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[
{
"title": "Complete Genome Sequence of the Cluster DJ Actinobacteriophage, Petito, isolated on the host Gordonia rubripertinca",
"abstract": "Gordonia phage Petito is a newly discovered siphovirus that infects Gordonia rubripertincta NRRL B-16540. The doublestranded DNA genome of this phage is 60,447 bp long with 93 predicted protein-coding genes and no tRNAs. Petito is a Cluster DJ phage.",
"full_author_list": "Elliot Benson, Micah Blount, Shria Chauhan, Jayden Ehrhart, Adelinn Foster, Abigail Ingber, Madeline Julian, Derika Kwansah, Trang Le, Emily May, Elizabeth Mazel, Esther Morency, Sierra Nelson, Casey O'Toole, Kaitlin Potter, Leandra Vita, Kirra Weigand, Denise Monti",
"short_author_list": "Benson et al",
"article_url": "https://www.micropublication.org/static/pdf/micropub-biology-001456.pdf",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39839714"
},
{
"title": "Isolation and Annotation of Arthrobacter globiformis Phage AWGoat",
"abstract": "AWGoat, a lytic bacteriophage that infects Arthrobacter globiformis, was isolated from a goat pen in Charlotte, NC. Its genome is 65,496 bp long, with a GC content of 67.1%. Based on gene content similarity, AWGoat is assigned to actinobacteriophage cluster AP. It encodes a putative toxin from a broadly distributed toxin/antitoxin pair and an unusually large minor tail protein.",
"full_author_list": "Caitlyn Bolling, Chloe Chervenic, Kate Drake, Zoe Griffin, Isha Jain, Hala Khabir, Tyler Ordon, Anthony Padilla, Rachel Showers, Jose Vences, Caelan Walsh, Wyatt Workman, Sharon Bullock, Michelle Pass, Tonya Bates, Ellen Wisner",
"short_author_list": "Bolling et al",
"article_url": "https://www.micropublication.org/static/pdf/micropub-biology-001433.pdf",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39897170"
},
{
"title": "Complete genome sequences of AZ Arthrobacter phages Wildwest and Sue2",
"abstract": "This announcement reports the complete genome sequences of two bacteriophages isolated from soil samples using the host Arthrobacter atrocyaneus Strain NRRL B-2883. These findings enhance our understanding of AZ1 cluster phages, particularly Wildwest and Sue2, with their unique genomic features.",
"full_author_list": "Isabella E. Cloud, Ava N. Ortega, Angelina M. Spencer, Varsha Upadhyayulla, Tamarah L. Adair",
"short_author_list": "Cloud et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01078-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39898625"
},
{
"title": "Complete Genome Sequences of Mycobacterium smegmatis Phages Dove and Issimir",
"abstract": "We announce the discovery of two mycobacteriophages isolated from soil in Rock Hill, South Carolina. Phage Dove has a genome sequence length of 108,976bp, a siphovirus morphology, and a predicted temperate lifecycle. Phage Issimir has a genome sequence length of 155,564bp, a myovirus morphology, and a predicted lytic lifecycle.",
"full_author_list": "Victoria Frost, Israel Bellinger, Riley Burn, Chastity Chisholm, Fisher Cobb, Hannah Duncan, Kalli Green, Madelynn Harding, Amari Johnson, Rachel Leek, Breanna Menard, Ciaran Murphy, Destiny Thompson, Gwendolyn Tomlin, Kristi Westover",
"short_author_list": "Frost et al",
"article_url": "https://www.micropublication.org/static/pdf/micropub-biology-001432.pdf",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39897166"
},
{
"title": "Genome Sequence of Gordonia terrae Bacteriophage Wheezy",
"abstract": "Bacteriophage Wheezy, a lytic phage with siphoviral morphology isolated using the host Gordonia terrae 3612, has a genome of 67,021 base pairs and is 65.9% GC. The genome sequence of Wheezy aligns most closely with subcluster CR2 phages Tracker and NatB6. Annotation of the full-length genome sequence of Phage Wheezy revealed 92 protein-coding genes and no tRNA genes.",
"full_author_list": "Rachel M Heyne, Catherine P Chia",
"short_author_list": "Heyne et al",
"article_url": "https://micropublication.org/static/pdf/micropub-biology-001407.pdf",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39845266"
},
{
"title": "Complete genome sequence of bacteriophage Godfather isolated from Microbacterium foliorum",
"abstract": "Microbacteriophage Godfather was collected from a soil sample in Stephenville, Texas. The 17,452-bp double-stranded genome contains 24 protein-coding genes. The genome shares >99% nucleotide sequence identity with cluster EE microbacteriophages Scamander, Danno, Kojax4, and Burgy.",
"full_author_list": "Joshua Hutchings, Lauren Bower, Ethan Collum, Timothy Hester, Melody Hunter, Chaney Kelly, Luke Reynolds, Cole Moore, Dustin Edwards",
"short_author_list": "Hutchings et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00888-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39817740"
},
{
"title": "Genome sequences of three temperate actinobacteriophages from clusters FA and AS",
"abstract": "Three novel temperate siphoviruses, Juno112, KHumphrey, and ChuckDuck, were isolated from soil at Stevenson University using the bacterium Arthrobacter globiformis B-2979. Based on gene content similarity, Juno112 and KHumphrey are assigned to actinobacteriophage cluster AS3 and ChuckDuck to cluster FA. All three phages encode tyrosine recombinases, with ChuckDuck encoding two.",
"full_author_list": "Jonathan G. Lawton, Alyssa D. Reddy, Victoria M. Herrera, Riley J. Strain, Elroie E. Mekonnen, Frank W. Stearns, Samuel G. Obae, Rivka L. Glaser",
"short_author_list": "Lawton et al",
"article_url": "https://micropublication.org/static/pdf/micropub-biology-001444.pdf",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39989906"
},
{
"title": "Lytic bacteriophages of Gordonia rubripertincta from topsoil in Lubbock, Texas: FlyingTortilla and ScarletRaider",
"abstract": "We isolated two environmental phages, as part of the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Sciences program, that infect Gordonia rubripertincta from topsoil in Lubbock, Texas. We report the complete genome sequences of lytic bacteriophages FlyingTortilla and ScarletRaider. Sequence similarity analysis reveals the viruses as a part of an unclassified order within the Caudoviricetes class.",
"full_author_list": "Laurissa N. Miller, Natalie Block, Whitney Dickens, Carson Bellew, Christian Deluna, Francesca Makilan, Malli Bhakta, Ashleigh Crawford, Trinity Criner, Chase Drucker, Aqsa Fayyaz, Jasmine Goh, Caitlyn Guetersloh, Claire Jansen, Dana Pham, Andrea Resendez, Austen Rowell, Fahareen B. Mosharraf, Allie C. Smith, Lisa M. Bono",
"short_author_list": "Miller et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01333-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "40231666"
},
{
"title": "Genome Sequence of Three Siphoviruses in the EE, GA and EA5 Actinobacteriophage Clusters: Biscayne, Bush and GreenIvy",
"abstract": "Bacteriophages Biscayne, Bush and GreenIvy were isolated from soil samples in Miami, FL using Microbacterium foliorum NRRL B-24224 as host. Transmission electron microscopy shows siphoviral morphologies for all three phages. Based on gene content similarity to other actinobacteriophages, they are assigned to the EE, GA and EA5 clusters, respectively.",
"full_author_list": "Xavier S Purroy, Betty R Sierra, Lara Becerra Reymundo, Victoria M Serradet, Alejandra M Camacho, Nicole A Briceno, Katherine Artiles, Pooja Lad, Nhan Phan, Alison Rodriguez Leiva, Jazlyn N Appolon, Akram Mikhail, Arianna M Ruiz, Carlos Rodriguez, David Vega, Gabriela Moyano, Grace Intrator, Kiryl Yasinski, Kristen Mclean, Nicole Gonzalez Giliberti, Erika Ramirez Ramirez, Victor Adolpho de Melo, Alexandra S Alsina, Maria Y Andino, Brian A Becker, Hillary Castellanos, Natalia A Castillo, Brandon S Fernandez, Jeremiah R Estinvil, Amanda A Gonzalez, Emily M Hernandez, Ayden Ho, Sheikh F Islam, Anna Liubenco, Lance Mejia, Sandra N Meesala, William Morales-Ramirez, Nathalie Morlote, Kevin Ramos-Homs, Jorge A Rodriguez, Leydis M Torres, Patricia Waikel, Jaime Mayoral",
"short_author_list": "Purroy et al",
"article_url": "https://www.micropublication.org/journals/biology/micropub-biology-001397",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39839715"
},
{
"title": "The complete genome sequence of the cluster BE1 Streptomyces Bacteriophage Riptide includes genes encoding ribosome-associated proteins",
"abstract": "This study isolated bacteriophage Riptide, a BE1 cluster siphovirus, from soil using <em>Streptomyces mirabilis</em> NRRL B-2400. Riptide follows a lytic life cycle contains a genome length of 132,142 bp encoding 236 protein coding genes including two with ribosomal-related functions, as well as genes that encode 39 tRNAs and 1 tmRNA.",
"full_author_list": "Alena Sagalovsky, Aniket Camarushi, Jeshuwin D. Prabakaran, Abdullah Shahzad, Nicholas Nguyen, Daniel Mirahmadian, Michelle A. Ibino, Ali Mutasim, Emmanuel Okusanya, Choudhury Zaki, Kimia Kardaniyazd, Hope Ramsey, Jariatu Kargbo, Beryl Fuamazeh, Dania Mahmood, James Anderson, Eni Adesola, Laure Elisabeth Fom Kembou, Cameron Hindle, Keyshawn Kontchou, Abdullah Najib, Gilbert Hernandez, 2024 UMBC Phage Hunters, Elana Frazier, Steven M. Caruso",
"short_author_list": "Sagalovsky et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00776-25",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "40938125"
},
{
"title": "Complete genome sequences of Streptomyces phages HazuAndZazu and Tubberson",
"abstract": "Bacteriophages HazuAndZazu and Tubberson, belonging to the BI1 and BC1 subclusters, are Caudoviricetes with a siphoviral morphology that infect Streptomyces species. They have GC contents of 59.5% and 71.5%, and genomes 55,823 and 39,028 bp long, respectively. Annotation of cluster BC phage Tubberson includes an immunity mechanism.",
"full_author_list": "Nisha Shah, Phoenix S Bryant, Meghna Chandrasekaran, Arya J Chaudhari, Ramsha A Chaudhary, Cole Cheng, Norah J X Jackson, Allison S Kende, Agnes Koodaly, Rohan S Kyasa, Iman Mahmood, Katherine J McHarg, Isabella S Naimi, Ayeoritse T Tuedon; 2024 UMBC Phage Hunters; Zachary M Smith, Steven M Caruso",
"short_author_list": "Shah et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00361-25",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "40488613"
},
{
"title": "Genome sequence of WestPM, a phage infecting Microbacterium foliorum isolated from beach environmental samples",
"abstract": "Bacteriophage WestPM is a siphoviral-like phage infecting Microbacterium foliorum isolated from environmental samples collected on Pensacola Beach, FL. The genome of this phage is 39,693 bp long and contains 59 predicted protein-coding genes and zero tRNA genes. Based on gene content similarity, WestPM is grouped in the actinobacteriophage EA11 subcluster.",
"full_author_list": "Charles J West, Brittany C Yencho, Andrew J Brown, Conor R Flannigan, Hui-Min Chung",
"short_author_list": "West et al",
"article_url": "https://micropublication.org/static/pdf/micropub-biology-001395.pdf",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2025",
"pubmed_id": "39839710"
},
{
"title": "Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta",
"abstract": "Novel actinobacteriophage Soos was isolated and purified from Southern Indiana soil using host Gordonia rubripertincta NRRL B-16540. Sequencing revealed a 57,509 bp circularly permuted genome encoding 87 predicted protein-coding genes. Soos is only the third phage in cluster CP, along with phages Clawz and Sting.",
"full_author_list": "Reese M. Adams, Holly A. Britton, Emily D. Bruce, Yucita De La Paz, Emily N. Kratz, Emma J. Pfeifer, Daisy E. Priddy, Brooklyn I. Schotter, Wyatt A. Stuffle, Jordyn Wagner, Meredith R. Weiss, Danielle K. Watt, Pamela L. Connerly, Elizabeth E. Rueschhoff https://orcid.org/0000-0002-8268-0905",
"short_author_list": "Adams et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01204-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38526095"
},
{
"title": "Genome sequence of Xenia2 a DV cluster phage that infects Gordonia rubripertincta",
"abstract": "Xenia2 is a DV cluster actinobacteriophage that infects Gordonia rubripertincta NRRL B-16540. The genome is 68,135bp, has a GC content of 57.9% and 98 predicted protein-coding genes, 33 of which have a predicted function. Xenia2 has a lysis cassette with an endolysin (lysin A) and four different holin-like transmembrane proteins.",
"full_author_list": "Carol Agaiby, Maha Ahmed, Aidan Argueta, Kyle Arrowood, Keelynn P. Barrier, Meghan W. Church, Cheryl R. Connell, Ken D. Dao, Kathleen Huyen T. Dao, Makenzie R. Davenport, Megan D. Edmondson, Makenzie I. Estabrook, Santoshi Gondhi, Patricia Gonzalez, Francine Leduc, Trang Ma, Adam Mansoor, Sara Mansoor, Lillian Mattley, Cyrus Meyer, Loc Nguyen, Emaan Niaz, Jenna M. Parker, Delaney C. Ross, Devin M. Scott, Brianna Semryck, Kyrillos Takla, Aishwarya Tiramdas, Sai Kaushik Upputuru, Richard S. Pollenz",
"short_author_list": "Agaiby et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00578-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39162485"
},
{
"title": "Genome Sequence of Arthrobacter globiformis B-2979 Phage JanetJ",
"abstract": "Phage JanetJ was isolated on Arthrobacter globiformis B-2979 and has siphovirus morphology. JanetJ's genome consists of 36,986 base pairs, encoding 52 putative protein-coding genes. JanetJ adds to the small number of previously isolated cluster FO phages, none of which encode identifiable immunity repressor or integrase functions, with the exception of phage Maja.",
"full_author_list": "Arib Ahsan, Ruby S Crosthwait, Josephine J Crosthwait, Srilekha Davuluri, Omoye N Ehimare, Yihao Fan, Tiarra Nikitha Joseph Philomen Raju, Jamie Kim, Alexander Y Lee, Nicholas K Odani, Mugil V Shanmugam, Anmol Singhal, Alana J Snyder, Jessica W Sy, Grace Y Wang, George W Zhou, and Christa T Bancroft",
"short_author_list": "Ahsan et al",
"article_url": "https://www.micropublication.org/journals/biology/micropub-biology-001351",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39583577"
},
{
"title": "Genome sequence of bacteriophage GiJojo, isolated using Streptomyces mirabilis in Catonsville, Maryland",
"abstract": "Bacteriophage GiJojo is a myovirus isolated from soil that infects Streptomyces mirabilis NRRL B-2400, with a genome length of 115,161 bp containing 180 genes and 29 tRNAs. Of those genes, 59 have been assigned functions. GiJojo is a member of the BS cluster of actinobacteriophages.",
"full_author_list": "Marie Louise P. Badiola, Kaela D. Befano, McKayla L. Berger, Claudine R. Blanco, Nhyira Ghunney, Jaehyun G. Lee, Lin P. Myat, James K. Nguyen, Ellison M. Ober, Karla M. Press-Porter, Brendan T. She, Justin S. Watkins, 2023 UMBC Phage Hunters, Steven M. Caruso",
"short_author_list": "Badiola et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00584-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39177367"
},
{
"title": "Complete genome sequence of Mycobacterium smegmatis phage Rummer, a subcluster A3 actinophage",
"abstract": "Bacteriophage Rummer is a siphovirus morphology actinophage isolated from Mycobacterium smegmatis. Rummer has a 50,908 base pair genome encoding 89 predicted protein-coding genes and three tRNAs. Based on gene content similarity to sequenced actinobacteriophages, Rummer is assigned to phage subcluster A3.",
"full_author_list": "Dondra S. Bailey, Dominique R. Dotson, Charlotte Berkes, Oluwanifemi Agbede, Marcelaine Augustin, Imani Blackman-Murray, Talaeya Chambers, Nicolas Felber, Dy'Mon Fleming, Loretta Frazier, Natalie Gray, Ayanna Harrison, Genesis Hernandez, Nina Iwuchukwu, Chika Iwuji, Taysha Jackson, Angelic Jefferson, Daya Jordan, Miracle Jordan, Brian Nicolas, Monae Person, Ga'Nayah Richardson, Ashley Roman, Christian Stevens, My'Sean Suggs, Nahshon Thompson, Summer Timmons-Smith, Shiaishea Wilfong, Micaela Wilson-Wheatley",
"short_author_list": "Bailey et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01268-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38466105"
},
{
"title": "Desert diversity: genome sequence of Gordonia rubripertincta cluster DJ phage Mossy and cluster DV phage Erutan",
"abstract": "Lytic bacteriophages Mossy and Erutan were directly isolated from desert soil on Gordonia rubripertincta and characterized by their morphologies and genomes. Mossy, part of the DJ cluster of Actinobacteriophage, has a genome of 61,183 bp. The genome of Erutan, part of the DV cluster, is 66,957 bp.",
"full_author_list": "October Barnes, Christopher J. Workman, Noah C. Patterson, Riley Oesch, Katie L. Johnson, Kaarin Goncz, Joel Sharbrough, Linda C. DeVeaux",
"short_author_list": "Barnes et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01245-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38470028"
},
{
"title": "Complete Genome Sequences of Phages EarickHC, Figueroism, FinalFrontier, SBlackberry, Skylord, and Slay isolated using Microbacterium foliorum",
"abstract": "Phages EarickHC, Figueroism, FinalFrontier, SBlackberry, Skylord, and Slay were isolated from soil samples collected around Southern California using the host Microbacterium foliorum. All six phages are lytic and have a siphoviral morphology. Genomes are 39,843 to 52,992 bp in length and contain 58 to 91 protein coding genes.",
"full_author_list": "Brianna Barruga, Sabrina Benitez, Emily Bouit, Tristan Bouit, Earick Cagang, Joshua Cantos, Dylan Carpio, Jaden Chen, Sungyoung Choi, Rita Dementyev, Ethan Dewri, Christian Dominguez, Alexandria Falvo, Christian Figueroa, Elva Garcia, Yannik Gibson, Dulce Guevara, Katie Jang, Michael Kelly, Caleb Kim, Nicole Kim, Raymond Kim, Julia Ko, Alyssa Lee, Yumin Lee, Rosalia Marenco, Moses Milano, Soojeong Moon, Kristen Ngo, Brian Nguyen, Eddie Nguyen, Ashley Perdomo, Elizabeth Paul, Ester Peiro, Daphne Prakash, Jennifer Ramon, Leslie Rodriguez, Emily Sandoval Plouffe, Joanna Shelim, Elizabeth Ton, Adam Tsao, Tabitha Usery, Madyson Vaca, Ethan Wang, Stuart Wettstein, Noboyuki Yano, Grace Young, Jiacheng Zhang, and Arturo Diaz",
"short_author_list": "Barruga et al",
"article_url": "https://www.micropublication.org/journals/biology/micropub-biology-001357",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": ""
},
{
"title": "Complete genome sequences of mycobacteriophages Ageofdapage, Aubs, BABullseye, CheetoDust, ShaboiShabazz, and TomBrady",
"abstract": "We report genome sequences of six mycobacteriophages. Each virus was isolated from a soil sample and belongs to the siphovirus morphology. Genomes are 41,901–60,613 bp in length, contain between 62 and 103 protein-coding genes, with up to 40% of those genes having a predicted function.",
"full_author_list": "Shelbie Bass, Danielle Coates, Nina Frasketi, Smeetha James, Vishnu Marella, Riya Pulla, Kyle Stoecker, Srichandra Tupurani, Allison A. Johnson",
"short_author_list": "Bass et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01253-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38334400"
},
{
"title": "Genome sequences of actinobacteriophages JorRay, Blocker23, Nibbles, and OlgasClover",
"abstract": "JorRay, Blocker23, Nibbles, and OlgasClover are actinobacteriophages belonging to clusters G1, B2, CT, and DJ, respectively. JorRay and Blocker23 were identified in host bacterium Mycobacterium smegmatis mc2155. Nibbles and OlgasClover were identified in host bacterium Gordonia rubripertincta NRRL B-16540.",
"full_author_list": "Breanna M. Baumgartner, Kayla A. Bono, Dawn R. McIntosh, Anna M. Vu, Chanel F. Adams, Brooklyn C. Benik, Jessica Chavez, Samantha J. Gresky, Andres Sotelo, Jordan I. Ray, Alexandra Peister, Kendra W. Kimberley, Chelsey C. McKenna, James R. Theoret, Earl J. Yoon, Erin J. Windsor",
"short_author_list": "Baumgartner et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01256-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38445868"
},
{
"title": "Complete genome sequence of Microbacterium paraoxydans phage Damascus",
"abstract": "Phage Damascus was isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The Damascus genome is 56,477 bp with 3′ single-stranded overhangs and 56.5% G+C content. Damascus was assigned to cluster EL and shares 42.6%–91.7% gene content with the three other phages in this cluster.",
"full_author_list": "Julisa M. Bearhart, Jenna L. Bethke, Cassie S. Christian, Faith N. Cour, Karleigh R. Creasey, Emily J. Crowe, Julia G. Dahl, Lindsey A. Hanson, Abby L. Jaecks, Vincent A. Lamantia, Mercedes Madison, Autumn L. Roskowiak, Justin D. Scheberl, Bekkah M. VanEperen, Morgan E. Wurst, Karen K. Klyczek",
"short_author_list": "Bearhart et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01287-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": ""
},
{
"title": "Genomic sequences of Mycobacterium smegmatis A cluster phages LBerry, Pembroke, and Zolita",
"abstract": "LBerry, Pembroke, and Zolita are newly isolated bacteriophages that infect Mycobacterium smegmatis mc²155. Based on gene content similarity, LBerry and Pembroke are assigned to cluster A3, and Zolita is assigned to cluster A5. LBerry and Pembroke are 99% identical to Anaysia and Caviar, and Zolita is 99% identical to SydNat.",
"full_author_list": "Nathan E. Berry, Marly S. Cassford, Colby J. Agostino, Ethan N. Dionne, Olivia J. Schmitt, Kristen A. Butela, Deborah Jacobs-Sera, Joseph A. DeGiorgis, Kathleen Cornely",
"short_author_list": "Berry et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00504-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "13",
"journal_issue": "8",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38980043"
},
{
"title": "Genome and characteristics of Arthrobacter globiformis AZ cluster phage London",
"abstract": "London is a predicted temperate bacteriophage with siphovirus morphology infecting Arthrobacter globiformis NRRL strain B-2880. Sequencing of the genome revealed a length of 43,599 bp comprising 69 predicted open-reading frames and no tRNA genes. It is categorized as a cluster AZ1 phage along with closely related actinobacteriophages Elezi, Eraser, and Niobe.",
"full_author_list": "Andrea R. Beyer, Hannah L. Hatke Hughes, Jasmae S. Flowers, Jacquelin Bullock, Demesha T. Daniels, Makayla Drew, Queen Lee-Mayes, Brianna M. Marshall, Vivica Remson, Micaelah Thomas",
"short_author_list": "Beyer et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00819-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "37906022"
},
{
"title": "Complete annotated genome sequence of Microbacterium paraoxydans phage Evcara, a cluster GI podovirus isolated from compost.",
"abstract": "Bacteriophage Evcara is a podovirus isolated on Microbacterium paraoxydans NRRL B-24275. Its genome is 16,285 bp in length and contains 22 predicted protein-coding genes. Evcara, has been assigned to cluster GI with Microbacterium foliorum phages PineapplePizza and Curie that share 10 homologues with the well-characterized Bacillus subtilis phage phi29.",
"full_author_list": "Hannah B. Bonogafsky, Kelly M. Freer, Taylor B. Sanderson, Kira A. Yost, Ayden J. Pyle, Ginavieve Rowley, and Maria D. Gainey",
"short_author_list": "Bonogafsky at al",
"article_url": "https://www.micropublication.org/journals/biology/micropub-biology-001398",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39717144"
},
{
"title": "Genome sequence and annotation of Arthrobacter globiformis phage Vulpecula (AS1) isolated from soil in Dahlonega, Georgia",
"abstract": "Vulpecula, a temperate bacteriophage collected from soil in Dahlonega, Georgia using host Arthrobacter globiformis, is an AS1 subcluster virus of 37,766 bp (67.7% GC). Genome annotation suggests 64 open reading frames, no predicted tRNA genes, and ~98% sequence similarity to AS1 phages Ruchi (from GA) and Jamun (New Hampshire).",
"full_author_list": "Lily Chuhran, Chase Whitlow, Carson Teems, Alison Kanak, Shane A. Webb",
"short_author_list": "Chuhran et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00090-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38385671"
},
{
"title": "Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3",
"abstract": "Background: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc2155 continue to be discovered.\r\nMaterials and Methods: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.\r\nResults: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4–67.5%) and 102–104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.\r\nConclusions: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.",
"full_author_list": "Véronique A. Delesalle, Ruusu E. Ankeriasniemi, Colin M. Lewis, Jehan M. Mody, Abigail M. Roy, Ward A. Sarvis, Duy D. Vo, Allison E. Walsh, and Rose J. Zappia",
"short_author_list": "Delesalle et al",
"article_url": "https://doi.org/10.1089/phage.2024.0004",
"journal": "PHAGE",
"journal_volume": "5",
"journal_issue": "2",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39119203"
},
{
"title": "Complete genomes of two cluster AK Arthrobacter phages isolated from soil samples in Newburgh, NY, United States",
"abstract": "Two phages belonging to Arthrobacter phage cluster AK were isolated from soil samples collected in Newburgh, NY in 2021. Both are lytic with a genome organization typical of siphoviruses except for two genes encoding minor tail proteins with pyocin-knob domains found early in the genome, before the terminase gene.",
"full_author_list": "Véronique A. Delesalle, Mariah A.K. King, Tabitha J. Rozario, Noah D. Wolf, Connor J. Stewart, Luke F. DeMato, Kevin F. Trafford, Saiman Adhikari, Van T. Dinh, Gina Caputo, Ashley Hunter, Michelle Licata, Misun Modell, Suparna Bhalla",
"short_author_list": "Delesalle et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00716-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39264183"
},
{
"title": "Genome sequence of Arthrobacter globiformis phage MaGuCo",
"abstract": "MaGuCo is a temperate phage isolated from soil collected in Alton, NH, USA, using Arthrobacter globiformis. Its genome is 43,924 base pairs long and contains 63 protein-encoding genes, 44 of which were assigned putative functions. MaCuGo is assigned to cluster AZ2 based on gene content similarity to actinobacteriophages.",
"full_author_list": "Amanda E. Diggins, Mary G. Gubitose, Elijah G. Hinrichsen, Patrick T. Jones, Brian S. Kearns, Caitlynn E. Lord, Mary T. Parsons, Rachel A. Pitt, Isabella A. Woods, Teagan R. Zarakotas, Beth M. Wilkes",
"short_author_list": "Diggins et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01179-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38376341"
},
{
"title": "Three Cluster O mycobacteriophages isolated in Philadelphia, PA",
"abstract": "We report here the discovery and characterization of three novel bacteriophages infecting Mycobacterium smegmatis. These siphoviruses were isolated from soil collected in urban areas around Saint Joseph's University in Philadelphia. Mycobacteriphages Idergollasper, FoulBall, and Schuy are assigned to actinobacteriophage cluster O based on gene content similarity, and have prolate capsids typical for this cluster.",
"full_author_list": "Alexander DiGiacomo, Nicole Bowen, Thientrinh Nguyen, Sophia Borrello, Naomi Brooks, Ella Bubeck, Cole Buker, Lauren Charboneau, Ariana Corapi, Katelyn Derstine, Leah Fries, Olivia Graveley, Isabella Jimenez, Paul Lacour, Ignacio Llorente Fernandez, Madeleine Malesich, Sydney Matusiak, Jacob McNelly, Skyler Reka, Simon Sheppard, Lauren Zile, Ava Smith, Jessalyn Aquilino, Danielle Niblock, Anne Winkler, Leya Givvines, C Nicole Sunnen, and Julia Lee-Soety",
"short_author_list": "DiGiacomo et al",
"article_url": "https://www.micropublication.org/journals/biology/micropub-biology-001375",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39606152"
},
{
"title": "Genome sequences of Arthrobacter globiformis phages JuneStar and Pumpkins in Bismarck, ND",
"abstract": "We report the isolation and characteristics of phages JuneStar and Pumpkins, siphoviruses isolated from soil in Bismarck, ND using Arthrobacter globiformis B2979-SEA. Based on gene content similarity, both phages are assigned to actinobacteriophage cluster AZ1. They encode a putative serine integrase that is conserved across cluster AZ1 phages, suggesting a temperate lifestyle.",
"full_author_list": "Madeline Dojs, Christine Fleischacker, Celia Brekken, Ethan Emineth, Allison Hughes, Sarah Rodriguez-Brandon, Corrina Vigness",
"short_author_list": "Dojs et al",
"article_url": "https://www.micropublication.org/journals/biology/micropub-biology-001378",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39606149"
},
{
"title": "The genomic characterization of three Microbacterium foliorum-specific bacteriophages,“Nucci,”“MCubed,” and “QMacho”",
"abstract": "Nucci, MCubed, and QMacho are microbacteriophages that were isolated from soil samples in Charlotte, NC. They were classified into EA10, EA2, and EB clusters, respectively. Nucci and MCubed each had 63 predicted genes, while QMacho had 73 predicted genes.",
"full_author_list": "Jennifer Cook Easterwood, Joanna Mantis Katsanos, Jenna Lloyd",
"short_author_list": "Easterwood et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00203-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38597796"
},
{
"title": "Complete genome sequence of Microbacterium foliorum singleton phage Magritte",
"abstract": "Actinobacteriophage Magritte was isolated from soil in Columbia, TN using Microbacterium foliorum as a host. Magritte is a singleton with a siphovirus morphology and a large genome of 133,228 bp encoding 250 predicted genes, including 26 tRNA genes.",
"full_author_list": "Elvira Eivazova, Jenna St. Pierre, Miriam Galindo, James Bautista, Annaleisa Matzirakis, Madalyn Falletti1, Elynor Fix, and Levi Fritsch",
"short_author_list": "Eivazova et al",
"article_url": "https://www.micropublication.org/journals/biology/micropub-biology-001377",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": ""
},
{
"title": "Nine Cluster E mycobacteriophages isolated from soil",
"abstract": "Mycobacteriophages FireRed, MISSy, MPhalcon, Murica, Sassay, Terminus, Willez, YassJohnny, and Youngblood were isolated from soil using Mycobacterium smegmatis as a host. Genome sequencing and annotation revealed that they belong to Actinobacteriophage Cluster E. Here, we describe the features of their genomes and discuss similarities within these Cluster E phages.",
"full_author_list": "Joseph M. Gaballa, Amanda Freise, Krisanavane Reddi, Jordan Moberg Parker",
"short_author_list": "Gaballa et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00463-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": ""
},
{
"title": "Complete genome sequences of five Ackermannviridae that infect Enterobacteriaceae hosts",
"abstract": "This announcement contains the whole genome sequences of five Ackermannviridae that infect members of the Enterobacteriaceae family of bacteria. Four of the five phages were isolated using Salmonella enterica serovar Typhimurium as a bacterial host: AR2819, Sajous1, SilasIsHot, and FrontPhageNews. ChubbyThor was isolated using Shigella boydii.",
"full_author_list": "Evan B. Harris, Laura B. Anthony, Sakhawat Ali, Hannah Atkin, Lucy C. Bowden, Steven W. Brugger, Emille L. Carr, Nathaniel Eberhard, Samuel Flor, Rochelle K. Gaertner, Austen Gleave, David Hess, Trevor Hoggan, Elisa Correa Lazaro, Katherine Leonard, Trek Lewis, Colleen R. Newey, Joshua Ramsey, Kayla R. Sajous, Daniel Schaeffer, Tyson Stoker, Sierra Stump, Daniel W. Thompson, Rachel Weyland, Julianne H. Grose",
"short_author_list": "Harris et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00950-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38323836"
},
{
"title": "Complete genome sequence of Microbacterium foliorum phage Curie, a podovirus isolated from soil in Spokane, Washington",
"abstract": "Bacteriophage Curie is a podovirus that infects Microbacterium foliorum. The Curie genome spans 16,810 bp, has 90 bp terminal inverted repeats, and includes 23 protein-coding genes. Its genome architecture resembles phage PineapplePizza and other phi29-like phages. Together, Curie and PineapplePizza form a new actinobacteriophage Cluster GI.",
"full_author_list": "Emma N. Horton, Erika K. Beach, Kathryn T. Cook, Kyra G. Cronin, Avery T. Haag, Sierra M. Salter, Nicole A. Stojanovic, Zoe E. Fry, Brian M. Connolly, Rebekah F. Hare, Ann-Scott H. Ettinger, Marianne K. Poxleitner, Kirk R. Anders",
"short_author_list": "Horton et al.",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00408-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39037314"
},
{
"title": "Genome characterization of BI2 subcluster Streptomyces scabiei bacteriophages GoblinVoyage and Doxi13",
"abstract": "We present the bacteriophages GoblinVoyage and Doxi13, siphoviruses isolated on Streptomyces scabiei RL-34. They belong to the BI2 cluster and have genomes consisting of 60.9% GC content with identical 3’ end sticky overhangs. The genome lengths of GoblinVoyage and Doxi13 are 43,540 bp and 43,696 bp, respectively.",
"full_author_list": "Hanna Jin, Nihal K. Chana, Annie L. Tang, Paramjit Kaur, Brishti Lamichhane, Sze Ching Leung, Diane Scheiderer, Vighnesh V. Sivaprakasam, Dannah T. Marcelino, Gregory J. Hull, Toma M. Kamara, 2023 UMBC Phage Hunters, STEM BUILD at UMBC Cohort 7, Maria C. Guimaro, Steven M. Caruso",
"short_author_list": "Jin et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00581-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39162451"
},
{
"title": "Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using Streptomyces mirabilis NRRL B-2400 in Columbia, MD",
"abstract": "Here, we present bacteriophage SoJo, a siphovirus infecting Streptomyces mirabilis, with a circularly permuted genome of 39 kbp and GC content of 71.5%. Its genome length and content are similar to that of other phages in the Actinobacteriophage Database BC cluster. SoJo was isolated from soil in Columbia, MD, USA.",
"full_author_list": "Soven Verma Kumar, Nicholas Schaffer, Zainab Bharmal, Quinn Mood, 2022 UMBC Phage Hunters, Ivan Erill, Steven M. Caruso",
"short_author_list": "Kumar et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00068-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38394246"
},
{
"title": "Genome sequence of Microbacterium foliorum phage CandC",
"abstract": "We report the discovery and genome sequence of CandC, a lytic bacter iophage with siphovirus morphology. CandC was isolated from a soil sample from Plattsburgh, NY, USA (Fall 2021). It has a genome size of 62,344 bp with 106 predicted protein-encoding genes, 30 of which are assigned putative functions.",
"full_author_list": "Joëlle C. Makhoul, Megan Valentine, Caila Campbell, Emma G. McLaughlin, Frank H. Vereline, Jenna M. Collins, Sophia I. G. Crandall, Emma L. Rabideau, Wesley J. Tender, Shaniah L. Fairweather, Carson J. Miller, Kori Q. Y. Mcleish, Justin D. Izquierdo, Leah N. Gallagher, Luke P. Tyrrell, Alyssa M. Gleichsner",
"short_author_list": "Makhoul et al",
"article_url": "https://journals.asm.org/doi/pdf/10.1128/mra.01117-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38231186"
},
{
"title": "Comparative genome analysis of cluster EF bacteriophages Ajin and OverHedge isolated from soil in Tennessee",
"abstract": "Bacteriophages Ajin and OverHedge were isolated from soil in Tennessee using the bacterium Microbacterium foliorum. Ajin and OverHedge (cluster EF) have a genome of 56,993 bp and 56,559 bp, containing 86 and 81 predicted genes, respectively. The Ajin genome has unique genes, phosphatase and glycosyltransferase, compared to the OverHedge.",
"full_author_list": "Sergei A. Markov, Paul Y. Atuahene, Clayton W. Barnes, Taquerra Butler, Stephan D. Cooper, Emma M. Covel, Kayla R. Diaz, Dalon Gadson, Anna C. Holt, Maegan A. Litchfield, Alexis J. Nefe, Comfort E. Ogbu, Kiara M. Rupp, Falisaty Simpson, Elyse Wood",
"short_author_list": "Markov et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00925-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39345199"
},
{
"title": "Complete genome sequences of Arthrobacter globiformis phages Uzumaki and Argan of cluster AU6",
"abstract": "Bacteriophages Uzumaki and Argan infect Arthrobacter globiformis B-2880 isolated from soil samples in Long Island, New York. These bacteriophages have lambda-like morphology with prolate capsid and share 97% gene content similarity. These traits place them in cluster AU6 with other related Arthrobacter phages.",
"full_author_list": "Brandon Mathew, Andrew Sean Lee, Katie Chen, Michael Kaczmarski, Nigel Oommen, Asweel Mehaboob, Vrushali Patel, Yamini Patel, Hannah Saji, Muhammad Ayaan Shamsi, Bryan Gibb",
"short_author_list": "Mathew et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00293-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38990022"
},
{
"title": "Complete genome sequence of the Microbacterium foliorum bacteriophage Garey24",
"abstract": "In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in Funes, Argentina. Its 41,522 bp circularly permuted genome contains 63 putative protein-coding genes. Based on gene content similarity, Garey24 was assigned to subcluster EA1.",
"full_author_list": "Matías R. Migueletti, Julieta García Rey, Josefina Micheloni, Camila Lomanto, Elisa Martelli, Gastón Sánchez, Julián M. Colombo, Luciano M. Vallecillo, Francisco Lamagni, Tomás Giusti, Fabrina Acosta, Franco Villagrán, Martín Gvozdenovich, Abril Pricco Frakich, Tulio Pianesi, Gonzalo Tulin, Florencia C. Mascali, Tomás D. Petitti, Mariano A. Torres Manno, Corina M. Fusari, Laura Buttigliero, María Florencia Giordana, Hugo Gramajo, Lautaro Diacovich, Martín Espariz, María Alejandra Mussi",
"short_author_list": "Migueletti et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01215-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38315107"
},
{
"title": "Complete genome sequence of the Streptomyces bacteriophage Amabiko",
"abstract": "Amabiko is a lytic subcluster BE2 bacteriophage that infects Streptomyces scabiei—a bacterium causing common scab in potatoes. Its 131,414 bp genome has a GC content of 49.5% and contains 245 putative protein-coding genes, 45 tRNAs, and one tmRNA. Amabiko is closely related to Streptomyces bacteriophage MindFlayer (gene content similarity: 86.5%).",
"full_author_list": "Mark Milhaven, Heba A. Bakry, Anuvi Batra, Amanda M. Bermingham, Gloria Grama, Jacob Kebe, Shawn S. Martinez, Rishika V. Mudunuri, Megan R. Nelson, Evie T. Nguyen, Mia M. Peterson, Alexis Pruitt, Kristan Tran, Akarshi Brar, Gabriella Cerna, Elaine Chaffee, Steven M. Caruso, Susanne P. Pfeifer",
"short_author_list": "Milhaven et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00182-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38651927"
},
{
"title": "Complete genome sequences of StopSmel and Aussie, two Mu-like bacteriophages of Sinorhizobium meliloti",
"abstract": "We report the complete genome sequences of two bacteriophages, Aussie and StopSmel, isolated from soil using the host Sinorhizobium meliloti NRRL L-50. The genomes are similar in length and gene content and share 76% nucleotide identity. Comparative analysis of Aussie and StopSmel identified core functional modules associated with Mu-like bacteriophages.",
"full_author_list": "Macy Nielander, Mya Maybank, Crissy Massimino, John Fitzgerald, Hannah Blossum, Cayce Douthitt, Chris Holland, Wayne B. Hunter, Megan Carrol, Tom D'Elia",
"short_author_list": "Nielander et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01230-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38385668"
},
{
"title": "Genome sequence of bacteriophage Djungelskog isolated from an Arthrobacter globiformis culture",
"abstract": "Actinobacteriophage Djungelskog was isolated from a sample of degraded organic material in Poughkeepsie, NY, using Arthrobacter globiformis B-2979. Its genome is 54,512 bp and encodes 86 putative protein-coding genes. Djungelskog has a siphovirus morphology and is assigned to cluster AW based on gene content similarity to actinobacteriophages.",
"full_author_list": "Abigail M. Oliveros, Shelby A. McDougall, Miles A. Snyder, Sara K. Snowden, Joseph D. Richard, Christopher M. Rao, Marybeth Ponce, Christopher J. Pitonza, Mira Ozcelik, Sofia S. Mannina, Juliana R. Magna, Andrew S. Lopez, Linnea C. Gustafson, Brynn K. Glackin, Abigail E. Dolge, Nate D. DeLancy, Andrew B. C. Davis, Thomas P. Davis, Max Blagodar, Sydney N. Natale, Megan K. Dennis, Elizabeth A. Godin",
"short_author_list": "Oliveros et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01294-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38376224"
},
{
"title": "Genome sequence of bacteriophage Janeemi isolated on Arthrobacter globiformis from soil collected in New York",
"abstract": "Janeemi is a bacteriophage that infects Arthrobacter globiformis B-2880, which was isolated from soil collected in New York City. The genome has a length of 43,877 bp and contains 69 predicted genes. Based on gene content similarity to phages in the actinobacteriophage database, Janeemi is assigned to phage cluster AZ1.",
"full_author_list": "Yamini Patel, Vrushali P. Patel, Amna Syeda, Hannah Saji, Bryan P. Gibb",
"short_author_list": "Patel et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00177-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38860811"
},
{
"title": "Mycobacteriophage maravista: a cluster F1 phage discovered on Cape Cod, Massachusetts",
"abstract": "Mycobacterium virus Maravista, a member of the family Gracegardnervirianae and species Cheoctovirus, is an F1 cluster phage that infects Mycobacterium smegmatis mc²155. The Maravista genome has 61.3% GC content, is 60,140 bp in length, and encodes 104 putative genes. Maravista encodes two putative glycosyltransferases, suggesting glycosylation of its capsid protein.",
"full_author_list": "Charles Pelagalli, Debbie-Jacobs Sera, Joseph A. DeGiorgis, Kathleen Cornely",
"short_author_list": "Pelagalli et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00502-24",
"journal": "Microbiology Resource Announcements",
"journal_volume": "13",
"journal_issue": "7",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38860805"
},
{
"title": "Genome Sequence of the Mycobacterium smegmatis Bacteriophage Eugenia",
"abstract": "We report the discovery and genome sequence of mycobacteriophage Eugenia, isolated from soil samples collected in Akron, OH. Eugenia is a double-stranded DNA virus with a genome size of 69,139 bp, featuring 104 predicted protein-encoding genes, with 32 of these genes assigned putative functions.",
"full_author_list": "Vipaporn Phuntumart, Lucia Boulos, Bella Nunnally, Isabella Lima, John Motter, Olivia Sidoti, Sam Rutherford, Hsin-Ho Wei, Raymond Larsen, and Jill H Zeilstra-Ryalls",
"short_author_list": "Phuntumart et al",
"article_url": "https://doi.org/10.17912/micropub.biology.001401",
"journal": "microPublication Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": ""
},
{
"title": "Complete genome sequences of nine Rhodococcus equi phages",
"abstract": "We report genomes of nine phages isolated from Actinobacteria Rhodococcus equi NRRL B-16538. Six of these phages belong to actinobacteriophage cluster CR, which otherwise contains Gordonia phages; two form the CF cluster; and one is a singleton. Genome lengths are 62,017–80,980 bp with 63.9%–67.3% GC content.",
"full_author_list": "Myles D. Radersma, Gabrielle Lathrop, Karena C. Moleakunnel, Luke A. Harlow, Aerin E. Baker, Alison J. Chen, Jason G. Churu, Carly A. Dole, Sophia L. Doorn, Ethan M. Hill, Anna Howland, Amanda Janvier, Catie M. Kramer, Matt J. Minasian, Jocelyn R. Nieze, Isabella K. Perezrios, Fiona J. Ramsey, Katie L. Seinen, Sierra K. Swierenga, Michael M. Veenstra, Grace E. Weaver, Alexandra C. White, Esther Yoon, John T. Wertz, Randall J. DeJong",
"short_author_list": "Radersma et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01088-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38179906"
},
{
"title": "Genome sequence of PSonyx, a singleton bacteriophage infecting Corynebacterium glutamicum",
"abstract": "PSonyx is a newly isolated phage that infects Corynebacterium glutamicum. This siphovirus was isolated from a French pond in the south of Paris by students from Paris-Saclay University. Its 80,277-bp singleton genome carries 136 protein-coding genes and 5 tRNAs.",
"full_author_list": "Ombeline Rossier, Cécile Labarre, Anne Lopes, Monique Auberdiac, Kevin Tambosco, Daniel Delaruelle, Hakima Abes, Ana A. Arteni, Malika Ouldali, Laura Pieri, Ryan Afgoun, Leonor Anacleto, Nathan Beaure, Meyssa Beghdad, Nolwenn Bellom, Elsa Ben Hamou-Kuijpers, Aïda Boukamel, James Carron, Vincent Carta, Lauriane Castelneau, Zoe Chadaillac, Elsa Chaouat, Soline Desmat, Keylian Favel, Eva Gabillot, Melissa Gargar, Madeleine Gautheret, Esther Gilles, Claire Lager, Amandine Le Deit, Yoann Le vay, Laure Lemercier, Anastassiya Litvinov, Samir Moussi, Marion Prevot, Marion Rehala, Chloë Rodrigues, Ramatoulaye Sambe, Ashvini Srimoorthy, Tiroumagale M. Tillay, Cerise Verhoeven, Pauline Vittaz, Jacqueline Wu, Christophe Regeard",
"short_author_list": "Rossier et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01155-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38236045"
},
{
"title": "Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth",
"abstract": "The genome sequences of thousands of bacteriophages have been determined and functions for many of the encoded genes have been assigned based on homology to characterized sequences. However, functions have not been assigned to more than two-thirds of the identified phage genes as they have no recognizable sequence features. Recent genome-wide overexpression screens have begun to identify bacteriophage genes that encode proteins that reduce or inhibit bacterial growth. This study describes the construction of a plasmid-based overexpression library of 76 genes encoded by Cluster K1 mycobacteriophage Amelie, which is genetically similar to cluster K phages Waterfoul and Hammy recently described in similar screens and closely related to phages that infect clinically important mycobacteria. Twenty-six out of the 76 genes evaluated in our screen, encompassing 34% of the genome, reduced growth of the host Mycobacterium smegmatis to various degrees. More than one-third of these 26 toxic genes have no known function, and 10 of the 26 genes almost completely abolished host growth upon overexpression. Notably, while several of the toxic genes identified in Amelie shared homologs with other Cluster K phages recently screened, this study uncovered 7 previously unknown gene families that exhibit cytotoxic properties, thereby broadening the repertoire of known phage-encoded growth inhibitors. This work, carried out under the HHMI-supported SEA-GENES project (Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists), underscores the importance of comprehensive overexpression screens in elucidating genome-wide patterns of phage gene function and novel interactions between phages and their hosts.",
"full_author_list": "Chelsea Tafoya, Brandon Ching, Elva Garcia, Alyssa Lee, Melissa Acevedo, Kelsey Bass, Elizabeth Chau, Heidi Lin, Kaitlyn Mamora, Michael Reeves, Madyllyne Vaca, William van Iderstein, Luis Velasco, Vivianna Williams, Grant Yonemoto, Tyler Yonemoto, Danielle M Heller, Arturo Diaz",
"short_author_list": "Tafoya et al",
"article_url": "https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae285/7917390?searchresult=1",
"journal": "G3",
"journal_volume": "15",
"journal_issue": "2",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "39657018"
},
{
"title": "Genome sequence and annotation of Arthrobacter globiformis phage Ruchi (AS1) isolated from soil in Lumpkin County, Georgia",
"abstract": "Ruchi, a temperate, AS1 subcluster bacteriophage isolated in Lumpkin County, Georgia using host Arthrobacter globiformis, possesses a genome of 38,571 bp and 67.7% GC. Annotation of this virus revealed 64 predicted reading frames, no predicted tRNA genes, and a close evolutionary relationship to AS1 phage Basilisk.",
"full_author_list": "Brooke Brooke Tatum, Payton Murray, Claire Bicknell, Shane A. Webb https://orcid.org/0009-0006-5669-404X, Alison Kanak, Payton Murray, Claire Bicknell, Shane A. Webb, Alison Kanak",
"short_author_list": "Tatum et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.01224-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38466103"
},
{
"title": "Complete genome sequences of seven Microbacterium foliorum phages Albedo, Kenzers, Swervy, Cranjis, JaimeB, Fullmetal, and Stormbreaker",
"abstract": "Seven bacteriophages were isolated from soil in Pennsylvania and Wisconsin using the host Microbacterium foliorum. These bacteriophages range in the number of predicted genes encoded, from 25 to 91, and are distributed across actinobacteriophage clusters EB, EC, EE, and EK.",
"full_author_list": "Keyshla Valentin Caban, Elizabeth Kalesnik, Kaitlyn A. Green, Christopher J. Negro, Ulises Nunez Rodriguez, Milan C. Peele, Casandra T. Nguyen, Sydney Cahill, Keara Dougherty, Melissa Logue, Star Hargraves, Hannah Radziak, Luke Willette, Esther Ogunyinka, Davia C. Campbell, Oluwatomiwa Adebamiro, Cecelia Schmeltzer, Jonathan Onimus, Hannah A. Asaka, Wilfred Bangura, Christina M. Shimp, Ameera Alade, Daekwon M. Sequira, Tommy Jimenez, Neumann University Phage Discovery Group, Sarah J. Swerdlow, Melinda K. Harrison, Patricia C. Fallest-Strobl, Matthew D. Mastropaolo",
"short_author_list": "Valentin Caban et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01251-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38451225"
},
{
"title": "Complete genome sequences of Mycobacterium smegmatis phages Ashballer and Bombitas",
"abstract": "We report the discovery of two mycobacteriophages isolated from soil in Rock Hill, South Carolina. Ashballer has a genome sequence length of 52,231 bp, while Bombitas is relatively larger at 110,129 bp. Both have siphovirus morphologies and have temperate lifecycles.",
"full_author_list": "Kristi M. Westover, Alexis R. Atkinson, Abby G. Bowers, Amaya L. Brown, James C. Ferebee, Chase A. Keisler, Kaylyn L. Lee, Amaya O. Payton, Lidia A. Peralta, Julianne V. Phu, Khamryn A. Pollock, Maya G. Scott, Bryson E. Vaughan, Karissa M. Wilczak, Victoria J. Frost",
"short_author_list": "Westover et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00990-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2024",
"pubmed_id": "38231182"
},
{
"title": "From compost to culver: genome sequence and annotation of a cluster CQ1 Gordonia phage",
"abstract": "Phage Culver, with a siphovirus morphology, was isolated using Gordonia terrae CAG3. Culver is assigned to phage cluster CQ1 based on gene content similarity to actinobacteriophages. Notably, Culver is predicted to encode eight tRNAs, lysin A by two adjacent genes, and, unlike other CQ1 phages, two putative integrase genes.",
"full_author_list": "William K. Alexander, Rianna R. Allen, Jaden D. Anderson, Amber N. Brumfield, Tiffany M. Cook, Giana M. Dana, Gregory J. Ethridge, Emily C. Gailey, Rebekah A. Netzley, Joshua V. Nguyen, Phillip J. Souza, Briggs M. Yoder, Jamie R. Wallen, Maria D. Gainey https://orcid.org/0000-0001-8853-2092, Tonya C. Bates, Ellen M. Wisner",
"short_author_list": "Alexander et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01066-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38132830"
},
{
"title": "Isolation and genome sequence annotation of KillerTomato, a newly discovered cluster EE bacteriophage infecting Microbacterium",
"abstract": "Discovered in Pocatello, Idaho, soil near a tomato garden, siphovirus KillerTomato infects Microbacterium foliorum NRRL B-24224. KillerTomato is a lytic cluster EE phage with a 17,442-bp genome and 68.6% GC content. Of 25 genes, 20 were assigned putative functions, including a putative tail assembly chaperone protein with a programmed frameshift and an endolysin.",
"full_author_list": "Omer Almahie, Breanna Danklefsen, R. Scott Graves, Sariah M. Hepworth, Rylee T. Mathison, Emily A. Sullivan, Paige R. Wood, Skylar Bartholomew, Reganne Brewster, Dylan J. Hunt, Carlos Serna, Jack F. Shurley, Anna S. Grinath, Michael A. Thomas",
"short_author_list": "Almahie et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00852-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37877714"
},
{
"title": "A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy",
"abstract": "During infection, bacteriophages produce diverse gene products to overcome bacterial antiphage defenses, to outcompete other phages, and to take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing ∼25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known antimycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.",
"full_author_list": "Isabel Amaya, Kaylia Edwards, Bethany M Wise, Ankita Bhattacharyya, Clint H D Pablo, Ember Mushrush, Amber N Coats, Sara Dao, Grace Dittmar, Taylor Gore, Taiya M Jarva, Giorgi Kenkebashvili, Sudiksha Rathan-Kumar, Gabriella M Reyes, Garrett L Watts, Victoria Kalene Watts, Deena Dubrow, Gabrielle Lewis, Benjamin H Stone, Bingjie Xue, Steven G Cresawn, Dmitri Mavrodi, Viknesh Sivanathan, Danielle Heller",
"short_author_list": "Amaya et al",
"article_url": "https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkad240/7338749",
"journal": "G3 Genes|Genomes|Genetics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37934806"
},
{
"title": "Genome Sequence of Gordonia rubripertincta Phage Survivors, a Cluster CT Siphovirus",
"abstract": "Bacteriophage Survivors is a siphovirus isolated from Gordonia rubripertincta NRRL B-16540. Survivors has a 45,436-bp genome encoding 69 predicted protein-coding genes, of which 32 have assigned functions. Based on gene content similarity to sequenced actinobacteriophages, Survivors is assigned to phage cluster CT.",
"full_author_list": "Amber M. Amend, Jacob P. Bifone, Justin C. Brewer, Makayla N. Denton, Eden B. Gilbert, Abigail C. Grimm, Jaden M. Hogan, Reagan M. Kelley, Lennon J. Kelly-Brooner, Jit A. Mukerji, Matthew Osterhoudt, Cody R. Senn, Bethanie R. Smith, Olive G. Stillwell, Jimmy Vo, Danielle K. Watt, Pamela L. Connerly, Elizabeth E. Rueschhoff",
"short_author_list": "Amend et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01086-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "36598273"
},
{
"title": "Genome Sequence of Gordonia terrae Phage APunk",
"abstract": "Gordonia phage APunk was isolated from soil collected in Grand Rapids (MI, USA) using Gordonia terrae 3612. The genome of APunk is 59,154 bp long, has a 67.7% GC content, and contains 32 protein-coding genes. Based on its gene content similarity to actinobacteriophages, APunk is assigned to phage cluster DE4.",
"full_author_list": "Emma Anderman, Theo Dini, Kenzi Eldbah, Tara Frino, Julia Milavec, Adam Sayed, Victoria Profrock, Rachel Virtue, Theodhora Qyshkollari, Melinda Harrison",
"short_author_list": "Anderman et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01220-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "36877085"
},
{
"title": "Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature",
"abstract": "We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-coding genes that have no close relatives among the actinobacteriophages.",
"full_author_list": "Kirk R. Anders, Antonio Abeyta, Christy C. Andrade, Carla Y. Bonilla, Amanda B. Braley, Alexandra G. Bratt, Kaya A. Duncan, Stephen G. Hayes, Ciara J. Robinson, Helen Smith-Flores, Ann-Scott H. Ettinger, William F. Ettinger, Marta M. Fay, Joseph Haydock, Sean K. McKenzie, Rebecca A. Garlena, Daniel A. Russell, Marianne K. Poxleitner",
"short_author_list": "Anders et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.01086-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38099681"
},
{
"title": "Complete genome sequences of microbacterium phages Tedro and BAjuniper",
"abstract": "We purified two novel bacteriophages from soil collected in Sioux County, Iowa: BAjuniper and Tedro. These bacteriophages were isolated from the host, Microbacterium foliorum. BAjuniper was assigned to cluster EB, and Tedro was assigned to cluster EF. Both phages display genomes typical of other phages in their clusters.",
"full_author_list": "Grace M. Anderson, Olivia E. Anderson, Clayton A. Bosma, Erin E. Brouwer, Kleyton M. DeGroot, Owen C. Hede, Daiki Jonouchi, Dylan J. Kirkeby, Jayron T. Klinghagen, Kate J. Kralik, Julia S. Kutz, Olivia F. Lott, Erika J. McKenney, Victoria L. Pavik, Cayli H. Penner, Garrett Raymon, Leah B. Rozeboom, Jett L. Skrien, Jessica K. Slight, Maegan J. Stokes, Jonas D. Tiensvold, Kyra J. Wajer, Alaena L. Trevino, Byron Noordewier, Sara S. Tolsma",
"short_author_list": "Anderson et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00793-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37905824"
},
{
"title": "From Cullowhee Creek to Conley: genome sequence and annotation of a cluster DJ Gordonia phage",
"abstract": "We report the discovery of Gordonia phage Conley, a siphovirus isolated from Cullowhee Creek in the Fall of 2022. The 60,078bp genome contains 90 predicted protein-coding genes all transcribed in the same direction and has been assigned to genetic cluster DJ based on gene content similarity.",
"full_author_list": "Mindy N. Andro, AJ J. Cansler, Olivia S. Conley, Naidelyn O. Cruz, Joshua A. Dionne, Jordan I. Edwards, Daniel Furtuna, Carlee J. Green, Miriam Huber, Gunnar J. Hudson, Isabella R. Humphries, Amanda A. Karazin, Patrizia I. Mombille, Montana M. Pell, Gabriela Shickle, Zahria J. Shipp, Chloe A. Timmons, Jasmine I. Trembush, Cameron D. Turnmire, Naa Yemoley Yemofio, Mathew D. Burleson, Maria D. Gainey",
"short_author_list": "Andro et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01176-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38133170"
},
{
"title": "Complete genome sequences and characteristics of mycobacteriophages Diminimus, Dulcita, Glaske16, and Koreni",
"abstract": "Complete genome sequences of four novel mycobacteriophages, Diminimus, Dulcita, Glaske16, and Koreni, isolated from soil are presented. All these bacteriophages belong to subcluster M1, except Koreni that belongs to subcluster A4. Moreover, all have siphovirus morphologies, with genome sizes ranging from 51,055 to 81,156 bp.",
"full_author_list": "Faith W. Baliraine, Kaitlyn E. Mathews, Emma G. Livingston, Clarissa A. Martinez, Olivia L. Donnelly, Taryn M. Pledger, Tadeen Feroz, Zoe J. Harbison, Sarah G. Schlimme, Camila Andrade, Keren N. Salazar, Elise C. Berryhill, Madelyn M. DeLosSantos, Hannah L. Foree, Wanjiru Gicheru, Adrienne M. Jett, Sofia N. Mendez, Toluwalope M. Odebiyi, Jacob I. Pitman, Michael J. Tan, Josh D. McLoud, Frederick N. Baliraine",
"short_author_list": "Baliraine et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01010-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38063427"
},
{
"title": "Characterization of the genomes of cluster CT Gordonia terrae phages, Horseradish and Yummy",
"abstract": "The genomes of lytic, cluster CT Gordonia terrae phages, Horseradish and Yummy, are 45,764 and 45,878 bp in length, respectively, and each encodes 71 protein-coding genes. The genomes are identical in sequence with the exception of a 38-bp insertion/deletion in the minor tail protein, gp26.",
"full_author_list": "Nicole Bazinet, Esther Biro, Ashley Geydoshek, Grace Hodgkin, Eric Jestel, Emily Klute, Clare MacDonald, Marcus Russano, Jayson Thatcher, Melody N. Neely, Sally Molloy",
"short_author_list": "Bazinet et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00747-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37982651"
},
{
"title": "Complete Genome Sequence of Bacteriophage vB_Hercules_Set, Which Infects Enteric Pathogen Salmonella enterica Serovar Typhimurium",
"abstract": "We report the isolation, sequencing, and annotation of bacteriophage vB_Hercules_Set, a kuttervirus infecting human pathogen Salmonella enterica. vB_Hercules_Set was isolated from a slurry of soil and deli meat collected in New Hampshire in 2021. The genome length is 157,338 nucleotides, containing 210 protein-coding genes and five tRNAs.",
"full_author_list": "Evan N. Bennett, Ibrahim Ayyash, Joshua Hughes, Teagen Comeau, Shallee T. Page",
"short_author_list": "Bennett et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01282-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "36927071"
},
{
"title": "Annotation of Secretariat and Hydrus, two DJ cluster phages isolated on Gordonia rubripertincta",
"abstract": "Secretariat and Hydrus are phages grouped into the DJ cluster that were isolated on Gordonia rubripertincta NRRL B-16540. The phages have 75% nucleotide identity and share 73% gene content. Secretariat has a genome with 84 predicted genes, while Hydrus has 91 predicted genes and can also infect Gordonia terrae 3612.",
"full_author_list": "Jackson Bland, Sydney Miller, Elijah D. Algarin-Martinez, Abbigail M. Biggs, Maria E. D. Cavasini, Michael A. Chase, Caitlyn Coleman, Victoria Correa, Don F. Danielson, Wynter R. Dean, Joseph L. French, Mae E. Horne, Breanna M. Macumber, Francesca Kristal Martini, Sydney G. Mazzei, Coen E. E. McGarrah, Oslow Odegaard, Indu S. Parameswaran, Corrisa Quarterman, Taylor M. Rand, Kira M. Ruiz-Houston, Ava R. Sciacchitano, Nina S. Seidensticker, Anna Soltys, Adrian E. Terron-Osorio, Allyson L. Todd, Audrey R. Wood, Maxwell D. Ungrey, Richard S. Pollenz",
"short_author_list": "Bland et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00623-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37750725"
},
{
"title": "Genome sequence of Streptomyces BM cluster phage Frankenweenie",
"abstract": "Frankenweenie is a newly isolated bacteriophage that infects Streptomyces scabiei RL-34. Frankenweenie was discovered in Gaithersburg, MD, and has 366 genes comprising a 200,048-bp genome. Frankenweenie is grouped in cluster BM and is predicted to possess a unique tailspike protein that potentially widens its host range.",
"full_author_list": "Katherine E. Cleary, Charles Pelagalli, Marly Cassford, Nathan Berry, Elizabeth Aguas, Brandon Kim, Tagide deCarvalho, Deborah Jacobs-Sera, Steven M. Caruso, Kathleen Cornely",
"short_author_list": "Cleary et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00592-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37830805"
},
{
"title": "Genome sequence of the lytic bacteriophage Alucard, a cluster EE actinophage",
"abstract": "Bacteriophage Alucard is a lytic phage isolated from the soil collected in southern Maine on Microbacterium foliorum NRRL B-24224. Alucard has siphovirus morphology with a 17,363-bp genome encoding 25 putative genes. Based on gene content similarity to actinobacteriophages, Alucard is assigned to cluster EE.",
"full_author_list": "Samuel R. Cousins, Gemma R. Dufour, Kendra Law, Robert M. Nichols, Bradi J. Sladek, Christopher R. Aniapam, Brian P. Tarbox, Emily F. Savage",
"short_author_list": "Cousins et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.01017-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38051077"
},
{
"title": "Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species",
"abstract": "Satellites are mobile genetic elements that are dependent upon the replication machinery of their helper viruses. Bacteriophages have provided many examples of satellite nucleic acids that utilize their helper morphogenic genes for propagation. Here we describe two novel satellite-helper phage systems, Mulch and Flayer, that infect Streptomyces species. The satellites in these systems encode for encapsidation machinery but have an absence of key replication genes, thus providing the first example of bacteriophage satellite viruses. We also show that codon usage of the satellites matches the tRNA gene content of the helpers. The satellite in one of these systems, Flayer, does not appear to integrate into the host genome, which represents the first example of a virulent satellite phage. The Flayer satellite has a unique tail adaptation that allows it to attach to its helper for simultaneous co-infection. These findings demonstrate an ever-increasing array of satellite strategies for genetic dependence on their helpers in the evolutionary arms race between satellite and helper phages.",
"full_author_list": "Tagide deCarvalho, Elia Mascolo, Steven M. Caruso, Júlia López-Pérez, Kathleen Weston-Hafer, Christopher Shaffer, and Ivan Erill",
"short_author_list": "deCarvalho et al, 2023",
"article_url": "https://www.nature.com/articles/s41396-023-01548-0",
"journal": "The ISME Journal",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": ""
},
{
"title": "Genome sequences of bacteriophage Shambre1 and Renna12, isolated from Arthrobacter globiformis",
"abstract": "Bacteriophages Shambre1 and Renna12 were isolated from soil in Bismarck, ND, using Arthrobacter globiformis. Genomic characterization and analyses allowed Renna12 to be assigned to phage cluster AS3, while Shambre1, which is not closely related to any phage, is a singleton.",
"full_author_list": "Madeline Dojs, Christine Fleischacker, Skylar Ackerman, Blaise Boyle, Shambre Feiring, Thomas Fleischacker, Jaycee Frank, Sarah Jackson, Ashlin Schaefbauer, Corinna Vigness, Rylie Webb",
"short_author_list": "Dojs et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00858-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38088575"
},
{
"title": "Genome sequence of cluster A15 Gordonia terrae bacteriophage Nebulosus",
"abstract": "The temperate Gordonia phage Nebulosus was isolated from soil on Gordonia terrae and is a siphovirus. The genome is 52,175 bp in length, has 62% GC content, and encodes 96 protein-coding genes. Nebulosus encodes a partitioning system, ParABS, which is likely involved in lysogeny maintenance.",
"full_author_list": "Veronica Doyle, Gabriella Giftos, Strix Kugler, Andrew Melanson, Dominic Needham, Ryleigh Raber, Justin Solomon, Apple Webster, Melody Neely, Sally Molloy",
"short_author_list": "Doyle et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00699-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37750701"
},
{
"title": "Genome sequences of 13 Bacillus anthracis Sterne bacteriophages isolated from soil in the western United States",
"abstract": "Bacillus anthracis, classified as a Tier 1 Select Agent by the Centers for Disease Control and Prevention (CDC), is the causative agent of anthrax in both humans and livestock. Herein, we report the full genome sequences of 13 bacteriophages that infect B. anthracis Sterne. These phages are grouped into four clusters and are similar to previously described Bacillus phages.",
"full_author_list": "Jacob D. Fairholm, Rebecca James, Emily D. Lavering, Benjamin H. Ogilvie, Trever L. Thurgood, Richard A. Robison, Julianne H. Grose",
"short_author_list": "Fairholm et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00207-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38032238"
},
{
"title": "Characterization and genome sequence of Microbacterium foliorum phage Morrigan, of cluster EA6 with siphovirus morphology",
"abstract": "Bacteriophage Morrigan, which was isolated from soil using Microbacterium foliorum NRRL B-24224, is lytic with siphovirus morphology. Morrigan’s 40,509-bp genome has a GC content of 62.8% and 66 putative protein-coding genes, of which 31 could be assigned putative functions. Based on gene content similarity to actinobacteriophages, Morrigan is assigned to subcluster EA6.",
"full_author_list": "Jennifer A. Guerrero, Nery Maldonado, Emmanuella O. Mbajiofor, Lisette Ramirez, Mary Jo Valencia, Creehan D. Healy, Alejandro A. Garza, Samantha A. Mizell, Brianna N. Jackson, Mayra Vargas Ayala",
"short_author_list": "Guerrero et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00719-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37975671"
},
{
"title": "Complete genome sequence of bacteriophage MrAaronian isolated from an Arthrobacter globiformis culture",
"abstract": "Arthrobacteriophage MrAaronian contains a 54,509 bp DNA genome with 87 predicted protein-coding genes. MrAaronian has siphovirus morphology and was collected from a flowerbed soil sample in Poughkeepsie, NY, and isolated on an Arthrobacter globiformis B-2979 culture. MrAaronian has > 99% nucleotide identity with cluster AW arthrobacteriophages Michelle, Stayer, Sloopyjoe, and StarLord.",
"full_author_list": "Ian Haines, Jessica Blakely, Ashley Branson, Diana Estrada, Rebeca Fernandez Robles, Katelyn Fitzgerald, Shelby Jeffers, Timyee Leung, Jasmine Munoz, Ashley Olivos, Anayeli Ramirez, Caressa Smith, Justin Spere, Idaleth Tavarez, Isabella Wood, Ethan Zavala, Madison Arrighi, Angelica Coronel-Galindo, Megan K. Dennis, Marlee Goppert, Dustin Edwards",
"short_author_list": "Haines et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00778-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37933970"
},
{
"title": "Models of classroom assessment for course-based research experiences",
"abstract": "Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessment—(1) Assessing Laboratory Work and Scientific Thinking; (2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; (3) Appraising Forms of Scientific Communication; and (4) Metacognition of Learning—along with a set of practices for each aim. These aims and practices of assessment were then integrated with previously developed models of course-based research instruction to reveal an assessment program in which instructors provide extensive feedback to support productive student engagement in research while grading those aspects of research that are necessary for the student to succeed. Assessment conducted in this way delicately balances the need to facilitate students’ ongoing research with the requirement of a final grade without undercutting the important aims of a CRE education.",
"full_author_list": "David Hanauer, Tong Zhang, Mark Graham, Sandra Adams, Yesmi Patricia Ahumada-Santos, Richard Alvey, Mauricio Antunes, Mary Ayuk, María Elena Báez-Flores, Christa Bancroft, Tonya Bates, Meghan Bechman, Elizabeth Behr, Andrea Beyer, Rebecca Bortz, Dane Bowder, Laura Briggs, Victoria Brown-Kennerly, Michael Buckholt, Sharon Bullock, Kristen Butela, Christine Byrum, Steven Caruso, Catherine Chia, Rebecca Chong, Hui-Min Chung, Kari Clase, Sean Coleman, D. Parks Collins, Stephanie Conant, Brett Condon, Pamela Connerly, Bernadette Connors, Jennifer Cook-Easterwood, Katie Crump, Tom D'Elia, Megan Dennis, Linda DeVeaux, Lautaro Diacovich, Iain Duffy, Nicholas Edgington, Dustin Edwards, Tenny Egwuatu, Elvira Eivazova, Patricia Fallest-Strobl, Christy Fillman, Ann Findley, Emily Fisher, Matthew Fisher, Marie Fogarty, Amanda Freise, Victoria Frost, Maria Gainey, Amaya Garcia Costas, Atenea Garza, Hannah Gavin, Raffaella Ghittoni, Bryan Gibb, Urszula Golebiewska, Anna Grinath, Susan Gurney, Rebekah Hare, Steven Heninger, John Hinz, Lee Hughes, Pradeepa Jayachandran, Kristen Johnson, Allison Johnson, Michelle Kanther , Margaret Kenna, Bridgette Kirkpatrick, Karen Klyczek, Kathryn Kohl, Michael Kuchka, Amber LaPeruta , Julia Lee-Soety, Lynn Lewis, Heather Lindberg, Jaclyn Madden, Sergei Markov, Matthew Mastropaolo, Vinayak Mathur, Sean McClory, Evan Merkhofer, Julie Merkle, Scott Michael, Jon Mitchell, Sally Molloy, Denise Monti, María Alejandra Mussi, Holly Nance, Fernando Nieto-Fernandez, Jillian Nissen, Imade Nsa, Mary O'Donnell, Shallee Page, Andrea Panagakis, Jesús Ricardo Parra-Unda, Tara Pelletier, Tiara Perez Morales, Nick Peters, Vipaporn Phuntumart , Richard Pollenz, Mary Preuss, David Puthoff, Muideen Raifu, Nathan Reyna, Claire Rinehart, Jessica Rocheleau, Ombeline Rossier, Adam Rudner, Elizabeth Rueschhoff, Amy Ryan, Sanghamitra Saha, Christopher Shaffer, Mary Ann Smith, Amy Sprenkle, Christy Strong, C. Nicole Sunnen, Brian Tarbox, Louise Temple, Kara Thoemke, Michael Thomas, Deborah Tobiason, Sara Tolsma, Julie Torruellas Garcia, Megan Valentine, Edwin Vazquez, Robert Ward, Catherine Ward, Vassie Ware, Marcie Warner, Jacqueline Washington , Daniel Westholm, Keith Wheaton, Beth Wilkes, Elizabeth Williams, William Biederman, Steven Cresawn, Danielle Heller, Deborah Jacobs-Sera, Graham Hatfull, David Asai, Viknesh Sivanathan",
"short_author_list": "Hanauer et alia",
"article_url": "https://www.frontiersin.org/articles/10.3389/feduc.2023.1279921/full",
"journal": "Frontiers in Education",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": ""
},
{
"title": "Sequence analysis of Discoknowium, an A5 mycobacteriophage",
"abstract": "Discoknowium is a temperate A5 bacteriophage that infects the bacterial host Mycobacterium smegmatis. Isolated from a rat fecal sample, Discoknowium’s genome is 50,222 bp in length, contains 84 genes and 1 tRNA, and shares 82%–98% nucleotide identity with other A5 subcluster phages.",
"full_author_list": "Kate B. R. Carline, Megan S. Fleeharty, Lin Fang, Mahima Shijo, Mitchell K. Doherty, Zoe A. Riddick, Marcus O. Royster, Amiyah R. Stukes, Bilalay V. Tchadi, Alana N. Thomas, Kurt E. Williamson, Margaret S. Saha",
"short_author_list": "Kate B. R. Carline, Megan S. Fleeharty, Lin Fang",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00920-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38047653"
},
{
"title": "Complete genome sequences of cluster F1 and cluster B1 Mycobacterium smegmatis phages Karhdo and Basato",
"abstract": "We present the complete genome sequences of Mycobacterium smegmatis phages Karhdo and Basato, isolated in Clark County, Nevada. The phages were isolated and annotated by students enrolled in undergraduate research courses over two semesters at the University of Nevada, Las Vegas.",
"full_author_list": "Jireh Kim, Carlos Herrera, Wai Yan Aung, Gino Pablo Gonzales Boyles, Carmina Chavez, Mona Cibulka, Emma Foley, Jose Guerra, Disha Byadarahalli Mohan Kumar, Willow Levrant, Lewis Lim, Jose Llanes, Zachary Kamuela O'Brien, Art Pagaduan, Justin Aaron Richardson, Khristian Rosales, James Schrecengost, Tommy Shin, Gabriel Strong-Lundquist, Winnie Tat, Fritz Vanderford, Isabelle Vrinceanu, Vicky Wang, Stephanie Yang, Christy Strong, Philippos K. Tsourkas, Kurt Regner",
"short_author_list": "Kim et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00938-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38051075"
},
{
"title": "Genome sequence of Microbacterium foliorum bacteriophage DumpQuist isolated from soil in Clarksville, Tennessee",
"abstract": "Bacteriophage DumpQuist was isolated from soil collected in Clarksville, TN, using the bacterium Microbacterium foliorum. Electron microscopy revealed that DumpQuist has a podovirus morphology. DumpQuist has a 53,924-bp genome that contains 54 predicted protein-coding genes and is most similar to phages in actinobacteriophage cluster EK1.",
"full_author_list": "Sergei A. Markov, Kehinde O. Olusoga, Patience O. Oni, Grace A. Henderson",
"short_author_list": "Markov et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00923-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37991355"
},
{
"title": "Genome Sequences of Five Microbacterium foliorum Phages, GaeCeo, NeumannU, Eightball, Chivey, and Hiddenleaf",
"abstract": "Five siphoviruses were isolated from soil in southeastern Pennsylvania using Microbacterium foliorum. Bacteriophages NeumannU and Eightball have 25 predicted genes, Chivey and Hiddenleaf have 87 genes, and GaeCeo has 60 genes. Based on gene content similarity to sequenced actinobacteriophages, these five phages are distributed across clusters EA, EE, and EF.",
"full_author_list": "Matthew D. Mastropaolo, Patricia C. Fallest-Strobl, DaeKwon M. Sequira, Davia D. Campbell, Christopher J. Negro, Kho S. Tuang, Ian M. Sigmund-Hamre, Courtney L. Womack, Thomas Mansbridge, Amanda L. Metzler, Emily G. Sasher, Colleen Collins, Nicholas K. Crowley, Victoria R. Dower, Megan Bates, Christian Bjorkelo, Hailey Johnson, Lauren R. Salvitti, Neumann University Phage Discovery Group",
"short_author_list": "Mastropaolo et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.01106-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "36861977"
},
{
"title": "Complete Genome Sequences of Chop, DelRio, and GrandSlam, Three Gordonia Phages Isolated from Soil in Central Arkansas",
"abstract": "Chop, DelRio, and GrandSlam are phage with a Siphoviridae morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage.",
"full_author_list": "Heidi N. Mathes, Elijah I. Christenson, John H. Crum, Emme M. Edmondson, Kassidy E. Gray, Luke W. Lawson, Lauren E. Lee, Michael P. Lee, Jackson A. Lipscomb, Morgan E. Masengale, Hannah G. Matthews, Charles M. McClain IV, Tuesday N. Melton, Trace H. Morrow, Alexis M. Perry, David R. Rainwater, Grace E. Renois, Maryann F. Rettig, Duncan C. Troup, Allie J. Wilson, Nathan S. Reyna, Ruth Plymale",
"short_author_list": "Mathes et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00023-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37036373"
},
{
"title": "Isolation and Annotation of Azira, a CT Cluster Phage That Infects Gordonia rubripertincta",
"abstract": "Azira is a CT cluster actinobacteriophage that infects Gordonia rubripertincta NRRL B-16540. The genome contains 67 predicted protein coding genes, of which 31 have a putative function. Azira has a lysis cassette encoding two endolysins and three transmembrane proteins. Azira contains four genes predicted to encode enzymes involved in thymine synthesis.",
"full_author_list": "Coen E. E. McGarrah, Elijah D. Algarin-Martinez, Maria E. D. Cavasini, Victoria Correa, Don F. Danielson, Wynter R. Dean, Joseph L. French, Naleena N. Gaskin, Urvi Jain, Jeanette Janvier, Breanna M. Macumber, Francesca Kristal Martini, Sydney G. Mazzei, Jennifer M. Mujica, Oslow Odegaard, Corissa Quaterman, Taylor M. Rand, Nina S. Seidensticker, Tyler Serrano, Anna Soltys, Maxwell D. Ungrey, Richard S. Pollenz",
"short_author_list": "McGarrah et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00347-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37347199"
},
{
"title": "Genome sequences of cluster GA phages Phonegingi and Dropshot",
"abstract": "Bacteriophages Phonegingi and Dropshot were isolated from soil in North Carolina using the host Microbacterium foliorum. Both phages have siphovirus morphologies. Based on gene content similarity to one another and to other actinobacteriophages, both phages are assigned to phage cluster GA.",
"full_author_list": "Natalie McLean, Tabitha Jackson, Yajat Govardhan, Aditi Dharanendiran, Caden Bost, Frederick Brown, Benjamin Cowen, Jenna Deselem, Nico Parkhurst, Jacob Stewart, Justin Leonard, D. Parks Collins",
"short_author_list": "McLean et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00918-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38014965"
},
{
"title": "Complete genome sequences of Gordonia rubripertincta phages OtterstedtS21 and Patos",
"abstract": "We report the genomes of two viruses with siphovirus morphology, OtterstedtS21 and Patos, from Albany, New York, using Gordonia rubripertincta. The genomes of OtterstedtS21 and Patos are ~68 kbp long with 58% GC content. Both phages group with cluster DV based on gene content similarity to phages in the Actinobacteriophage database.",
"full_author_list": "Bowen Meng, Alexander Bleau, Riddhi R. Bombaywala, Audrey S. DeGraw, Manjot S. Deol, Kendall E. Dollard, Nicolas Gentile, Julianna Jebaraj, Gregory N. Kayayan, Briana C. Miranda, Ayobamidele E. Momoh, Elias Morales, Amalia C. Nunes, Antonia M. Oropallo, Sophia C. Otterstedt, Anna T. Pridell, Jenna I. Roberts, Gabriel A. Ruiz, Dhatri Sangasani, Renee D. Smith, Mahad Tarar, Vir Singh, Pradeepa Jayachandran",
"short_author_list": "Meng et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00718-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37772859"
},
{
"title": "Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions",
"abstract": "Bacteriophages are being widely harnessed as an alternative to antibiotics due to the global emergence of drug-resistant pathogens. To guide the usage of these bactericidal agents, characterization of their host specificity is vital—however, host range information remains limited for many bacteriophages. This is particularly the case for bacteriophages infecting the Microbacterium genus, despite their importance in agriculture, biomedicine, and biotechnology. Here, we elucidate the phylogenomic relationships between 125 Microbacterium cluster EA bacteriophages—including members from 11 sub-clusters (EA1 to EA11)—and infer their putative host ranges using insights from codon usage bias patterns as well as predictions from both exploratory and confirmatory computational methods. Our computational analyses suggest that cluster EA bacteriophages have a shared infection history across the Microbacterium clade. Interestingly, bacteriophages of all sub-clusters exhibit codon usage preference patterns that resemble those of bacterial strains different from ones used for isolation, suggesting that they might be able to infect additional hosts. Furthermore, host range predictions indicate that certain sub-clusters may be better suited in prospective biotechnological and medical applications such as phage therapy.",
"full_author_list": "Mark Milhaven, Cyril J. Versoza, Aman Garg, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Jackelyn Lobatos, Corinne Mitra, Maria Strasser, Susanne P. Pfeifer",
"short_author_list": "Milhaven et al",
"article_url": "https://www.mdpi.com/2076-2607/11/1/170",
"journal": "Microorganisms",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "36677462"
},
{
"title": "Complete Genome Sequence of the Microbacterium Bacteriophage Chako",
"abstract": "We characterized the complete genome sequence of Chako, an obligate lytic bacteriophage with siphovirus morphology from subcluster EA1 that infects Microbacterium foliorum NRRL B-24224. Its 41.6-kb genome contains 62 putative protein-coding genes and is highly similar to that of bacteriophage HanSolo (99.26% nucleotide identity).",
"full_author_list": "Mark Milhaven, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Aman Garg, Jackelyn Lobatos, Corinne Mitra, Maria Strasser, Robert Harms, Susanne P. Pfeifer",
"short_author_list": "Milhaven et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01251-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "36645290"
},
{
"title": "Complete Genome Sequences of Subcluster C1 Mycobacteriophages Blackbrain, Cactojaque, Kboogie, Trinitium, and YoungMoneyMata",
"abstract": "Five subcluster C1 mycobacteriophages, Blackbrain, Cactojaque, Kboogie, Trinitium, and YoungMoneyMata, were isolated from soil using the host Mycobacterium smegmatis mc2155. The genome sizes range from 154,512 to 156,223 bp. The largest genome encodes 237 predicted proteins, 34 tRNAs, and 1 transfer-messenger RNA (tmRNA).",
"full_author_list": "Madison M. Moore, Mary A. Ayuk, Amber A. Johnson, Triniti Sims, Sanaa Haamen, Ramata Haidara, Adrian D. Allen, Leon A. Dickson, Somiranjan Ghosh, Ayele Gugssa, Hemayet Ullah, Glory B. Bassey, Lourds M. Fernando, Laricca Y. London, Esohe G. Irabor, Swagota D. Roy, Benedict K. Quagraine, Michael Smith, Howard University SEA-PHAGES Students, Winston A. Anderson, Courtney J. Robinson",
"short_author_list": "Moore et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00253-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37255446"
},
{
"title": "Genomic sequence identification of Arthrobacter phage Ascela",
"abstract": "Arthrobacter phage Ascela was isolated in North Georgia. Its genome is 44,192 bp with 71 open reading frames and a GC content of 67.4%. It shares 99.29% nucleotide identity with Arthrobacter phage Iter. Actinobacteriophages that share over 50% nucleotide identity are sorted into clusters, with Ascela in cluster AZ and subcluster AZ1.",
"full_author_list": "Audrey E. Nesbit, Alison E. Kanak",
"short_author_list": "Nesbit et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00776-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37905911"
},
{
"title": "Isolating and characterizing cluster AB Mycobacteriophage NoShow, which encodes lysis proteins shared with cluster H2 phages",
"abstract": "We present here Mycobacteriophage NoShow, isolated from a soil sample collected on the Maguire Campus of Saint Joseph’s University in Merion Station, Pennsylvania. Even though NoShow’s 52,825 bp genome is most similar to phages in cluster AB, its lysA and lysB genes are most similar to phages in cluster H2.",
"full_author_list": "Danielle J. Niblock, Anne R. Winkler, Caroline E. Curtin, Jacqui F. Kokinda, Walter A. Danker, IV, Ignacio Llorente Fernandez, Ava R. Smith, Asad Ali, Gabrielle G. Cruz, Leya C. Givvines, Julia Y. Lee-Soety",
"short_author_list": "Niblock et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00649-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37747255"
},
{
"title": "Genome sequences of Microbacterium foliorum phages, BabyYoda and Lynlen",
"abstract": "BabyYoda and Lynlen are two cluster EB phages that were discovered at Thiel College using Microbacterium foliorum NRRL B-24224. Both BabyYoda and Lynlen are predicted to be lytic, with siphovirus morphologies, with genome sizes of 41,557 and 41,448 base pairs, respectively.",
"full_author_list": "Ashley E. Prout, Sarah J. Swerdlow",
"short_author_list": "Prout et al",
"article_url": "https://journals.asm.org/doi/pdf/10.1128/mra.01006-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38132671"
},
{
"title": "Genome sequences of six cluster CT and two cluster DJ bacteriophages that infect Gordonia rubripertincta",
"abstract": "We report the genome sequences of eight bacteriophages isolated using Gordonia rubripertincta NRRL B-16540-SEA. Based on gene content similarity to phages in the Actinobacteriophage database, six of the phages are assigned to phage cluster CT while two are assigned to cluster DJ.",
"full_author_list": "Xavier F. Rodriguez, Daniel C. Williams https, Catherine P. Chia",
"short_author_list": "Rodriguez et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00736-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37905830"
},
{
"title": "Complete genome sequences of cluster G1 and cluster K4 Mycobacterium smegmatis phages omnicritical and Barkley26",
"abstract": "We present the complete genome sequence of two Actinobacteriophages, OmniCritical and Barkley26, isolated in Clark County, NV. Over two semesters, The University of Nevada, Las Vegas (UNLV) students isolated and purified phages and manually annotated the genomes. The courses follow the HHMI Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) curricula.",
"full_author_list": "Ojas Sali, Dave M. Patel, Michaelangelo C. Ortega, Sydnee Han, Hanford Gerille Esperanza Gonzales, Omar Sulaiman Haneefzai, Carlos Herrera, Jireh Kim, Brooke Knoles, Abigail Lopez, Justin Aaron Richardson, David Andres Roach, Maxene Vergonia-Fehlman, Jessica Vincent, Sang Ho Yim, Leo I. C. Cutter, Christy Strong, Philippos K. Tsourkas, Kurt Regner",
"short_author_list": "Sali et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00274-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37671868"
},
{
"title": "Genome sequence of bacteriophage Aoka, a cluster FO phage isolated using Arthrobacter globiformis",
"abstract": "We report the discovery and genome sequence of bacteriophage Aoka, an actinobacteriophage isolated from a soil sample in Pueblo, Colorado using Arthrobacter globiformis, B2880-SEA. Its genome length is 36,744 base pairs with 54 protein-coding genes. Based on gene content similarity to other actinobacteriophages, Aoka is assigned to cluster FO.",
"full_author_list": "Aidan Sasaoka, Olivia Arellano, Xavier R. Hatch, Amaya M. Garcia Costas",
"short_author_list": "Sasaoka et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00454-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37737618"
},
{
"title": "Complete genome sequences of Streptomyces griseus phages Spelly and Phredrick",
"abstract": "We present the complete genome sequences of two viruses with siphovirus morphology, isolated from soils collected in Southwestern Indiana using the host Streptomyces griseus. Spelly is a BE2 cluster phage with a 131,347-bp genome. Phredrick is a BK1 cluster phage with a 128,873-bp genome.",
"full_author_list": "Joyce Stamm, Julie A. Merkle, Ava Abernathy, Elizabeth Ackerman, John Brown, Abbey Harris, Kayli Hoffman, Ashleigh Hoskins, Abbie Jahn, Nathan Jones, Ashley Kitch, Nandini Mathavan, Nat Rose, Joey Taylor",
"short_author_list": "Stamm et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01049-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "38112473"
},
{
"title": "Isolation and genome sequence annotation of SallyK, a newly discovered cluster EG bacteriophage infecting Microbacterium",
"abstract": "Discovered from soil in a flower planter in Pocatello, Idaho and using Microbacterium foliorum, SallyK is a lytic bacteriophage with a siphovirus morphology. It has a 62,883 bp-long genome with 103 putative genes. Based on gene content similarity to actinobacteriophages, SallyK is assigned to cluster EG.",
"full_author_list": "Paige R. Wood, Emily A. Sullivan, Rylee T. Mathison, Sariah M. Hepworth, R. Scott Graves, Breanna Danklefsen, Omer Almahie, Carlos Serna, Dylan J. Hunt, Reganne Brewster, Skylar Bartholomew, Jack F. Shurley, Anna S. Grinath, Michael A. Thomas",
"short_author_list": "Wood et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00943-23",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2023",
"pubmed_id": "37991360"
},
{
"title": "Genome Sequences of Two Gordonia rubripertincta Cluster DJ Bacteriophages, Pherobrine and Burley",
"abstract": "herobrine and Burley are siphoviruses infecting Gordonia rubripertincta. Pherobrine has a 60,305-bp genome with 89 predicted protein-coding genes, and Burley has a 60,111-bp genome with 90 predicted protein-coding genes. Both phages are assigned to cluster DJ, where they share 78% gene content similarity with each other.",
"full_author_list": "Aaron J. Adams, Michael Bell, Marie J. Bennett, Umar N. Chaudhry, Jennifer N. Daniels, James E. Herman, Sophia A. Oh, Fedora Parra, Cynthia R. Reagan, Borna Zareiesfandabadi, Marie P. Fogarty",
"short_author_list": "Aaron J. Adams, et al",
"article_url": "https://pubmed.ncbi.nlm.nih.gov/34989620/",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36346246"
},
{
"title": "Complete Genome Sequences of Actinobacteriophages Anaysia and Caviar",
"abstract": "Anaysia and Caviar are temperate siphoviruses isolated from soil using Gordonia terrae 3612 and Mycobacterium smegmatis mc2155, respectively. Anaysia’s 52,861-bp genome carries 102 genes, while Caviar’s 47,074-bp genome carries 79 genes. Based on gene content similarity, Anaysia and Caviar are assigned to phage clusters A15 and A3, respectively.",
"full_author_list": "Zain U. Abidin, Joselyne E. Aucapina, Shante Beauzil, Christina M. Berotte, Andrews O. Bonsu, Gabriella Y. Burgos, Solomon Tin Chi Chak, Anaya Collymore, Ethan R. Daley, Raphael Defarias, Veronica Ghobrial, Shivraj S. Gill, Jose M. Huertas-Arias, Hadassah Joseph, Navjot Kaur, Ummay Khan, Connor J. Klein, Horlando Lazo, Yeehen Li, Olivia B. Miller, Javier J. Muñoz, Fernando E. Nieto-Fernandez, Lisa-Marie Nisbett, Darren Owens, Samay M. Patel, Edraine J. Paulino, Samori Pender, Shania M. Perkins, Anjoli Persaud, Tamahina Pierrot, Ibrahim Raja, Kayla L. Riley, Sasha Romero, Paola G. Sarmiento, Kanaja Shorter, Steven Smith, Warda Tahir, Chisom A. Ukekwe",
"short_author_list": "Abidin et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00944-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36287003"
},
{
"title": "Complete Genome Sequence of Bacteriophage Fizzles, Isolated from Microbacterium foliorum",
"abstract": "Microbacteriophage Fizzles has a 62,078-bp linear double-stranded DNA genome sequence, predicted to contain 104 protein-coding genes. Fizzles is a Siphoviridae actinobacteriophage isolated from an ant hill soil sample collected in Stephenville, TX. Microbacteriophage Fizzles has >83.6% nucleotide identity with microbacteriophages Squash and Nike.",
"full_author_list": "Skyler Adams, Gabrielle Spotz, Riley Babcock, Chloe Butler, Samantha Conger, Madison Crew, Stephanie Garcia, , Joanna Gonzalez, Jocelyn Hodges, Alondra Martinez, Samuel Munoz, Chloe O’Grady, Abigail Quirl, Kristin Sefcik, Tanner Taylor, Gustavo Vazquez, Faith Cox, Dustin Edwards",
"short_author_list": "Adams et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.01079-21?af=R",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "34989620"
},
{
"title": "Annotation of the Complete Genome Sequences of Bacteriophages Sara and Birdfeeder",
"abstract": "Sara is a siphovirus with a linear 17,362bp genome containing 25 genes. Birdfeeder is a podovirus with a circularly permuted 53,897bp genome containing 52 genes. Sara and Birdfeeder were isolated from environmental samples in Plattsburgh, NY, USA and Forest Hill, MD, USA, respectively, using Microbacterium foliorum NRRL B-24224.",
"full_author_list": "Benjamin M. Adams, Joseph B. Adams, Reganne L. Brewster, Michael S. Cutler, Anthony E. Davis, Abby H. Gallegos, Jeremy S. Hernandez, Luke H. May, Emma G. Montoya, Andrew T. Reagan, Jack F. Shurley, Anna S. Grinath, Michael A. Thomas",
"short_author_list": "Adams et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00780-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36121218"
},
{
"title": "Genome Sequence and Annotation of Bacteriophage Tokki Isolated on Arthrobacter globiformis B-2979",
"abstract": "Arthrobacter phage Tokki is a siphovirus isolated from soil in River Falls, Wisconsin. The genome contains 57,652-bp encoding 98 proteins, of which 23 were assigned a function. Tokki’s genome structure and content is typical of other AU2 subcluster phages, except for the lack of an identifiable acetyltransferase.",
"full_author_list": "Alicia Aguilera Marti, Nicholas D. Bullock, Samuel B. Everett, Tonya C. Bates, Ellen M. Wisner",
"short_author_list": "Aguilera Marti et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00803-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36121232"
},
{
"title": "Complete Genome Sequences of Cluster F1 Mycobacteriophages Akhila and MilanaBonita",
"abstract": "Akhila and MilanaBonita are mycobacteriophages that were isolated from soil in New York using Mycobacterium smegmatis. Both phages have genomes that are 56,251 bp long and contain 99 genes; the genomes differ by only 1 nucleotide. Based on gene content similarity to phages in the Actinobacteriophage Database, both phages are assigned to cluster F1.",
"full_author_list": "Umer Ahsan, Nimra Ali, Chelsea Akintunde, Mohamed Ali, Caroline Bond, Brittney Canada, Soban Choudhry, Dennis Cortez, Nia Dennis, Tamia Gomez, Seerat Hameed, Daniel Higgins, Keisha Lacayo, Zeeshan Memon, Shubh Patel, Joel Philip, Ramon Polanco, Anshika Rajput, Malaika Raza, Anthony Recenello, Benjamin Scariah, Emmaline Seide, Stephany Shaji, Ariel Shalonov, Emaan Tariq, Zainab Tariq, Blessy Thomas, Rita Reddy, Fernando E. Nieto-Fernandez, Jillian C. Nissen",
"short_author_list": "Ahsan et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01191-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36537788"
},
{
"title": "Genome Sequence of Singleton Gordonia terrae Bacteriophage Finkle",
"abstract": "Bacteriophage Finkle is a temperate siphovirus isolated from soil on Gordonia terrae. The 47,895-bp genome has a GC content of 66.6% and encodes 84 protein-coding genes. The genome is not closely related to sequences in the Actinobacteriophage database, sharing less than 35% gene content, and was classified as a singleton.",
"full_author_list": "Seth Ashby, Gavin Bressette, Sydney Brown, Sophie Charles, Melissa Maginnis, Sally D. Molloy, Melody N. Neely",
"short_author_list": "Ashby et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00693-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36005761"
},
{
"title": "Genome Sequences of Microbacterium foliorum Phages Anseraureola, Pondwater, and Yasuo",
"abstract": "Anseraureola, Pondwater, and Yasuo are bacteriophages with siphovirus morphology that infect Microbacterium foliorum NRRL B-24224. They were isolated from soil collected in Amherst, Massachusetts, and have genome lengths between 17,362 bp and 17,453 bp. These phages each contain 25 predicted protein-coding genes and are assigned to phage cluster EE.",
"full_author_list": "David Bamgbowu, John Bsoumai, Jessica Butura, Emma Cady, Gabriella Cholod, Isaac Collibee, Lois Dompreh, Sydney Eisner, Maxim Elmaleh, Katelan Fitzgerald, Eric Gillis, Anna Horgan, Dylan Judd, Julia Keefe, Erika Kovalski, Kylie LaBianca, Patrick Lee, Fengkai Lin, Heather Maiuri, Chloe McDonald, Arden McKnight, Meghan Meseerole, Farah Mizra, Elizabeth Monger, Evelyn Moore, Nina Nguyen, Bettina Noel, Daniel O’Connor, Ruben Pagani, Makenzie Palmgren, Karin Pan, Bondita Pech, Jeanne Qian, Sheida Rastegar, Brittney Simas, Adeline Southard, Matt Tracy, Harry Vuong, Sean Whelan, Angela Zou, Elizabeth Punska, Robert Pause, Fengqiu Zhang, Alexander Ribbe, Peter Chien, Jessica Rocheleau",
"short_author_list": "Bamgbowu et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00849-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36227095"
},
{
"title": "Complete Genome Sequence of Gordonia rubripertincta Bacteriophage Hexbug Suggests Potential for a New CT Subcluster",
"abstract": "Through the SEA-PHAGES program at Tufts University, a bacteriophage infecting Gordonia rubripertincta NRRL B-16540 was isolated and characterized. Hexbug is a lytic phage and is currently one of 44 phages belonging to cluster CT. The Hexbug genome shares >96% nucleotide identity with cluster CT phage Orla.",
"full_author_list": "Daniel J Barszczak, Maxwell J Allison, Yaqi Cai, Lily Forman, Joshua M Goldstein, Sarrah M Hakimjee, Matthew T Scapicchio, Ruben Torres, Hannah E Gavin",
"short_author_list": "Barszczak et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00773-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36321919"
},
{
"title": "Complete Genome Sequences of Microbacterium Phages Clayda5 and Gshelby23 and Gordonia Phages Wrigley and Santhid",
"abstract": "Bacteriophages Clayda5, Gshelby23, Wrigley, and Santhid were isolated from soil samples collected in Iowa, with genomes typical of actinobacteriophages from clusters EB, EM, CY, and DY, respectively. Wrigley and Santhid were isolated on Gordonia terrae and are likely to be temperate. Clayda5 and Gshelby23 were isolated on Microbacterium foliorum.",
"full_author_list": "Abigail M. Bastian, Marcus J. Blankespoor, Gideon K. Fynaardt, Sadie A. Gilmeister, Emily E. Hurley, Madison Jones, Erika J. McKenney, Alexa N. Olguin, Micah N. Rens, Garrett Snyder, Anneka E. Sterk, Sophie M. Swart, Alaena Trevino, Ashley N. Van Egdom, Morgan C. Veach, Kip Cullinan, Kaarina Van Berkum, Lauren R. Pavich, Krista Starr, Byron Noordewier, Sara S. Tolsma",
"short_author_list": "Bastian et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00789-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36214689"
},
{
"title": "Complete Genome Sequences of Microbacterium paraoxydans Phages Cassita and Fransoyer",
"abstract": "Phages Cassita and Fransoyer were isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The genomes of Cassita and Fransoyer are 61,868 bp and 62,277 bp, respectively, with direct terminal repeats. Both phages exhibit siphoviral morphology and are predicted to have lytic life cycles.",
"full_author_list": "Brynn R. Bauer, Madelyn G. Brookins, Spencer Fobbe, Jade R. Fredrickson, Aidan D. Fretland, Nicole D. Grant, Abigail S. Katzenberger, Ali I. Khan, Brea L. Kieffer, Andrew M. Loken, Ignacio Lopez, Lindsay J. Lutton, Samantha A. Marquette, MaKayla J. Mears, Cadence M. Moe, Alexandra K. Parent, Rodrick P. Payne, Ida K. Peterson, Hailey L. Pucillo, Brina E. L. Rickman, Maddie A. Stubson, Elizabeth M. Zimmerman, Ashlyn M. Spring, Karen K. Klyczek",
"short_author_list": "Bauer et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00885-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36287072"
},
{
"title": "Genome Sequence of a Cluster DN1 Gordonia terrae Phage, Periwinkle",
"abstract": "Periwinkle is a temperate bacteriophage that was isolated on the host Gordonia terrae 3612. The genome has a length of 55,657 bp and a GC content of 62.9% and contains 109 protein-coding genes and no tRNA genes. An 8-kb region after the structural protein genes encodes eight membrane proteins, a tyrosine integrase, and an immunity repressor.",
"full_author_list": "Emma M. Boudreaux, Sophie B. Childs, Abigail Dichiara, Amy Hardy, Sam Kovacs, Alison F. Kueck, Parker M. Landesbergen, Melody Neely, Sally Molloy",
"short_author_list": "Boudreaux et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00696-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36005762"
},
{
"title": "Genome Sequences of Arthrobacter globiformis B-2979 Phages GlobiWarming and TaylorSipht",
"abstract": "Phages GlobiWarming and TaylorSipht are siphoviruses isolated on Arthrobacter globiformis B-2979. GlobiWarming has a 42,691 bp long genome that encodes 74 genes, whereas TaylorSipht has a 39,051 bp genome that encodes 65 genes. Both phages encode functions typical of temperate phages, with each including an immunity repressor, integrase, and excise.",
"full_author_list": "Miguel B. Bugayong, Aileen Cha, Carly L. Hamel, Ryan R. Johnson, James Kim, Joseph J. Kim, Andrew S. Levy, Kenneth D. Nguyen, Luc H. Pham, Anusha Sapre, Aidan C. Scanlan, Brandon Ye, Christa Bancroft",
"short_author_list": "Bugayong et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00923-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36197292"
},
{
"title": "Complete Genome Sequence of Finnry, a Subcluster L3 Mycobacteriophage from Charleston, South Carolina",
"abstract": "Subcluster L3 bacteriophage Finnry was isolated from soil collected in Charleston, South Carolina, using Mycobacterium smegmatis mc2155 as a host. The genome of this temperate siphovirus is 75,632 bp long (130 predicted protein-coding genes, 9 tRNAs, and no transfer-messenger RNAs), and BLASTn alignment revealed 99.86% identity with the genome of L3 mycobacteriophage Samty.",
"full_author_list": "Christine A. Byrum, Véronique A. Delesalle, Claudia L. Gold, Daniel J. Bennett, B. Conner Fox, Brandon M. Houston, Harrison E. Koller, Peyton G. Russell, Pavi Sreekumar, Bradley R. Teasley, Eva Vandoros, Anastasia M. Zimmerman, Mouna S. DiBenedetto, Christopher A. Korey",
"short_author_list": "Byrum et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00636-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35969062"
},
{
"title": "Genome Annotation for Pinkcreek, a C1 Subcluster Mycobacteriophage from New Orleans, Louisiana",
"abstract": "The mycobacteriophage Pinkcreek (C1 subcluster) was extracted from soil collected on the Dr. Norman C. Francis Parkway Bike Trail in New Orleans, Louisiana. It is a member of the family Myoviridae and infects Mycobacterium smegmatis mc2155. The Pinkcreek genome is 153,184 bp and contains 216 predicted protein-coding genes, 29 tRNAs, and 1 transfer-messenger RNA.",
"full_author_list": "Christine A. Byrum, Maximiliano F. Flota, Jackson A. Derrick, Steven Grant Dixon, Andre S. Gagliano, Halee S. Gibson, Paige A. Loose, Ashley Montero, Jessica L. Mugford, Emily E. Mullner, Briana C. Pope, Christopher A. Korey",
"short_author_list": "Byrum et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00576-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35980182"
},
{
"title": "Genome Sequence of a Cluster CR2 Gordonia terrae Phage, StarStruck",
"abstract": "Bacteriophage StarStruck is a lytic Siphoviridae phage that infects Gordonia terrae 3612. The 68,128-bp genome of StarStruck has a GC content of 65.4% and contains 92 protein-coding genes, including the gene for a HicA-like toxin. StarStruck was assigned to subcluster CR2 based on >35% shared gene content with other cluster CR genomes in the Actinobacteriophage Database.",
"full_author_list": "Wyatt Cannell, Eleanor Carrolton, Julia Coombs, Addison Gambol, McHenna Martin, Melody Neely, Sally Molloy",
"short_author_list": "Cannell et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00694-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36040147"
},
{
"title": "Genome Sequences of 14 Siphophages That Infect Serratia marcescens",
"abstract": "We announce the complete genome sequences of 14 Serratia bacteriophages isolated from wastewater treatment plants. These phages define two previously undescribed types which we call the Carrot-like phage cluster (phages Carrot, BigDog, LittleDog, Niamh, Opt-148, Opt-169, PhooPhighters, Rovert, Serratianator, Stoker, Swain, and Ulliraptor) and Tlacuache-like phage cluster (Tlacuache and Opt-155).",
"full_author_list": "Emilee L. Carr, McKay E. Wilson, Stephen T. Adams, Daniel K. Arens, Moroni Ayala, Hayden Ayers, Austin Barker, SHOW ALL (44 AUTHORS), Victoria Beecroft, Emily Bishop, Braden Brundage, Melany J. Carroll, Jacob Chow, Hunter Cobbley, Rhen Davis, Christopher Fajardo, Samuel Flor, David Fuhriman, Rochelle Gaertner Tullis, Austen Gleave, Ciara Green, Tyler Hanis, Trevor Hoggan, Liam Johnson, Jared L. Kruger, Andrew Lambert, Elvira Correa Lazaro, Emily Loertscher, Naomi Marshall, Elise Melhado, Riley Sarabia, Ruchira Sharma, Austin Steffensen, Jared B. Stewart, Tyson Stoker, Andrew Swain, Simeon Toronto, Daniel W. Thompson, J. Zachary Todd, Jamison Walker, Andrew Wilkey, Derrek Wilson, Cynthia L. Hallen, Sherwood R. Casjens, Julianne H. Grose",
"short_author_list": "Carr et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01212-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35412361"
},
{
"title": "Genome Sequence of Arthrobacter globiformis Phage KeAlii from Hawaiʻi",
"abstract": "Here, we report the genome sequence of bacteriophage KeAlii, a Siphoviridae that infects Arthrobacter globiformis strain B-2979, from Honolulu, Hawaiʻi. The 41,850-bp genome contains 66 predicted protein-coding genes and 1 gene that encodes a tRNA for tryptophan. Genome comparisons suggest KeAlii is closely related to actinobacteriophage Adolin.",
"full_author_list": "Rebecca A. Chong, University of Hawaiʻi at Mānoa SEA-PHAGES students, Stuart P. Donachie, Floyd A. Reed, Megan L. Porter",
"short_author_list": "Chong et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00439-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": ""
},
{
"title": "Genome Sequence of Arthrobacter Phage NathanVaag",
"abstract": "We report the genome sequence of bacteriophage NathanVaag, an actinobacteriophage isolated from soil in El Paso, Texas, that infects Arthrobacter sp. strain ATCC 21022. The 49,645-bp genome contains 73 predicted protein-coding genes. Based on gene content similarity to phages in the Actinobacteriophage Database, NathanVaag is assigned to phage cluster AO1.",
"full_author_list": "Rebecca A. Chong, Charlie M. Cosse, Viviana Gaytan, Dylan S. Green, Cade J. Kane, Kirsten A. Kasal, Zarek K. Kon, Rosa E. Maxwell, Vlas Olaru, Tuan D. Pham, MeiLin F. Precourt, Joseph R. Romero, Wellington J. Rothschild, Shantelle N. Sales, Troy D. Sensano, Wesley E. Simko, Inugiksuq J. Smith, Mika A. Toor, Adelaide R. Wilson, Megan L. Porter",
"short_author_list": "Chong et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00940-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36250873"
},
{
"title": "Mycobacteriophage Tarkin: a Cluster E Phage",
"abstract": "Mycobacteriophage Tarkin is a newly isolated phage that infects Mycobacterium smegmatis mc2155. Tarkin was discovered in Providence, RI, and has a 75,998-bp genome sequence. Tarkin is predicted to have 142 protein coding genes and 2 tRNA genes. Based on gene content similarity, Tarkin is grouped with mycobacteriophages in cluster E.",
"full_author_list": "Katherine E. Cleary, Anna M. Fakhri, Ethan N. Dionne, Marcie Warner, Joseph A. DeGiorgis, Kathleen Cornely",
"short_author_list": "Cleary et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00961-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36409114"
},
{
"title": "Complete Genome Sequence of Bacteriophage Eula, Isolated on Microbacterium foliorum",
"abstract": "Eula is a lytic microbacteriophage extracted from a soil sample collected in Statesville, NC, and isolated on Microbacterium foliorum NRRL B-24224. The Eula double-stranded DNA genome is 41,379 bp, with 69 predicted protein-coding genes and 1 tRNA. Based on gene content similarity, Eula was assigned to bacteriophage cluster EB.",
"full_author_list": "Travis Cook, Sophie Raffan, Taylor Born, Chloe Breece, Isaac Chandler, Henry DiLeo, Allison Eudy, Kaitlyn Lyon, Christian Nicholson, Adilene Serrano, Madeline Sigmon, Sydney Stevenson, Karli Townsell, Grace Van Patten, Justin E. Leonard, D. Parks Collins",
"short_author_list": "Cook et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00728-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36154145"
},
{
"title": "The Genomic Characterization of Two Microbacterium foliorum–Specific Bacteriophages, QuadZero and AnnaLie",
"abstract": "The microbacteriophages QuadZero and AnnaLie were isolated from soil samples from Charlotte, NC, and were classified into EA and EB clusters, respectively. QuadZero has a 40,140 base-pair double-stranded DNA genome with 62 predicted protein coding genes, whereas AnnaLie has a 41,665-bp genome with 71 predicted protein coding genes.",
"full_author_list": "Jennifer Cook-Easterwood, Donovan J. Bethel, Irene Kurikose, Joanna Katsanos",
"short_author_list": "Cook-Easterwood et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00208-22?af=R",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35658534"
},
{
"title": "Complete Genome Sequence of Arthrobacter Phage ScienceWizSam",
"abstract": "Phage ScienceWizSam was isolated from soil using Arthrobacter sp. strain ATCC 21022. The phage genome is 58,217 bp with 96 open reading frames (ORFs). All of the ORFs are transcribed rightwards. Based on gene content similarity, ScienceWizSam is assigned to phage subcluster AU1.",
"full_author_list": "Samantha Coplen, Charmaine Lopez-Davis, Hari Kotturi",
"short_author_list": "Coplen et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00927-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36342275"
},
{
"title": "Genome Sequences of Gordonia rubripertincta Bacteriophages AnarQue and Figliar",
"abstract": "AnarQue and Figliar are bacteriophages identified from the host bacterium Gordonia rubripertincta NRRL B-16540. AnarQue is circularly permuted and has a length of 61,822 bp; it is assigned to cluster DR. Figliar has a 3' sticky overhang and a length of 61,147 bp; it is assigned to cluster DJ.",
"full_author_list": "Ethan Curran, Sabrina E Callaway, Ramel R Dumanlang, Anna V Harshaw, Paula N Palacio, Yuta Nakamura, Kendra W Kimberley, James R Theoret, Earl J Yoon, Erin J Windsor, Chelsey C McKenna",
"short_author_list": "Curran et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01085-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35049345"
},
{
"title": "Genome Sequence of the Cluster CD Gordonia Phage Widow",
"abstract": "Widow is a novel cluster CD bacteriophage isolated from a soil sample using the bacterial host Gordonia terrae. The Widow genome is 43,656 bp in length and encodes 64 protein-coding genes and no tRNAs. The genome shares 52 to 92% gene content with other cluster CD members.",
"full_author_list": "Ben Curtis, Bayarjavkhlan Ganbaatar, Griffin Lawrence, Wyatt Oglesby, Jaylee Rice, Emelia Tremblay, Melissa Maginnis, Sally D. Molloy, Melody N. Neely",
"short_author_list": "Curtis et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36066262"
},
{
"title": "Characterization and Genome Sequence of Arthrobacter Phage Iter",
"abstract": "Arthrobacter phage Iter was isolated in North Georgia. Its genome is 43,963 bp with 70 open reading frames (ORFs) and a GC content of 67.4%. It shares 89.11% nucleotide identity with Arthrobacter phage Phives. Actinobacteriophages that share over 50% nucleotide identity are sorted into clusters, with Iter in cluster AZ.",
"full_author_list": "Kathleen A. Daly, Audrey E. Nesbit, Jacob D. Buchholz, Alison E. Kanak",
"short_author_list": "Daly et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36066250"
},
{
"title": "Genomic Sequence and Characteristics of EmiRose, a Bacteriophage Isolated on Corynebacterium flavescens",
"abstract": "Bacteriophage EmiRose is a siphovirus infecting Corynebacterium flavescens. The EmiRose genome is 37,431 bp long and composed of 47 protein-coding genes. Based on gene content similarity, EmiRose is not closely related to any previously sequenced bacteriophages in the actinobacteriophage database to date, including other corynebacteriophages. EmiRose is classified as a singleton.",
"full_author_list": "Emily Rose Davis, Blesyn Perry-Richardson, Aleem Mohamed, Ilzat Ali, Danielle Heller, Viknesh Sivanathan",
"short_author_list": "Davis et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00080-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35234508"
},
{
"title": "Genome Sequences of Streptomyces Bacteriophages Fabian, FlowerPower, Geostin, RetrieverFever, and Vorvolakos",
"abstract": "This paper reports the genome sequences of five bacteriophages that were isolated using Streptomyces scabiei. Phages Fabian, FlowerPower, Geostin, RetrieverFever, and Vorvolakos were assigned to actinobacteriophage cluster BF based on shared gene content, with each phage containing between 16 and 21 tRNA genes.",
"full_author_list": "Faith Davis, Baily Kakacek, Delaram Doorandish, Tamar Goldwasser, Neyiasuo Agboha, 2021 UMBC Phage Hunters, STEM BUILD at UMBC Cohort 6, Steven M. Caruso, Ivan Erill",
"short_author_list": "Davis et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00998-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36326493"
},
{
"title": "Genome Sequences of Gordonia Phages GrootJr and NovumRegina",
"abstract": "Two Gordonia bacteriophages, GrootJr and NovumRegina, were discovered, sequenced, and annotated. These phages were isolated from distinct soil and water samples, respectively, on Gordonia terrae 3612. These phages belong to the CR2 subcluster and are similar in genome size and gene content.",
"full_author_list": "Erin L. Doyle, Georgia M. Elliott, Sean J. Hummel, Katelyn A. Jindra, Ashley T. Marsh, Dane M. Bowder",
"short_author_list": "Doyle et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00703-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36342305"
},
{
"title": "Genome Sequences of Gordonia rubripertincta Phages LilyPad and PokyPuppy",
"abstract": "Two lytic phages infecting Gordonia rubripertincta were isolated from irrigated desert soil. Phage LilyPad and PokyPuppy have 64,158-bp and 77,065-bp genomes, respectively. Based on gene content similarity to phages in the Actinobacteriophage database, LilyPad is assigned to phage subcluster DG1 and PokyPuppy to subcluster CS2.",
"full_author_list": "Ella Eleven, Casia Esparza, Alivia Abernathy, Ashley Bradshaw, Marisa Garcia, Nathaniel Jobe, Kennedi Pyper, Cassandra Skaar, Kaarin Goncz, Joel Sharbrough, Linda C. DeVeaux",
"short_author_list": "Eleven et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00958-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36314913"
},
{
"title": "Genome Sequences of Elezi, Asa16, and Niobe, Three Cluster AZ Phages Isolated Using Arthrobacter globiformis B-2979",
"abstract": "The Actinobacteriophages Elezi, Asa16, and Niobe infect Arthrobacter globiformis B-2979 and are closely related to Eraser and London in Cluster AZ. They have flexible noncontractile tails, are predicted to be temperate phages, and their genome sizes range between 43,471 bp and 43,602 bp.",
"full_author_list": "Emanuela Elezi, Erica Sellers, Alia Abdulla, Marisa A. DeCiucis, Brielle R. Lynch, Mark Nowak, Jamie Outlaw, Camila Ramos, Jacklyn Ramos-Arvelo, Sophia Rokas, Yadinitza Torres-Cintrón, Simon Uka, Stefan Uka, Luz D. Vargas, Nicholas P. Edgington",
"short_author_list": "Elezi et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00368-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35943260"
},
{
"title": "Complete Genome Sequences of Five Bacteriophages That Infect Enterobacteriales Hosts",
"abstract": "Full genome sequences of five bacteriophages that were isolated from raw sewage samples and infect Enterobacteriales hosts are presented. Brookers is a P22-like Proteus phage, OddieOddie is a 9g-like Escherichia coli phage, Diencephelon is a Kp3-like Klebsiella phage, and Rgz1 and Lilpapawes are classic T4-like and T7-like virulent Proteus phages, respectively.",
"full_author_list": "Full genome sequences of five bacteriophages that were isolated from raw sewage samples and infect Enterobacteriales hosts are presented. Brookers is a P22-like Proteus phage, OddieOddie is a 9g-like Escherichia coli phage, Diencephelon is a Kp3-like Klebsiella phage, and Rgz1 and Lilpapawes are classic T4-like and T7-like virulent Proteus phages, respectively.",
"short_author_list": "Evans et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01223-21?af=R",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35343780"
},
{
"title": "Complete Annotated Genome Sequences of Two Novel Microbacteriophages, Gingerbug and HerculesXL, from Western Oregon, USA",
"abstract": "Bacteriophages Gingerbug and HerculesXL are siphoviruses that were isolated from soil in western Oregon, USA, using the actinobacterium Microbacterium foliorum. The genomes of Gingerbug and HerculesXL are similar in length and, based on gene content similarity to actinobacteriophages, were assigned to phage clusters GF and EA11, respectively.",
"full_author_list": "Matthew R. Fisher, Chyanna G. Blackburn, Hope T. Poet, Rebecca Meisner",
"short_author_list": "Fisher et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00919-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36286998"
},
{
"title": "Isolation and Annotation of the Genome Sequences of Bacteriophages InvictusManeo (Subcluster K5) and Netyap (Subcluster L2)",
"abstract": "The mycobacteriophages InvictusManeo (K5 subcluster) and Netyap (L2 subcluster) were isolated from soils in Cullowhee Creek, Cullowhee, North Carolina. Both exhibit Siphoviridae morphology and infect Mycobacterium smegmatis mc2155. The InvictusManeo genome is 61,147 bp and contains 96 predicted protein-coding genes, whereas the Netyap genome is 76,366 bp with 131 predicted protein-coding genes.",
"full_author_list": "Maximiliano F Flota, Véronique A Delesalle, Caitlyn R Moss, Davis S Beeson, Andrew M Bogatkevich, Clarissa C Burgess, Noemi Carretero Lazcano, Jayda A Carroll-Deaton, Hayden A Deprill, Ivy S Dickens, Maria D Gainey, Sophia G Gierszal, Avery A Goff, Brooke K Harris, John B LeBrun, Jim Lin, Molly R McLaughlin, Brian C Metts, Kristen L O'Rear, Maria A Osorio Hernandez, Isabella E Raieta, Erica D Schmidt, Thomas D Sinkway, Kimberly S Sok, Michael A Ulrich, Isaiah T Velez, Jamie R Wallen, Ayden R Wardius, Christine A Byrum",
"short_author_list": "Flota et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00160-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "11",
"journal_issue": "6",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35536032"
},
{
"title": "Complete Genome Sequences of Mycobacterium smegmatis Phages MelsMeow, Yorick, Virgeve, and Mikro",
"abstract": "Mycobacterium phages Mikro, Yorick, Virgeve, and MelsMeow were isolated from soil in Rock Hill, South Carolina. Mikro is a myovirus with a comparatively large genome of 157,166 bp. The remainder are siphoviruses with genome lengths ranging from 59,227 bp to 68,563 bp. All phages were isolated on Mycobacterium smegmatis.",
"full_author_list": "Victoria J. Frost, Jada E. Fogle, Ryan N. Harris, Brooke Jewell, Kaylee E. Mills, Jessica E. Morgan, Precious T. Thompson, Emi Umemoto, Kristi M. Westover",
"short_author_list": "Frost et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00758-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36154149"
},
{
"title": "Instructional Models for Course-Based Research Experience (CRE) Teaching",
"abstract": "The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.",
"full_author_list": "David I. Hanauer, Mark J. Graham, Rachel J. Arnold, Mary A. Ayuk, Mitchell F. Balish, Andrea R. Beyer, Kristen A. Butela, Christine A. Byrum, Catherine P. Chia, Hui-Min Chung, Kari L. Clase, Stephanie Conant, Roy J. Coomans, Tom D’Elia, Jason Diaz, Arturo Diaz, Jean A. Doty, Nicholas P. Edgington, Dustin C. Edwards, Elvira Eivazova, Christine B. Emmons, Kayla M. Fast, Emily J. Fisher, Christine L. Fleischacker, Gregory D. Frederick, Amanda C. Freise, Maria D. Gainey, Chris R. Gissendanner, Urszula P. Golebiewska, Nancy A. Guild, Heather L. Hendrickson, Christopher D. Herren, Margaret S. Hopson-Fernandes Lee E. Hughes, Deborah Jacobs-Sera, Allison A. Johnson, Bridgette L. Kirkpatrick, Karen K. Klyczek, Ann P. Koga, Hari Kotturi, Janine LeBlanc-Straceski, Julia Y. Lee-Soety, Justin E. Leonard, Matthew D. Mastropaolo, Evan C. Merkhofer, Scott F. Michael, Jon C. Mitchell, Swarna Mohan, Denise L. Monti, Christos Noutsos, Imade Y. Nsa, Nick T. Peters, Ruth Plymale, Richard S. Pollenz, Megan L. Porter, Claire A. Rinehart, German Rosas-Acosta, Joseph F. Ross, Michael R. Rubin, Anne E. Scherer, Stephanie C. Schroeder, Christopher D. Shaffer, Amy B. Sprenkle, C. Nicole Sunnen, Sarah J. Swerdlow, Deborah Tobiason, Sara S. Tolsma, Philippos K. Tsourkas, Robert E. Ward, Vassie C. Ware, Marcie H. Warner, Jacqueline M. Washington, Kristi M. Westover, Simon J. White, JoAnn L. Whitefleet-Smith, Daniel C. Williams, Michael J. Wolyniak, Jill H. Zeilstra-Ryalls, David J. Asai, Graham F. Hatfull, and Viknesh Sivanathan",
"short_author_list": "Hanauer et al",
"article_url": "https://www.lifescied.org/doi/10.1187/cbe.21-03-0057",
"journal": "CBE—Life Sciences Education",
"journal_volume": "21",
"journal_issue": "1",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "34978921"
},
{
"title": "Systematic overexpression of genes encoded by mycobacteriophage Waterfoul reveals novel inhibitors of mycobacterial growth",
"abstract": "Bacteriophages represent an enormous reservoir of novel genes, many of which are unrelated to existing entries in public databases and cannot be assigned a predicted function. Characterization of these genes can provide important insights into the intricacies of phage–host interactions and may offer new strategies to manipulate bacterial growth and behavior. Overexpression is a useful tool in the study of gene-mediated effects, and we describe here the construction of a plasmid-based overexpression library of a complete set of genes for Waterfoul, a mycobacteriophage closely related to those infecting clinically important strains of Mycobacterium tuberculosis and/or Mycobacterium abscessus. The arrayed Waterfoul gene library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 32 Waterfoul gene products capable of inhibiting the growth of the host Mycobacterium smegmatis and providing a first look at the frequency and distribution of cytotoxic products encoded within a single mycobacteriophage genome. Several of these Waterfoul gene products were observed to confer potent anti-mycobacterial effects, making them interesting candidates for follow-up mechanistic studies.",
"full_author_list": "Danielle Heller, Isabel Amaya, Aleem Mohamed, Ilzat Ali, Dmitri Mavrodi, Padraig Deighan, Viknesh Sivanathan",
"short_author_list": "Heller et al",
"article_url": "https://academic.oup.com/g3journal/article/12/8/jkac140/6612092",
"journal": "G3 Genes|Genomes|Genetics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35727726"
},
{
"title": "Genome Characteristics of Vardy, a Cluster DJ Actinobacteriophage Isolated on Gordonia rubripertincta in Western North Carolina",
"abstract": "Phage Vardy is a lytic siphovirus isolated from creek soil in Cullowhee, NC, using Gordonia rubripertincta NRRL B-16540. Vardy’s 60,144-bp genome contains 90 predicted genes and five copies of a 50-bp motif that may regulate gene expression. Based on gene content similarity, Vardy is assigned to cluster DJ.",
"full_author_list": "Montana Henson, Matteo Fratarcangeli, Serim Park, Ashley Minot, Maria D. Gainey",
"short_author_list": "Henson et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00704-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36255294"
},
{
"title": "Genome Sequences of Microbacterium foliorum Bacteriophages StrawberryJamm, Quammi, Teehee, and Casend",
"abstract": "Four microbacteriophages infecting the host Microbacterium foliorum were isolated at Gonzaga University as part of the SEA-PHAGES program. Phages Teehee, StrawberryJamm, Quammi, and Casend are in the EG cluster, with average genome sizes of 62,263 bp and GC contents of 67.2%, with other interesting characteristics.",
"full_author_list": "Thomas P. Hoag, Joshua P. DeKlotz, Brian Steele, William F. Ettinger, Kristen A. Butela, Kirk R. Anders, Marianne Poxleitner",
"short_author_list": "Hoag et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00185-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35384701"
},
{
"title": "Complete Genome Sequence of the Cluster P Mycobacteriophage Phegasus",
"abstract": "We characterized the complete genome of the cluster P mycobacteriophage Phegasus. Its 47.5-kb genome contains 81 protein-coding genes, 36 of which could be assigned a putative function. Phegasus is most closely related to two subcluster P1 bacteriophages, Mangethe and Majeke, with an average nucleotide identity of 99.63% each.",
"full_author_list": "Abigail A. Howell, Cyril J. Versoza, Gabriella Cerna, Tyler Johnston, Shriya Kakde, Keith Karuku, Maria Kowal, Jasmine Monahan, Jillian Murray, Teresa Nguyen, Aurely Sanchez Carreon, Elizabeth Song, Abigail Streiff, Blake Su, Faith Youkhana, Saige Munig, Zeel Patel, Minerva So, Makena Sy, Sarah Weiss, Yang Zhou, Susanne P. Pfeifer",
"short_author_list": "Howell et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00540-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35924939"
},
{
"title": "Genome Sequences of Three Actinobacteriophage from Cluster FH Isolated Using Arthrobacter globiformis",
"abstract": "We report the discovery and genome sequences of three FH cluster actinophage infecting Arthrobacter globiformis B2979. Lilmac1015 and Klevey were isolated from riverbank soil and Prairie from soil collected below a tree. Their respective genome lengths are 49,978, 50,075, and 49,392 bp, with 80, 81, and 78 predicted protein-coding genes.",
"full_author_list": "Shannon Isenhart, Adam Gillison, Darien Brown, Auremie Kleven, Macayla Allen, Brittany Bohn, Lee Anne Martínez, Amaya García Costas",
"short_author_list": "Isenhart et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00805-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36301118"
},
{
"title": "Complete Genome Sequence of Mycobacteriophage IgnatiusPatJac",
"abstract": "IgnatiusPatJac is a Siphoviridae mycobacteriophage capable of lytic infection\r\nin Mycobacterium smegmatis and Mycobacterium tuberculosis. It was isolated from damp\r\nsoil in Johannesburg, South Africa. The 51,164-bp double-stranded DNA genome has a\r\nGC content of 63.6%, predicted to encode 93 genes. IgnatiusPatJac is classified as an A1\r\nsubcluster mycobacteriophage.",
"full_author_list": "Olivia Jacobs, Nikki Gentle, Christopher Ealand, Bavesh Kanaa",
"short_author_list": "Jacobs, O., et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00664-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36129274"
},
{
"title": "Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages",
"abstract": "Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages–Powerpuff, Lego, and YesChef–which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ, Microbacterium Cluster EH, and the former Microbacterium singleton Zeta1847 exhibited low nucleotide similarity. However, their gene content similarity was in excess of the recently adopted Microbacterium clustering parameter, which ultimately resulted in the reassignment of Zeta1847 to Cluster EH. This finding further highlights the importance of using multiple metrics to capture phage relatedness. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle. In the first experimental verification of a Cluster AZ phage’s life cycle, we show that phage Powerpuff is a true temperate phage. It forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages may be temperate as well. Our findings provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.",
"full_author_list": "Andrew Kapinos, Pauline Aghamalian, Erika Capehart, Anya Alag, Heather Angel, Eddie Briseno, Byron Corado Perez, Emily Farag, Hilory Foster, Abbas Hakim, Daisy Hernandez-Casas, Calvin Huang, Derek Lam, Maya Mendez, Ashley Min, Nikki Nguyen, Alexa L. Omholt, Emily Ortiz, Lizbeth Shelly Saldivar, Jack Arthur Shannon, Rachel Smith, Mihika V. Sridhar, An Ta, Malavika C. Theophilus, Ryan Ngo, Canela Torres, Krisanavane Reddi, Amanda C. Freise, Jordan Moberg Parker",
"short_author_list": "Kapinos et al",
"article_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0262556",
"journal": "PLOS ONE",
"journal_volume": "17",
"journal_issue": "1",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35025964"
},
{
"title": "The ReBUILDetroit program and SEA PHAGES increases student attitudes towards research and sense of belonging for both ReBUILDetroit Scholars and non-BUILD students",
"abstract": "Increasing the overall diversity of the biomedical scientific community is an issue that impacts all\r\nlevels of STEM (science, technology, engineering, and mathematics) education, scientific\r\nresearch, and the future of scientific discovery. Large-scale initiatives, such as the NIH Building\r\nInfrastructure Leading to Diversity (BUILD) program, have been established to facilitate\r\nimprovements in diversity across the scientific community by supporting the training of STEM\r\nstudents early in their research careers. One of these BUILD sites, ReBUILDetroit, is a four-year\r\nundergraduate program that supports Scholars throughout their undergraduate careers and\r\nduring the transition to their next career step. To prepare for mentored research experiences in\r\nthe summer after their first year of college, all ReBUILDetroit Scholars participate in a first-year,\r\ncourse-embedded research sequence in biology, chemistry, or social science. Here, we describe\r\nthe pairing of the SEA PHAGES curriculum (which is a national CURE iREC) with the first-year\r\nresearch curricular goals of the ReBUILDetroit program, along with the impact of this first-year\r\nresearch course on both ReBUILDetroit Scholars and non-BUILD students who enrolled in the\r\nyearlong SEA PHAGES course sequence. We found that both groups of students report a similar\r\nincrease in research understanding and belonging, indicating that the ReBUILDetroit program\r\nimpacts students beyond the Scholars directly enrolled in the program. Establishing early intervention research experiences provides research experience for a large group of students\r\nand contributes to overall retention and persistence within STEM majors.",
"full_author_list": "Kaylen Little, Yamere Lloyd, Melanie Hwalek, Victoria Straub, Stephanie B. Conant, Jacob D. Kagey",
"short_author_list": "Kaylen Little, Yamere Lloyd, Melanie Hwalek, Victoria Straub",
"article_url": "https://www.understandinginterventionsjournal.org/article/74167-the-rebuildetroit-program-and-sea-phages-increases-student-attitudes-towards-research-and-sense-of-belonging-for-both-rebuildetroit-scho",
"journal": "Undergraduate and Community College Interventions",
"journal_volume": "13",
"journal_issue": "2",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": ""
},
{
"title": "Genome Characterization of Gordonia Phage Amore2",
"abstract": "Novel Gordonia phage Amore2 was isolated from Pittsburgh, Pennsylvania and infects Gordonia terrae 3612. Amore2 was placed into Actinobacteria cluster CS1. Its genome is 73,842 bp with 105 predicted open reading frames and 56.6% GC content. The closest similarity of Amore2 is Gordonia phage Austin, with a 98% nucleotide identity.",
"full_author_list": "Caroline M. Lantis, Emily C. Mattison, Sarah E. Miller, Alexandria J. Williams, Alison E. Kanak",
"short_author_list": "Lantis et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00537-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36169313"
},
{
"title": "Genomic Characterization of the Cluster CZ4 Gordonia terrae Phage Oregano",
"abstract": "Oregano is a novel cluster CZ4 bacteriophage isolated from the soil using the bacterial host Gordonia terrae. The Oregano genome is 47,575 bp long and encodes two tyrosine integrases and a toxin/antitoxin system. It shares an immunity repressor with both Gordonia and Mycobacterium phages that spans 7 clusters.",
"full_author_list": "Hannah Lembree, Oyku Goktug, Dorian Royal, Alexander Russell, Annika Savage, Makayla Sisco, Maple Waltner, Veronica Chun, Melody N. Neely, Sally D. Molloy",
"short_author_list": "Lembree et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00679-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36098529"
},
{
"title": "Genome Sequence of Cluster BI1 Streptomyces griseus Phage TaidaOne",
"abstract": "Bacteriophage TaidaOne was isolated from soil collected in Taipei, Taiwan, using the host Streptomyces griseus. It is a siphovirus with a 56,183-bp genome that contains 86 protein-coding genes. Based on gene content similarity, it was assigned to actinobacteriophage subcluster BI1, within which only TaidaOne and GirlPower genomes contain an acetyltransferase homolog gene.",
"full_author_list": "Nai-Chun Lin, Chieh-Ling Liao, Che-Yu Cheng, Ping-Hua Chen, Shi-Wing Chen, Kuang-Chun Cheng, Marwin Fernandez, Ting-Kai Hou, Bo-Chen Jiang, Nai-Shun Liao, Tien Pao, Ying-Ying Wong, Hsiang-Yu Yang, Hui-Min Chung",
"short_author_list": "Lin et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00905-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36314918"
},
{
"title": "Complete Genome Sequences of Mycobacteriophages SynergyX, Abinghost, Bananafish, and Delton",
"abstract": "Four lytic mycobacteriophages, namely, SynergyX, Abinghost, Bananafish, and Delton, were isolated from soil in Washington, DC, using the bacterial host Mycobacterium smegmatis mc2155. Analysis of the genomes revealed that they belong to two subclusters of actinobacteriophage cluster B (subclusters B2 and B3) and subcluster D1 of cluster D.",
"full_author_list": "Laricca Y. London, Mary A. Ayuk, Amia C. Black, Laraine Cheung, Delandra M. Robinson, D’nai N. Thomas, Marcie H. Warner, SHOW ALL (22 AUTHORS), Adrian D. Allen, Somiranjan Ghosh, Ayele Gugssa, Hemayet Ullah, Glory B. Bassey, Lourds M. Fernando, Madison M. Moore, Jerome J. Oliver, Esohe G. Irabor, Swagota D. Roy, Benedict K. Quagraine, Michael Smith, Howard University SEA-PHAGES Students, Winston A. Anderson, Courtney J. Robinson",
"short_author_list": "London et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00286-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35863046"
},
{
"title": "Complete Genome Sequence of Microbacterium foliorum Bacteriophage Librie",
"abstract": "Bacteriophage Librie was isolated from a soil sample from Clarksville, TN, using the bacterium Microbacterium foliorum. Librie has a 39,941 bp genome with 62 predicted protein-coding genes and 1 predicted gene for tRNA. Based on its gene content similarity to actinobacteriophages, Librie is grouped with phages in cluster EA5.",
"full_author_list": "Sergei A. Markov, Nygil L. Arms, Kayla J. Boyce, Melody R. Cardona Pendleton, Angilena M. Couch, Leigh E. Duncan, Osamiabe I. Enodiana, Jaci N. Gibson, Kendall J. Greer, Claudine M. Habib, Ugonna G. Isaac, Tamia C. Johnson, Gabriella G. Lewis, Summer K. Long, Isela A. Ogas, Kehinde O. Olusoga, Patience O. Oni, Kim-Ngan H. Victory, Robin J. Zimmer",
"short_author_list": "Markov et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00918-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36121231"
},
{
"title": "A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence",
"abstract": "Regulation of bacteriophage gene expression involves repressor proteins that bind and downregulate early lytic promoters. A large group of mycobacteriophages code for repressors that are unusual in also terminating transcription elongation at numerous binding sites (stoperators) distributed across the phage genome. Here we provide the X-ray crystal structure of a mycobacteriophage immunity repressor bound to DNA, which reveals the binding of a monomer to an asymmetric DNA sequence using two independent DNA binding domains. The structure is supported by small-angle X-ray scattering, DNA binding, molecular dynamics, and in vivo immunity assays. We propose a model for how dual DNA binding domains facilitate regulation of both transcription initiation and elongation, while enabling evolution of other superinfection immune specificities.",
"full_author_list": "Reliza J. McGinnis, Chad A. Brambley, Brandon Stamey, William C. Green, Kimberly N. Gragg, Erin R. Cafferty, Thomas C. Terwilliger, Michal Hammel, Thomas J. Hollis, Justin M. Miller, Maria D. Gainey & Jamie R. Wallen",
"short_author_list": "McGinnis et al",
"article_url": "https://www.nature.com/articles/s41467-022-31678-6",
"journal": "nature communications",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35835745"
},
{
"title": "Complete Genome Sequences of the Novel Cluster BP Phages Infecting Streptomyces sanglieri, AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra",
"abstract": "The Streptomyces sanglieri bacteriophages AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra form a novel actinobacteriophage cluster, BP. These siphoviruses have circularly permuted genomes with an average size of 37,700 bp and a GC content of 71%. Each genome contains approximately 58 protein-coding genes, with no tRNAs.",
"full_author_list": "Sreemoye Nath, Ahmad Sulaiman, Jindanuch Maneekul, Swapan Bhuiyan, Sonya Layton, Carolina Menchaca, Subhayu Nayek, Juan Acosta, Alejandro Coronado, Alexandra Drake, Isaac Eastland, Monserrat Gallegos, Misti Gutierrez-Langa, Naomi Jefferson, Kennede Johnson, Erin Klokker, Marie Muniz, Diana Hernandez Olmos, Grace Pascarella, Tucker Richardson, Taylor Setliff, Alyssa N. Stiles, Eliza Sun, Melisa Tokel, Jessica M. Vondra, Lee E. Hughes",
"short_author_list": "Nath et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00751-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36102645"
},
{
"title": "Complete Genome Sequence of Cluster C Mycobacteriophage McGee",
"abstract": "Mycobacteriophage McGee is a myovirus isolated from a wet soil sample collected at Manassas, VA, using Mycobacterium smegmatis mc2155. McGee has a genome 156,008 bp long, containing 237 protein-coding genes, 31 tRNA genes, and 1 transfer-messenger RNA (tmRNA) gene. McGee shares high gene content similarity to phages in actinobacteriophage cluster C1.",
"full_author_list": "Imade Y. Nsa, Ayodeji A. Odunsi, Chioma V. Okorie, Seun D. Bamisaye, Rashidat O. Abass, Dennis O. Amadi, Joshua E. Ebitigha, Oluwafemi O. Kadiri, Temidayo M. Makinwa, Solape O. Olaiya, Josephine O. Oluwafemi, Tomilayo L. Owoeye, Zainab A. Sekoni, Abisoye F. Olubajo, Tenny O. G. Egwuatu, Ganiyu O. Oyetibo, Matthew O. Ilori",
"short_author_list": "Nsa et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00768-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36073918"
},
{
"title": "Complete Genome Sequence of Bacteriophage Loca, Isolated on a Microbacterium foliorum Culture",
"abstract": "Microbacteriophage Loca was extracted from a shopping cart handle swab sample in Stephenville, TX, and isolated on a Microbacterium foliorum NRRL-24224 culture. The 17,475-bp double-stranded DNA genome contains 25 predicted protein-coding genes and has >96% nucleotide identity to bacteriophages Quaker and Livingwater.",
"full_author_list": "Aurod Ounsinegad, Megan Ashcraft, Emily Bliss, Dasire Brawley, Grace Clements, Austin Densmore, Alexis Gastin, Marisol Luciano, Cole Moore, Virginia Munoz, Aryana Pernarelli, Maci Pitner, Esmae Velsen, Kara Wiggam, Marlee Goppert, Dustin Edwards",
"short_author_list": "Ounsinegad et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00783-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36066260"
},
{
"title": "Complete Genome Sequences of Streptomyces Bacteriophages Annihilus, TonyStarch, Thiqqums, CricKo, ClubPenguin, RosaAsantewaa, and PherryCruz",
"abstract": "Seven siphoviruses were isolated from soil using Streptomyces hosts. Their genome sequences ranged from 42,730 to 57,624 bp long and had a GC content of approximately 60%. Based on their gene content similarity to actinobacteriophages, all seven phages were assigned to cluster BI. For several of these phages, multiple ribosomal frameshifts were identified.",
"full_author_list": "Yvette Genie Park, Gillian Faith McCarthy, Hadeeqa Mustafa, Gemma M. Feild, Snigdha Puram, Hager Aly Younes, Danyah Imam, 2021 UMBC Phage Hunters, STEM BUILD at UMBC Cohort 5, Ivan Erill",
"short_author_list": "Park et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00922-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36286992"
},
{
"title": "Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)",
"abstract": "Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.",
"full_author_list": "Jolene Ramsey, Brenley McIntosh, Daniel Renfro, Suzanne A. Aleksander, Sandra LaBonte, Curtis Ross ,Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades, Tanya Z. Berardini, Jennifer A. Bennett, Siobhan Brady, Robert Britton, Seth Carbon, Steven M. Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L. Doyle, Iddo Friedberg, Susan M. R. Gurney, Lee Hughes, Allison Johnson, Jason M. Kowalski, Donghui Li, Ruth C. Lovering, Tamara L. Mans, Fiona McCarthy, Sean D. Moore, Rebecca Murphy, Timothy D. Paustian, Sarah Perdue, Celeste N. Peterson, Birgit M. Prüß, Margaret S. Saha, Robert R. Sheehy, John T. Tansey, Louise Temple, Alexander William Thorman, Saul Trevino, Amy Cheng Vollmer, Virginia Walbot, Joanne Willey, Deborah A. Siegele, James C. Hu",
"short_author_list": "Ramsey et al",
"article_url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009463",
"journal": "PLOS Computational Biology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "34710081"
},
{
"title": "Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta",
"abstract": "Holins are bacteriophage-encoded transmembrane proteins that function to control the timing of bacterial lysis event, assist with the destabilization of the membrane proton motive force and in some models, generate large “pores” in the cell membrane to allow the exit of the phage-encoded endolysin so they can access the peptidoglycan components of the cell wall. The lysis mechanism has been rigorously evaluated through biochemical and genetic studies in very few phages, and the results indicate that phages utilize endolysins, holins and accessory proteins to the outer membrane to achieve cell lysis through several distinct operational models. This observation suggests the possibility that phages may evolve novel variations of how the lysis proteins functionally interact in an effort to improve fitness or evade host defenses. To begin to address this hypothesis, the current study utilized a comprehensive bioinformatic approach to systematically identify the proteins encoded by the genes within the lysis cassettes in 16 genetically diverse phages that infect the Gram-positive Gordonia rubripertincta NRLL B-16540 strain. The results show that there is a high level of diversity of the various lysis genes and 16 different genome organizations of the putative lysis cassette, many which have never been described. Thirty-four different genes encoding holin-like proteins were identified as well as a potential holin-major capsid fusion protein. The holin-like proteins contained between 1–4 transmembrane helices, were not shared to a high degree amongst the different phages and are present in the lysis cassette in a wide range of combinations of up to 4 genes in which none are duplicated. Detailed evaluation of the transmembrane domains and predicted membrane topologies of the holin-like proteins show that many have novel structures that have not been previously characterized. These results provide compelling support that there are novel operational lysis models yet to be discovered.",
"full_author_list": "Richard S. Pollenz, Jackson Bland, Welkin H. Pope",
"short_author_list": "Richard S. Pollenz, Jackson Bland, Welkin H. Pope",
"article_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0276603",
"journal": "PLOS ONE",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36395171"
},
{
"title": "Complete Genome Sequences of Cluster S Mycobacteriophages Beelzebub, Raela, and RedRaider77",
"abstract": "We isolated three mycobacteriophages that belong to cluster S, namely, Beelzebub, Raela, and RedRaider77. Annotation revealed a genome structure typical of cluster S phages, including an atypical location of two minor tail protein genes in the right arm of these viral genomes.",
"full_author_list": "Kristina Sevcik, Peace Preston, Michaela Aulner, Byron Noordewier, Sara S. Tolsma",
"short_author_list": "Sevcik et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.01173-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36507676"
},
{
"title": "Complete Genome Sequences of Arthrobacter Phages Eraser, Kaylissa, and Phives",
"abstract": "Bacteriophages Phives, Kaylissa, and Eraser are siphoviruses infecting Arthrobacter globiformis B-2880 that were isolated in fall 2019 in Long Island, New York, from soil samples collected in Old Westbury, New York. All three bacteriophages are assigned to phage cluster AZ based on gene content similarity. While many aspects of the genomes are similar across the three phages, the endolysin genes for the phages are different and are located in different locations within the genomes.",
"full_author_list": "Srinidhi Gadula, Nayan Pallothu, Rodrigue Jean-Baptiste Jr., Joseph Holloway, Leonidas Salichos, Bryan Gibb",
"short_author_list": "Srinidhi Gadula, Nayan Pallothu, Rodrigue Jean-Bapt",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00178-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35389259"
},
{
"title": "Complete Genome Sequences of Genamy16 and NovaSharks, Two Gordonia rubripertincta Bacteriophages Isolated from Soil in Southeastern Florida",
"abstract": "We report on two actinobacteriophages, Genamy16 and NovaSharks, that were isolated from soil in Florida using Gordonia rubripertincta NRRL B-16540. The genomes of both phages are ~65,000 bp, with similar GC contents, and, based on gene content similarity to phages in the Actinobacteriophage Database, were assigned to phage cluster DV.",
"full_author_list": "Julie Torruellas Garcia, Sarah Ballarin, Neel Balusa, Melissa Bell, Samia Caballero, Joshua Chan, Maria Farez, Ashley Guillen-Tapia, Kristin Parent, Nashrah Pierre-Louis, Victoria Polishuk, Bhavya Soni, Sundharraman Subramanian, Katie Crump",
"short_author_list": "Torruellas Garcia et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00973-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36326520"
},
{
"title": "Characterization of Phages YuuY, KaiHaiDragon, and OneinaGillian Isolated from Microbacterium foliorum",
"abstract": "Microbacterium foliorum is a Gram-positive bacteria found in organic matter. Three lytic bacteriophages, KaiHaiDragon, OneinaGillian, and YuuY, were isolated from M. foliorum strain NRRL B-24224. Phage YuuY in particular expresses a broad host range as it possesses the ability to infect closely related bacterial species Microbacterium aerolatum at a high plating efficiency. Characterization tests were performed on all three Microbacterium phage to assess morphology, genomic characteristics, pH and thermal stabilities, life cycle, and the type of receptor used for infection. All three phages showed similar pH stability, ranging from pH 5–11, except for KaiHaiDragon, which had a reduced infection effectiveness at a pH of 11. YuuY possessed a significantly higher temperature tolerance compared to the other Microbacterium phages as some phage particles remained viable after incubation temperatures of up to 80 °C. Based on the one-step growth curve assay, all three Microbacterium phages possessed a relatively short latent period of 90 min and an approximately two-fold burst size factor. Moreover, all three phages utilize a carbohydrate receptor to initiate infection. Based on bioinformatics analysis, YuuY, KaiHaiDragon and OneinaGillian were assigned to clusters EA10, EC, and EG, respectively.",
"full_author_list": "Uylae Kim, Elizabeth S Paul, and Arturo Diaz",
"short_author_list": "Uylae Kim, Elizabeth S Paul, and Arturo Diaz",
"article_url": "https://www.mdpi.com/1422-0067/23/12/6609/htm",
"journal": "International Journal of Molecular Sciences",
"journal_volume": "23",
"journal_issue": "12",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35743053"
},
{
"title": "Genome Sequence and Characteristics of the Microbacterium foliorum Cluster EE Bacteriophage Burgy",
"abstract": "Burgy is a siphovirus that was isolated from compost soil near Fremont Township, Iowa, using Microbacterium foliorum NRRL B-24224. The genome has a length of 17,453 bp and contains 25 total protein-coding genes, 20 of which were assigned functions. Based on gene content, Burgy was assigned to actinobacteriophage cluster EE.",
"full_author_list": "Halle F. Van Roekel, Jacob J. Georgen, Rainy A. Kock, Sean T. Coleman",
"short_author_list": "Van Roekel et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00912-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36197284"
},
{
"title": "Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages",
"abstract": "Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera—from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies.",
"full_author_list": "Cyril J Versoza, Abigail A Howell, Tanya Aftab, Madison Blanco, Akarshi Brar, Elaine Chaffee, Nicholas Howell, Willow Leach, Jackelyn Lobatos, Michael Luca, Meghna Maddineni, Ruchira Mirji, Corinne Mitra, Maria Strasser, Saige Munig, Zeel Patel, Minerva So, Makena Sy, Sarah Weiss, Susanne P Pfeifer",
"short_author_list": "Versoza et al",
"article_url": "https://www.mdpi.com/1999-4915/14/8/1647",
"journal": "Viruses",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36016269"
},
{
"title": "Complete Genome Sequence of the Gordonia Bacteriophage BiggityBass",
"abstract": "Here, we characterized the complete genome of the Siphoviridae BiggityBass, a lytic subcluster DR bacteriophage infecting Gordonia terrae CAG3. Its 63.2-kb genome contains 84 protein-coding genes, of which 40 could be assigned a putative function. BiggityBass is related most closely to AnClar and Yago84 with 90.61% and 90.52% nucleotide identity, respectively.",
"full_author_list": "Cyril J. Versoza, Abigail A. Howell, Tanya Aftab, Madison Blanco, Akarshi Brar, Elaine Chaffee, Nicholas Howell, Willow Leach, Jackelyn Lobatos, Michael Luca, Meghna Maddineni, Ruchira Mirji, Corinne Mitra, Maria Strasser, Saige Munig, Zeel Patel, Minerva So, Makena Sy, Sarah Weiss, Christopher D. Herren, Martha Smith Caldas, Susanne P. Pfeifer",
"short_author_list": "Versoza et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00469-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35938821"
},
{
"title": "Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States",
"abstract": "Background: Despite their importance to microbial dynamics involving Bacillus subtilis, we have a limited understanding of the diversity of phages that can lyse this model organism.\r\n\r\nMaterials and Methods: Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild B. subtilis strain. Their genomes were assembled, characterized, and bioinformatically compared.\r\n\r\nResults: Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86–91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes.\r\n\r\nConclusions: A comparative approach provides insights into phage evolution, including the role of indels in protein folding.",
"full_author_list": "Albert C. Vill, Véronique A. Delesalle, Brianne E. Tomko, Katherine B. Lichty, Madison S. Strine, Alexandra A. Guffey, Elizabeth A. Burton, Natalie T. Tanke, and Greg P. Krukonis",
"short_author_list": "Vill et al",
"article_url": "https://www.liebertpub.com/doi/full/10.1089/phage.2022.0030",
"journal": "PHAGE",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": ""
},
{
"title": "Genome Sequence of CaiB, a DR Cluster Actinobacteriophage That Infects Gordonia rubripertincta",
"abstract": "CaiB is a DR cluster actinobacteriophage that was isolated from soil in Florida using Gordonia rubripertincta NRRL B-16540 as the host. The genome is 61,620 bp, has a GC content of 68.6%, and contains 85 predicted protein coding genes. CaiB has several putative operons and has repeated intergenic regions that may be involved in gene regulation.",
"full_author_list": "Bienna Welsh, Nader M. Abdalla, Esteban Aldana, Veronica M. Alvarado Fernandez, Bruna Arenales Salgado de Oliveira, Diane Fakhre, Amelia J. Haymond, SHOW ALL (25 AUTHORS), Katelyn M. Helton, Aditi Kanchibhatta, Jahwanza Knight, Sydney Marshall, Maomi Laine N. Martinez, Arielle Merkher, Savannah E. Morrow, Katie P. Nguyen, Jahanvi J. Patel, Somesh R. Patel, Pravalika Rayala, Kira M. Ruiz-Houston, Aarya P. Satardekar, Shifa M. Shaikh, Adrian E. Terron Osorio, Rachel C. Weitz, Louis Otero, Richard S. Pollenz",
"short_author_list": "Welsh et al",
"article_url": "https://journals.asm.org/doi/10.1128/mra.00376-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "35758688"
},
{
"title": "Complete Genome Sequence and Characteristics of Mycobacteriophage IkeLoa",
"abstract": "Mycobacteriophage IkeLoa is a lytic myovirus. It has a circularly permuted 155,280-bp genome containing 233 putative protein-coding genes, 32 tRNA genes, one tmRNA gene, and 64.7% G+C content. The RNA genes are distributed in five clusters across the genome. Only 28% of IkeLoa’s protein-coding genes can be assigned functions.",
"full_author_list": "Hannah R. Wheatley, Sarah R. Kushner, Frederick N. Baliraine",
"short_author_list": "Wheatley et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00985-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36287013"
},
{
"title": "Complete Genome Sequence of Arthrobacter Phage GantcherGoblin Exhibits Both Conservation with Subcluster AU6 Phages and Genetic Novelty",
"abstract": "GantcherGoblin is a lytic siphovirus that was isolated on Arthrobacter globiformis B-2979 from soil collected in Massachusetts. The 55,368-bp genome has a GC content of 50.1% and 91 predicted protein-coding genes. Based on gene content similarity to phages in the Actinobacteriophage Database, GantcherGoblin was assigned to phage subcluster AU6.",
"full_author_list": "J. J. Wheeler, Carina M. Carlos, Helen A. Cedzidlo, Xingfeiyang Liu, Massimo S. Modica, Izaiah D. Rhodes, Leah F. Truskinovsky, Ethan M. VanGosen, Hannah E. Gavin",
"short_author_list": "Wheeler et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00771-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36321902"
},
{
"title": "Genome Sequences and Characteristics of Six Cluster B1 Mycobacteriophages Discovered at Saint Joseph’s University",
"abstract": "We report on six new siphoviruses infecting Mycobacterium smegmatis that were isolated from soil samples collected on the campus of Saint Joseph’s University, on the western edge of Philadelphia, Pennsylvania. All phages have circularly permuted genomes that are 68,721 to 68,929 bp long, with an average G+C content of 66.4%.",
"full_author_list": "Anne Winkler, April Pivonka, Aidan Conry-Murray, Cecilia Petruconis, Isabella Patterne, Bernadette Bergman, Elizabeth Binder, Joshua Blackley, Rachel Brown, Katherine Commale, Emily Costello, Taylor Cromer, Jasmine Davila, Olivia DeSanto, Mary Agnus Dunn, Deborah Duong, Sophia Feingold, Kayla Flanders, Mary Frattara, Tate Fryczynski, Leya Givvines, Dana Glavin, Reid Hartman, Julia Iacovella, Katherine Koestler, Caroline Kominick, Andy Lam, Sharon Mashkovich, Jordan McCarthy, Corinne Merlino, Alexa Mihaita, Kara Moulton, Thientrinh Nguyen, Danielle Niblock, Isabella Paoli, Skye Rodriguez, Isabella Stefanic, Jenna Stoneroad, Caren Teague, Fabiana Tort-Umpierre, Arianna Varano, Alexandra Vlahovic, John Braverman, Christina King-Smith, Julia Y. Lee-Soety",
"short_author_list": "Winkler et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/mra.00754-22",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2022",
"pubmed_id": "36135363"
},
{
"title": "Genome Sequence and Characteristics of Cluster C1 Mycobacterium smegmatis Phage EasyJones",
"abstract": "Bacteriophage EasyJones is a myovirus infecting Mycobacterium smegmatis mc2155, with a genome length and gene content similar to those of phages grouped in subcluster C1. Interestingly, EasyJones contains a gene found in a subset of C1 genomes that is similar to the well-characterized immunity repressor of subcluster A1 mycobacteriophage Bxb1.",
"full_author_list": "Isabel Amaya, Duyen Bui, Ariel Egbunine, Ember Mushrush, Maggie Viland, Deborah Jacobs-Sera, Danielle Heller, Viknesh Sivanathan",
"short_author_list": "Amaya et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00997-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34817211"
},
{
"title": "Genome Sequence of Bacteriophage Adumb2043, Isolated from Arthrobacter globiformis in Southern Colorado",
"abstract": "Genome Sequence of Bacteriophage Adumb2043, Isolated from Arthrobacter globiformis in Southern Colorado",
"full_author_list": "Darien Brown, Shannon Isenhart, Auremie Kleven, Adam Gillison, Lee Anne Martínez, and Amaya García Costas",
"short_author_list": "Brown et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00776-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34647808"
},
{
"title": "Complete Genome Sequence of the Cluster B4 Mycobacteriophage Lolalove, Isolated in Charleston, South Carolina",
"abstract": "Lolalove, a B4 subcluster soil bacteriophage of Mycobacterium smegmatis, was isolated in Charleston, SC. It possesses a 71,111-bp linear double-stranded DNA (dsDNA) genome with 99 protein-coding genes and a GC content of 68.9%. genome BLASTn alignments indicate high sequence identity to the related B4 subcluster M. smegmatis phages BrownCNA, Mithril, and Hangman.",
"full_author_list": "Christine A. Byrum, Hannah Marie Rozier, Toni E. Allison, Emilia Ballou, Lauren Bergen, Reilley A. Chamness, Madison E. Davis, , Mouna S. DiBenedetto, Nathaniel C. Elston, Lyric A. Graham, Keiana L. Haigh, Tessa M. Jansen, Gabrielle S. Kostur, Nicholas A. Larson, Fiona L. Lewis, Carlo Negroni, Isabella V. Rupert, Isabel S. Wood, Anastasia M. Zimmerman, and Veronique A. Delesalle",
"short_author_list": "Byrum et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00493-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34197200"
},
{
"title": "Complete Genome Sequences of Mycobacterium Phages Tripl3t and Zeuska",
"abstract": "Tripl3t and Zeuska are siphoviral bacteriophages that were isolated from Mycobacterium smegmatis mc2 155 and contain double-stranded DNA genomes 53,565 bp and 53,598 bp in length, respectively. Tripl3t and Zeuska were annotated by students at Bluff Dale High School (Bluff Dale, TX) and Tolar High School (Tolar, TX) in community engagement with Tarleton State University.",
"full_author_list": "Faith Cox, Tiffany Lujan, Matthew Bristerpostma, Rheaven Sandoval, Haze Murphy, Leah Dowell, Jaime Merrill, Julie Edwards, and Dustin Edwards",
"short_author_list": "Cox et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34382828"
},
{
"title": "Complete Genome Sequence of Mycobacteriophage Joy99",
"abstract": "Joy99 is a siphoviral mycobacteriophage with a 59,837-base pair double-stranded DNA genome and is predicted to contain 97 protein-coding genes and a single tRNA gene. Joy99 was isolated in Saint Louis, MO, and annotated by students at Bluff Dale High School in community engagement with Tarleton State University.",
"full_author_list": "Faith Cox, Josh Katuri, Megan Adams, Danielle Bachhofer, Ashleigh Cooper, Jessica Doty, Miranda Fuentes, Leeila Hanson, Travis Miller, Jonathan Musgrave, Aleksey Palumbo, Camille Trautman, Julie Edwards, and Dustin Edwards",
"short_author_list": "Cox et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00556-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34382830"
},
{
"title": "Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages",
"abstract": "Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections but also offering novel insights into pathogen genetics and evolution. A prominent example is cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative nonpathogenic relatives, such as Mycobacterium smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate subcluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with Mycobacterium leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, subcluster K1 mycobacteriophages are able to integrate into the genomes of Mycobacterium abscessus and Mycobacterium marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance.",
"full_author_list": "Adele Crane, Cyril J Versoza, Tiana Hua, Rohan Kapoor, Lillian Lloyd, Rithik Mehta, Jueliet Menolascino, Abraham Morais, Saige Munig, Zeel Patel, Daniel Sackett, Brandon Schmit, Makena Sy, Susanne P Pfeifer",
"short_author_list": "Crane et al",
"article_url": "https://doi.org/10.1093/g3journal/jkab291",
"journal": "G3 : Genes | Genomes | Genetics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34849792"
},
{
"title": "Genome Sequences of Mycobacterium smegmatis Phages Fefferhead and ShamWow",
"abstract": "Fefferhead and ShamWow are temperate mycobacteriophages in the K6 and E clusters, respectively. The length of the Fefferhead genome is 61,366 bp, with 98 predicted genes. The ShamWow genome has a length of 75,933 bp, with 143 predicted genes, 3 of which are duplicates.",
"full_author_list": "Valerie L Dao, Lily Xia, Christa T Bancroft",
"short_author_list": "Dao et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00973-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34817212"
},
{
"title": "BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE",
"abstract": "Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of related Mycobacteria and Arthrobacter phage genomes relied on nucleotide identity thresholds but, more recently, clustering of Gordonia and Microbacterium phages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novel Arthrobacter phage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity with Arthrobacter phages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clustering Gordonia and Microbacterium phages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE.",
"full_author_list": "Stephanie Demo, Andrew Kapinos, Aaron Bernardino, Kristina Guardino, Blake Hobbs, Kimberly Hoh, Edward Lee, Iphen Vuong, Krisanavane Reddi, Amanda C. Freise, Jordan Moberg Parker",
"short_author_list": "Demo et al",
"article_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0248418",
"journal": "PLOS ONE",
"journal_volume": "16",
"journal_issue": "3",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33711060"
},
{
"title": "Genome Sequences of Akoni, Ashton, and Truong, Podoviridae Bacteriophages Isolated from Microbacterium foliorum",
"abstract": "Cluster EK2 Akoni, Ashton, and Truong are lytic Podoviridae actinobacteriophages that were isolated from soil in Florida using Microbacterium foliorum NRRL B-24224 as the host. The genomes are 54,307 bp, 54,560 bp, and 54,309 bp, respectively, and are 60% GC rich. Each genome contains a novel 13,464-bp gene that encompasses 25% of the genome.",
"full_author_list": "Fadia Fakhre, Raquel M Gonzalez, Elisabeth K Howells, Louis Otero, Kaili N Pegoraro, Kobe C Robichaux, Alexandra Rodier, Carter L Sadowski, Victoria P Carter, Amber D Gray, Grace C Klein, Catherine Lebosada, Chris M Miklaszewski, Sydnen, Michael A Chase, Caitlyn N Coleman, Brooke Corbett, Manoela O Cunha, Marshall Daffner, Caitlyn J Deam, Laura J Deloso, Anthony M DeSomma, Juan Pinera Gallardo, Mae E Horne, Olivia Kanahan, Victor Lam, Ryan T Morgan, Emilee M Mustor, Migdalia Ricardo-Iglesias, Chloe J Sartorio, Ava R Sciacchitano, Alex W Tvenstrup, Audrey R Wood, Richard S Pollenz",
"short_author_list": "Fakhre et al",
"article_url": "https://pubmed.ncbi.nlm.nih.gov/34264121/",
"journal": "Microbiology Resource Announcements",
"journal_volume": "10",
"journal_issue": "28",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34264121"
},
{
"title": "Genome Sequences of Subcluster M2 Mycobacteriophages Estes and Aziz",
"abstract": "Estes and Aziz are mycobacteriophages that were isolated on Mycolicibacterium smegmatis mc2155 at room temperature from soil samples collected in Spokane, WA. Their genome sequences are 83,601 and 83,412 bp long, respectively, and they are members of subcluster M2. Each contains 21 tRNA genes and short conserved repeats characteristic of cluster M phages.",
"full_author_list": "Sara K. Fitzgerald, Eleanor H. Johnson, Sophie H. R. Storz, Claire Ballard, Samantha Battaglia, Mikelle Boice, Joshua Bramwell-Butcher, Megan Dedinsky, Joshua DeKlotz, Izabel Diaz, Andrew Engley, Lindsey Ernst, Erica Gonzales, Alyssa Groscost, Paige Grosser, Alicia Haider, Morgan Harrison, Kurt Husler, Jalisa Lau, Melina Monlux, Jason Paratore, Trevor Ruesch, Mikaela Schlesinger, Anthony Scholes, Marianne K. Poxleitner and Kirk R. Anders",
"short_author_list": "Fitzgerald et al",
"article_url": "https://mra.asm.org/content/10/10/e00104-21?ct",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33707327"
},
{
"title": "Evaluation of Genome Sequences of the Bacteriophages JeTaime and Luna22",
"abstract": "The mycobacteriophages JeTaime (E cluster) and Luna22 (Q cluster) were isolated from soil in Providence, Rhode Island, and Charleston, South Carolina, respectively, using a Mycobacterium smegmatis mc2 155 host. The genome of JeTaime is 75,099 bp (142 predicted genes), and that of Luna22 is 53,730 bp (87 predicted genes). Both phages exhibit Siphoviridae morphology.",
"full_author_list": "Maximiliano F. Flota, Caitlyn R. Moss, Mitchell F. Balish, Nikki Chen, Kristen C. Cherry, Kathleen A. Cornely, Hayley M. D’Alessandro, , Mouna S. DiBenedetto, Joseph A. DeGiorgis, Steven Grant Dixon, Emily G. Dombrowski, Megan K. Edwards, Jonathan C. Eskew-Martin, Isabel E. P. Finnegan, Abanob G. Hanna, Sarah E. Hunter, Sabrina L. Johnson, Virginia A. L. Kenan, Chanelle Kendrick, Lucas C. Licaj, Victoria C. Maldonado, Megan G. Mazzei, Gracen E. Mitrick, Bradford L. J. Nelson, Jui S. Patel, Alexander I. Parry, Kacey M. Smekrud, Kirsten K. Snyder, Jonathan A. Stewart, Fredrick K. Swiger, Madison K. Thomas, Josiah C. Waters, and Christine A. Byrum",
"short_author_list": "Flota et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00746-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34617782"
},
{
"title": "Genome Sequence of VanLee, a Singleton Actinobacteriophage That Infects Multiple Gordonia Strains",
"abstract": "VanLee is a singleton phage that was isolated from soil in Florida using Gordonia rubripertincta NRRL B-16540 as the host. The genome is 84,560 bp and has a GC content of 67.8%. VanLee has 164 predicted protein-coding genes and one tRNA. VanLee can infect Gordonia terrae with the same efficiency as G. rubripertincta.",
"full_author_list": "Vanessa Franco, Kaylee Barnhill, Abbigail Biggs, Jackson Bland, Harris Choudhary, Trey Crogan, Alyssa Finocchiaro, , Thomas Fuller, Christopher Hanwacker, Zoe Howard, Mohammed Iqbal, Ann Mathew, Sydney Miller, Shivani Padhye, Emily Rainey, Arianna Rodriguez, Emma Stewart, Michael Chase, Louis Otero, and Richard S. Pollenz",
"short_author_list": "Franco et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00519-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34323611"
},
{
"title": "Genome Sequences of Gordonia Bacteriophages Jodelie19, BlingBling, and Burnsey",
"abstract": "Jodelie19, BlingBling, and Burnsey are bacteriophages identified using host bacteria of the genus Gordonia. Jodelie19 is a lytic phage found in Gordonia rubripertincta NRRL B-16540. The temperate phage BlingBling and lytic phage Burnsey were both isolated using the host bacterium Gordonia terrae 3612.",
"full_author_list": "Harrington DL, Barten HR, Audannio EI, Bragg FA, Garcia KA, Niswonger KM, MacAllister JR, McCarroll AM, O'Sullivan DM, Torres SE, Stanley CD, Yalzadeh D, Kimberley KW, McKenna CC, Theoret JR, Yoon EJ, Windsor EJ",
"short_author_list": "Harrington et al",
"article_url": "https://mra.asm.org/content/ga/10/5/e01280-20.full.pdf",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33541874"
},
{
"title": "Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages",
"abstract": "Bacteriophages typically infect a small set of related bacterial strains. The transfer of bacteriophages between more distant clades of bacteria has often been postulated, but remains mostly unaddressed. In this work we leverage the sequencing of a novel cluster of phages infecting Streptomyces bacteria and the availability of large numbers of complete phage genomes in public repositories to address this question. Using phylogenetic and comparative genomics methods, we show that several clusters of Actinobacteria-infecting phages are more closely related between them, and with a small group of Firmicutes phages, than with any other actinobacteriophage lineage. These data indicate that this heterogeneous group of phages shares a common ancestor with well-defined genome structure. Analysis of genomic %GC content and codon usage bias shows that these actinobacteriophages are poorly adapted to their Actinobacteria hosts, suggesting that this phage lineage could have originated in an ancestor of the Firmicutes, adapted to the low %GC content members of this phylum, and later migrated to the Actinobacteria, or that selective pressure for enhanced translational throughput is significantly lower for phages infecting Actinobacteria hosts.",
"full_author_list": "Koert, Matthew; López-Pérez, Júlia; Mattson, Courtney; Caruso, Steven; Erill, Ivan",
"short_author_list": "Koert et al",
"article_url": "https://peercommunityjournal.org/articles/10.24072/pcjournal.25/",
"journal": "Peer Community Journal",
"journal_volume": "1",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": ""
},
{
"title": "Complete Genome Sequences of Bacillus cereus Group Phages AaronPhadgers, ALPS, Beyonphe, Bubs, KamFam, OmnioDeoPrimus, Phireball, PPIsBest, YungSlug, and Zainny",
"abstract": "Here, we report genome sequences of 10 Bacillus cereus group-infecting bacteriophages. Each virus was isolated from an environmental sample, contained a double-stranded DNA genome, and belonged to the Myoviridae family. Nine phages exhibit a conserved genome structure, and one phage appears novel in genome structure, sequence, and protein content.",
"full_author_list": "Nora Kostyk, Oluchi Chigbu, Erin Cochran, Jackson Davis, Jacob Essig, Linda Do, Nashwan Farooque, Zainab Gbadamosi, Arathi Gnanodayan, Andrew Hale, Nasita Islam, Ahmed Ismail, Andreus Jordan, Krishna Karamsetty, Perry Tanner, Rahul Warrier, Hasib Zaman, Allison A Johnson, 2017 to 2020 VCU Phage Hunters",
"short_author_list": "Kostyk et al",
"article_url": "https://journals.asm.org/doi/10.1128/MRA.00300-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34410150"
},
{
"title": "Complete Genome Sequence of Mycobacteriophage Fulbright",
"abstract": "Mycobacteriophage Fulbright was isolated from soil in central Oklahoma using Mycobacterium smegmatis mc2115. The genome of phage Fulbright is 42,396 bp long and contains 70 open reading frames (ORFs), with 33 having predicted functions and 37 having hypothetical proteins. It belongs to cluster N and shares 99% nucleotide identity with mycobacteriophage Phloss.",
"full_author_list": "Hari Kotturi, Umar Sahi, Cameron Kedy, Ahmed K. Ali",
"short_author_list": "Kotturi et al",
"article_url": "https://mra.asm.org/content/10/11/e00123-21?ct",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": ""
},
{
"title": "Complete Genome Sequences of Mycobacteriophages Dallas and Jonghyun",
"abstract": "Two temperate mycobacteriophages, Dallas and Jonghyun, were isolated from soil in Washington, DC, using the bacterial host Mycobacterium smegmatis mc2155. Analysis of the genomes revealed that Dallas and Jonghyun belong to clusters J and G, respectively. The structures of the genomes are typical of their respective clusters.",
"full_author_list": "Laricca Y London, Mary A Ayuk, Diana Effiom, Folasade Fashina, Briana J Louis, Sara S Tolsma, Adrian D Allen, Leon A Dickson, Somiranjan Ghosh, Ayele Gugssa, Hemayet Ullah, Glory B Bassey, Lourds M Fernando, Madison M Moore, Jerome J Oliver, Esohe G Irabor, Swagota D Roy, Benedict K Quagraine, Michael Smith, Howard University SEA-PHAGES Students, Winston A Anderson, Courtney J Robinson",
"short_author_list": "London et al",
"article_url": "https://journals.asm.org/doi/10.1128/MRA.00304-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34236221"
},
{
"title": "Complete Genome Sequences of Microbacterium Bacteriophages Danno, Otwor, and Scumberland, Isolated in Clarksville, Tennessee",
"abstract": "This paper reports the genome sequences of bacteriophages isolated from soil samples using Microbacterium foliorum. Phages Danno and Otwor (cluster EE) have genomes of 17,452 bp and 17,454 bp, respectively, and 25 predicted genes. The phage Scumberland (cluster EC) has a genome of 53,276 bp with 92 predicted genes.",
"full_author_list": "Sergei A. Markov, James C. Church, Leong Lee, Cole M. Bell, Sarah D. Binkley, Kevin M. Bouma, Kaitlin M. Hutson, Gregory S. Markov, Elizabeth C. Mason, Gabrielle B. Rueff, Taiwo O. Sennuga, Montana H. Simpson, Robin J. Zimmer, Diana G. Villalpando",
"short_author_list": "Markov et al",
"article_url": "https://mra.asm.org/content/10/13/e00209-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33795346"
},
{
"title": "Complete Genome Sequence of Microbacterium Bacteriophage Erla",
"abstract": "We characterized the complete genome sequence of Siphoviridae bacteriophage Erla, an obligatory lytic subcluster EA1 bacteriophage infecting Microbacterium foliorum NRRL B-24224, with a capsid width of 65 nm and a tail length of 112 nm. The 41.5-kb genome, encompassing 62 predicted protein-coding genes, is highly similar (99.52% identity) to that of bacteriophage Calix.",
"full_author_list": "Milhaven M, Hastings E, Brister D, Cevallos L, Chilukuri S, Diyya A, Garg A, Hernandez R, Kelly D, Lazo K, Le J, Maag G, Marfatia PD, Mehta R, Nejad A, Porche J, Queiroz A, Sackett D, Santos Molina P, Slade T, So M, Thakur K, Urquidez Negrete A, Wackett S, Weiss S, McCarthy L, Wheaton K, Rudner AD, McCutcheon JP, Pfeifer SP",
"short_author_list": "Milhaven et al",
"article_url": "https://mra.asm.org/content/10/3/e01354-20?ct",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33479002"
},
{
"title": "Complete Genome Sequences of Mycobacteriophages HarryOW and Peeb",
"abstract": "HarryOW and Peeb are Mycobacterium smegmatis mc2 155 Siphoviridae temperate phages with 52,935 and 41,876 base pairs in genome length, respectively. HarryOW belongs to the A1 subcluster and Peeb to the G1 subcluster. They were isolated and annotated by students from the SUNY Old Westbury Science and Technology Entry Program.",
"full_author_list": "Fernando E. Nieto-Fernandez, Christos Noutsos, John Kleopoulos, Olubusola Babalola, Belle L. Connaught, Balquees Shafique, Shannon Farnum, , Hammad Nawaz, Raymond Catapano, Rita M. Reddy, Jorge Morales, Patricia Roccanova, and Shirley Barrera",
"short_author_list": "Nieto-Fernandez et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00112-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33833023"
},
{
"title": "Genome Sequences of Mycobacterium smegmatis Phages Purgamenstris and PhancyPhin",
"abstract": "Two novel mycobacteriophages, PhancyPhin and Purgamenstris, were isolated from the Houston, Texas, area. They were isolated in the same year with the soil enrichment method using the host Mycobacterium smegmatis mc2 155. They exhibit a 99.55% nucleotide identity with each other.",
"full_author_list": "Ramirez Rendon AD, Diaz-Sanchez A, Pool RJ, Ahmed F, Mendez A, Medellin RC, Mendoza FA, Anderson R, Sanchez MA, Ramos JR, Sadana R, Saha S",
"short_author_list": "Ramirez Rendon et al",
"article_url": "https://mra.asm.org/content/10/9/e01288-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33664137"
},
{
"title": "Undergraduate Virtual Engagement in Community Genome Annotation Provides Flexibility to Overcome Course Disruptions",
"abstract": "Recently, students and faculty have been forced to deal with unprecedented disruptions to their courses and broader uncertainties that have presented serious challenges to quality instruction. We present a flexible, team-based approach to teaching and learning that can transition seamlessly between face-to-face, hybrid, and fully online instruction when disruptions occur. We have built a community genome annotation program that can be implemented as a module in a biology course, as an entire course, or as directed research projects. This approach maintains an engaging and supportive educational environment and provides students the opportunity to learn and contribute to science with undergraduate research. Students are provided guidance through multiple interactions with faculty and peer mentors to support their progress and encourage learning. Integration of the developed instructional tools with available technology ensures that students can contribute remotely. Through this process, students seamlessly continue their annotation coursework, participate in undergraduate research, and prepare abstracts and posters for virtual conferences. Importantly, this strategy does not impose any additional burden or workload on students, who may already be overwhelmed with the additional work associated with the transition to remote learning. Here, we present tips for implementing this instructional platform, provide an overview of tools that facilitate instruction, and discuss expected educational outcomes.",
"full_author_list": "Surya Saha, Teresa D. Shippy, Susan J. Brown, Joshua B. Benoit, and Tom D’Elia",
"short_author_list": "Saha et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8011878/",
"journal": "Journal of Microbiology & Biology Education",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33884059"
},
{
"title": "Complete Genome Sequences of Two Mycobacterium smegmatis Bacteriophages",
"abstract": "Mycobacterium smegmatis, an acid-fast bacterial species in the phylum Actinobacteria, has often been used as a substitute for pathogenic mycobacteria in research. Here, we describe the isolation and characterization of two M. smegmatis bacteriophages, Penelope2018 and Miniwave.",
"full_author_list": "Sanchez D, Acosta A, Skoumpourdis N; Dominican College SEA-PHAGES Annotators, Alvarez R, Connors BJ",
"short_author_list": "Sanchez et al",
"article_url": "https://pubmed.ncbi.nlm.nih.gov/33414321/",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33414321"
},
{
"title": "Complete Genome Sequence of Bacteriophage IndyLu, Isolated from a Microbacterium foliorum Culture",
"abstract": "Microbacteriophage IndyLu was isolated from Microbacterium foliorum NRRL B-24224. The 41,958-bp double-stranded DNA genome has 71 predicted protein coding genes and 1 tRNA. The lytic actinobacteriophage was extracted from soil samples collected in Stephenville, TX, and is related to cluster EB bacteriophages Didgeridoo and Lahqtemish.",
"full_author_list": "Ashley Suris, Selina Alvarado, Tommy Butler, Carlos Canales, Matthew Castro, Julia Gaston, Marlee Goppert, , Raylon Huckaby, Jesse Laposky, Jessica Lee, Elizabeth Mullins, Damla Ustundag, Josue Zuniga, Faith Cox, Dustin Edwards",
"short_author_list": "Suris et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.01079-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34913713"
},
{
"title": "Complete Genome Sequences of Cluster A6 and Cluster G1 Mycobacterium smegmatis Phages Hoot and Jolene",
"abstract": "We present the complete genome sequences of Mycobacterium smegmatis phages Hoot and Jolene, isolated in Las Vegas, NV. The phages were isolated and annotated by students enrolled in an undergraduate research course at the University of Nevada, Las Vegas. Hoot is a cluster A6 mycobacteriophage, while Jolene is in cluster G1.",
"full_author_list": "Jon Thompson, Asli Özdemir, Arsen M. Topchyan, Maxwell Torosian, Victoria Z. Thymianos, Angelica Eagle, Juliana McCormick, Leon Kyle G. Boyles, Azucena A. Benito, Kurt Regner, Christy Strong, and Philippos K. Tsourkas",
"short_author_list": "Thompson et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00578-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34672710"
},
{
"title": "Closed Genome Sequence of Yavru, a Novel Arthrobacter globiformis Phage",
"abstract": "We characterized the complete genome sequence of actinobacteriophage Yavru (Siphoviridae), a cluster FE bacteriophage infecting Arthrobacter globiformis NRRL B-2979; it was 89.5% identical to cluster FE phage Whytu, with a capsid width of 50 nm and a tail length of 90 nm. The genome was 15,193 bp in length, with 23 predicted protein-coding genes.",
"full_author_list": "Meliha Ulker, Fardeen A. Siddiqui, Thomas J. Gerton, Rachel E. Anastasi, Dylan J. Conroy, Ethan G. Edwards, Isabelle E. Laizure, Joshua D. Reynolds, Kelsie Duggan, Kristen C. Johnson, and Kyle S. MacLea",
"short_author_list": "Ulker et al",
"article_url": "https://journals.asm.org/doi/full/10.1128/MRA.00986-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "34761957"
},
{
"title": "Complete Genome Sequences of Microbacterium liquefaciens Phages Mercedes, Leafus, Nebulous, and Ixel",
"abstract": "Microbacterium phages Mercedes, Leafus, Nebulous, and Ixel were isolated from soil in Rock Hill, SC. All are lytic phages with Siphoviridae morphotypes and similar genome sequence lengths that range from 40,200 bp to 42,000 bp. The four bacteriophages were isolated using the host Microbacterium liquefaciens.",
"full_author_list": "Victoria J. Frost, Kristi M. Westover",
"short_author_list": "Victoria J. Frost, Kristi M. Westover",
"article_url": "https://mra.asm.org/content/10/11/e00068-21",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2021",
"pubmed_id": "33737355"
},
{
"title": "Complete Genome Sequence of the Streptomyces-Specific Bacteriophage BRock",
"abstract": "The Streptomyces bacteriophage Abt2graduatex2 is a double-stranded DNA (dsDNA) Siphoviridae isolated from soil collected in Baltimore, MD, and harvested using Streptomyces griseus subsp. griseus. Abt2graduatex2, a cluster BG phage, encodes an HicA-like toxin.",
"full_author_list": "Stephen F. Baron, Ashley N. Crossman, Shikha Malik, Parveen Sidhu, Kiran Nehra, Pragati Jamdagni, Ivan Erill, Louise M. Temple",
"short_author_list": "Baron et al",
"article_url": "http://mra.asm.org/content/9/35/e00624-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32855246"
},
{
"title": "Complete Genome Sequence of the Cluster F1 Mycobacteriophage KingMidas",
"abstract": "Subcluster F1 bacteriophage KingMidas was isolated from soil collected in Providence, Rhode Island, using Mycobacterium smegmatis mc2155 as the host. The genome is 57,386 bp and contains 105 predicted protein-coding genes but no transfer-messenger RNAs or tRNAs. This siphovirus has an icosahedral head, with a genome 99.1% identical to that of F1 mycobacteriophage Scottish.",
"full_author_list": "Christine A. Byrum, Christopher A. Korey, Zachary Jordan, Yang Zhou, Sarah Taylor, Joas Alfajardo, Veronique A. Delesalle",
"short_author_list": "Byrum et al",
"article_url": "https://mra.asm.org/content/9/7/e01557-19",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32054715"
},
{
"title": "Characterization and Genome Sequence of the Mycobacteriophage Donny",
"abstract": "We report the discovery of the novel bacteriophage Donny, a Siphoviridae virus that infects Mycobacterium smegmatis mc2155. Donny has a genome length of 69,691 bp and a G+C content of 68.5%. Donny shares 99% and 93% nucleotide identity with bacteriophages Acadian and Baee, respectively.",
"full_author_list": "Lauren E. Colston, Miriam Segura-Totten, Ryan A. Shanks",
"short_author_list": "Colston et al",
"article_url": "https://mra.asm.org/content/9/30/e00373-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32703827"
},
{
"title": "Genome Sequences of the Mycobacteriophages Awesomesauce and LastJedi",
"abstract": "Bacteriophages Awesomesauce and LastJedi infect Mycobacterium smegmatis mc2155. While the Awesomesauce genome is 57,054 bp with 94 protein-coding genes, the LastJedi genome is 55,149 bp with 94 protein-coding genes. Nucleotide sequence comparison in Phamerator detected synteny between Awesomesauce gp49 to gp61 and singleton LilSpotty. Whole-genome BLASTn alignments revealed that LastJedi strongly resembles Clifton (99.41% identity).",
"full_author_list": "Madison E. Davis, Véronique A. Delesalle, Kayla D. Blankenship, Jeffrey T. Good, Clayr M. Kroenke, Gabrielle M. Kuba, Sean P. Sweeney and Christine A. Byrum",
"short_author_list": "Davis et al",
"article_url": "http://mra.asm.org/content/9/34/e00707-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32816978"
},
{
"title": "Complete Genome Sequences of Mycobacteriophages Apex and Gophee",
"abstract": "Apex and Gophee are mycobacteriophages directly isolated from soil using the host Mycobacterium smegmatis mc2155. Apex has a 71,244-bp double-stranded DNA (dsDNA) genome encoding 98 putative proteins, and Gophee has a 68,556-bp dsDNA genome encoding 101 putative proteins.",
"full_author_list": "Denzel Edwards, Tara Carney, Yunia Alvarez, Justin Pagan, Emma Sarro, Regina Alvarez, Bernadette J. Connors",
"short_author_list": "Edwards et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "33154015"
},
{
"title": "Genome Sequences of Microbacteriophages Zada and Ioannes",
"abstract": "Microbacteriophages Zada and Ioannes were isolated from soil and characterized. Genomes were then sequenced and annotated. This was done using the host bacterium Microbacterium foliorum. Zada and Ioannes are both lytic phages with a Siphoviridae morphotype.",
"full_author_list": "Razan El Yaman, Jayla S. Anderson, Tania M. Anderson, Michael A. Avalos Jr., Sheku K. Bangurah, Ken B. Dada, Kiefer R. Degener, Mohammad N. Hadeed, Leen H. Issa, Akhteyar S. Jaeran, Katelynn M. Kowalski, Yamere T. Lloyd, Demitra P. Loucopoulos, Vanessa J. Manzo, Nicolas M. Nunez, Andrea M. Sandoval, Semaj Shelton Jr., Steven M. Taddei, Ali A. Zamat, Stephanie B. Conant, Jonathan S. Finkel, Jacob D. Kagey",
"short_author_list": "El Yaman et al",
"article_url": "https://mra.asm.org/content/9/45/e01012-20?ct",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "33154009"
},
{
"title": "Complete Genome Sequences of Mycobacteriophages OKaNui and DroogsArmy",
"abstract": "Mycobacteriophages OKaNui and DroogsArmy were isolated from soil using the bacterial host Mycobacterium smegmatis mc2155, which belongs to the phylum Actinobacteria. OKaNui was discovered in east Mississippi and DroogsArmy in west Alabama in the United States. The genomes of OKaNui and DroogsArmy were 51,424 bp and 53,254 bp long, respectively.",
"full_author_list": "Kayla M. Fast, Kadaisha G. Johnson, Kaitlyn N. Mayfield, Leah A. Stephens, T. Hunter Reid, Emma D. Ryan, Tracy W. Keener and Michael W. Sandel",
"short_author_list": "Fast et al",
"article_url": "http://mra.asm.org/content/9/33/e00791-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32817159"
},
{
"title": "Complete Genome Sequence of Mycobacteriophage Faze9",
"abstract": "Mycobacteriophage Faze9 is a novel lytic phage that was isolated from soil collected in Scranton, PA, using the host Mycobacterium smegmatis mc2155. Faze9 has a double-stranded DNA genome composed of 67,503 kbp, has a G+C content of 68.9\\%, encodes 91 predicted proteins, and is closely related to mycobacteriophages in the B2 subcluster.",
"full_author_list": "John Grossi, John Shebby, Christopher W. Brey Marywood University SEA-PHAGES 2016–2017 Hunters",
"short_author_list": "Grossi et al",
"article_url": "https://mra.asm.org/content/9/3/e01372-19",
"journal": "Microbiology Resource Announcements",
"journal_volume": "9",
"journal_issue": "3",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "31948961"
},
{
"title": "Genome Sequences of Gordonia rubripertincta Bacteriophages Jellybones and NHagos",
"abstract": "Jellybones and NHagos are bacteriophages that were identified in the host bacterium Gordonia rubripertincta NRRL B-16540. Jellybones has a direct terminal repeat and was assigned to the CS2 subcluster with a length of 77,514 bp. NHagos is circularly permuted and was assigned to the DR cluster with a length of 59,580 bp.",
"full_author_list": "D'Andrew L. Harrington, Jennifer L. Stevens, Mia J. Johnson, Samantha J. Pochiro, Michelle M. Moriarty, Miriam E. Robertson, Andy Sanchez, Orin G. Whitby, Kendra W. Kimberley, Chelsey C. McKenna, James R. Theoret, Erin J. Windsor, Earl J. Yoon",
"short_author_list": "Harrington et al",
"article_url": "https://mra.asm.org/content/9/40/e00935-20?ct",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "33004457"
},
{
"title": "Genome Sequence of Arthrobacter sp. Phage Scuttle",
"abstract": "Arthrobacter phage Scuttle was isolated by enrichment from a dry soil sample (collected in Upper Darby, Pennsylvania) on host Arthrobacter sp. ATCC 21022. The genome of this phage is 43,729 bp long, has a GC content of 61.1%, and has 61 annotated protein-coding genes.",
"full_author_list": "Melinda Harrison, Matthew D. Mastropaolo, Andrew Conboy",
"short_author_list": "Harrison et al",
"article_url": "https://mra.asm.org/content/9/26/e00577-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32586860"
},
{
"title": "Genome Sequences of Mycobacteriophages Joselito, Patt, and Tydolla",
"abstract": "Mycobacteriophages Joselito, Patt, and Tydolla were isolated from different soil or water samples using Mycobacterium smegmatis mc2155 as the host. Each was obtained using direct isolation techniques, purified, and then sequenced using the deconvolution of genomes after en masse sequencing (DOGEMS) method.",
"full_author_list": "Christina Jacob, Yunia Alvarez, Tara Carney, Cynthia Castro, Regina Alvarez, Bernadette J. Connors",
"short_author_list": "Jacob et al",
"article_url": "https://mra.asm.org/content/9/23/e00519-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32499357"
},
{
"title": "Genomic diversity of bacteriophages infecting Microbacterium spp",
"abstract": "The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.",
"full_author_list": "Deborah Jacobs-Sera, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A. Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M. R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis N. Mavrich, Angela L. McKinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy, Denise L. Monti, Dana A. Pape-Zambito, Richard S. Pollenz, Welkin H. Pope, Nathan S. Reyna, Claire A. Rinehart, Daniel A. Russell, Christopher D. Shaffer, Viknesh Sivanathan, Ty H. Stoner, Joseph Stukey, C. Nicole Sunnen, Sara S. Tolsma, Philippos K. Tsourkas, Jamie R. Wallen, Vassie C. Ware, Marcie H. Warner, Jacqueline M. Washington, Kristi M. Westover, JoAnn L. Whitefleet-Smith, Helen I. Wiersma-Koch, Daniel C. Williams, Kira M. Zack, Graham F. Hatfull",
"short_author_list": "Jacobs-Sera et al",
"article_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234636",
"journal": "PLoS ONE",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32555720"
},
{
"title": "Genome Sequences of Two F1 Subcluster Bacteriophages, Burwell21 and Nivrat, Isolated Using the Bacterial Host Mycobacterium smegmatis",
"abstract": "The mycobacteriophages Burwell21 and Nivrat are two F1 cluster bacteriophages isolated from different soil samples in Charlotte, NC. Burwell21 has a 58,098-base-pair double-stranded DNA genome, with 99 protein-coding genes predicted, whereas Nivrat has a 58,009-base-pair genome, with 102 protein-coding genes predicted.",
"full_author_list": "Joanna Katsanos, Chioma Ngene, Jennifer Cook-Easterwood",
"short_author_list": "Katsanos et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32165393"
},
{
"title": "Genome Sequences of Bacteriophages ClearAsMud and Kauala, Isolated from Microbacterium foliorum",
"abstract": "Cluster EC ClearAsMud and cluster EA4 Kauala are lytic Siphoviridae bacteriophages that were isolated from soil in southern California using Microbacterium foliorum NRRL B-24224 as the host. The ClearAsMud and Kauala genomes are 52,987 bp and 39,378 bp, respectively, and contain 92 and 56 predicted protein-coding genes, respectively.",
"full_author_list": "Heidi Lin, Michael Reeves, Melissa Acevedo, Kelsey Bass, Elizabeth Chau, Brandon Ching, Elisaelena Enriquez, Skylar Evans, Kaitlyn Mamora, Caitlyn Pang, Michelle Santos, Chelsea Tafoya, Madyllyne Vaca, Wiliam Van Iderstein, Luis Velasco, Vivianna Williams, Grant Yonemoto, Tyler Yonemoto, Jessica Choi, Natasha Dean, Arturo Diaz",
"short_author_list": "Lin et al",
"article_url": "https://mra.asm.org/content/9/46/e01026-20?ct",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "33184160"
},
{
"title": "pdm_utils: a SEA-PHAGES MySQL phage database management toolkit",
"abstract": "Bacteriophages (phages) are incredibly abundant and genetically diverse. The volume of phage genomics data is rapidly increasing, driven in part by the SEA-PHAGES program, which isolates, sequences, and manually annotates hundreds of phage genomes each year. With an ever-expanding genomics dataset, there are many opportunities for generating new biological insights through comparative genomic and bioinformatic analyses. As a result, there is a growing need to be able to store, update, explore, and analyze phage genomics data. The package pdm_utils provides a collection of tools for MySQL phage database management designed to meet specific needs in the SEA-PHAGES program and phage genomics generally.",
"full_author_list": "Mavrich T, Gauthier C, Abad L, Bowman C, Cresawn S, Hatfull G",
"short_author_list": "Mavrich et al",
"article_url": "https://pubmed.ncbi.nlm.nih.gov/33226064/",
"journal": "Bioinformatics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "33226064"
},
{
"title": "Complete Genome Sequence of Rahel, a C1 Cluster Mycobacteriophage",
"abstract": "Rahel is a lytic Myoviridae bacteriophage that infects Mycobacterium smegmatis mc2155. It has 1,555,955 bp and 64.7% G+C content. Rahel has a circularly permuted genome with 270 genes, 53 of them of known function, 33 tRNAs, and 1 transfer-messenger RNA (tmRNA). Only five genes are coded on the reverse strand.",
"full_author_list": "Fernando E. Nieto-Fernandez, Christos Noutsos, Jillian Nissen, Yara Abdelsalam, Jessica Ackloo, Navpreet Banger, Hason Chan, Tarana Chittineedi, Isabel Duplessy, Mark Dyce, Daesha Garrison, Jaime Gonzalez, Sandra John, Imanjot Kahlon, Tania Kumar, Adwoa Lewis, Karthik Madhira, Rivka Mullokandova, Nellie Pirzadeh, Iman Raja, Kevin Ram, Ravi Ramdhari, Rita Reddy, Briana S. Saed, Phalan Smith, Steeve Sproul, Jane Thomas, Avia Yossefi, Jorge Morales",
"short_author_list": "Nieto-Fernandez et al",
"article_url": "https://mra.asm.org/content/9/45/e01071-20?ct",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "33154012"
},
{
"title": "Genome Sequences of 20 Bacteriophages Isolated on Gordonia terrae",
"abstract": "We report here the sequences of 20 bacteriophages isolated on Gordonia terrae 3612. These phages span considerable sequence diversity, represent 12 clusters and a singleton genome, and range in genome length from 16.2 kbp to 151.3 kbp. Phages Pupper and SCentae are the first reported Myoviridae phages of Gordonia spp.",
"full_author_list": "Welkin H. Pope, Kristen A. Butela, Rebecca A. Garlena, Deborah Jacobs-Sera, Daniel A. Russell, Marcie H. Warner, University of Pittsburgh SEA-PHAGES, Graham F. Hatfull",
"short_author_list": "Pope et al",
"article_url": "https://mra.asm.org/content/9/3/e01489-19",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "31948974"
},
{
"title": "Characterization and Genome Sequence of Mycobacterium Phage XianYue",
"abstract": "Novel mycobacteriophage XianYue was isolated in Northeast Georgia and infects Mycobacteria smegmatis mc2155. Actinobacteriophages which share at least 50% nucleotide identity are grouped into clusters, with XianYue in cluster A2. Its genome is 52,907 bp with 91 open reading frames (ORFs) and 62.9% GC content, and it shares 86.51% nucleotide identity with mycobacteriophage Trixie.",
"full_author_list": "Wesley D. Rhinehart, Amanda J. Laidlaw, Alexis M. O’Neal, Jessica A. Toller, Miriam Segura-Totten, Ryan A. Shanks, Alison E. Kanak",
"short_author_list": "Rhinehart et al",
"article_url": "https://mra.asm.org/content/9/25/e00459-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32554787"
},
{
"title": "Complete Genome Sequences of Cluster G Mycobacteriophage Darionha, Cluster A Mycobacteriophage Salz, and Cluster J Mycobacteriophage ThreeRngTarjay",
"abstract": "Mycobacteriophages Darionha, Salz, and ThreeRngTarjay are mycobacteriophages isolated using the host Mycobacterium smegmatis mc2155. Following isolation from soil samples, all three siphoviridae phages were characterized, and their genomes were sequenced and annotated.",
"full_author_list": "Andrea M. Sandoval, Amber M. Abram, Zahraa M. Alhabib, Angelina S. Antonyan, Salar M. Brikho, Sarah I. Buhay, Griffin E. Craig, Karen G. Crile, Nour El Yaman, Lizbeth Garcia-Leon, Zahraa B. Hammoud, Anthony R. Huffman, Ali H. Issa, Alexander B. Jackman, Victoria K. Krajcz, Yamiya J. Lloyd, Marcel L. Jones, Diana L. McMahon, Briana A. D. Murdock, Jada J. Nelson, Tulsi T. Patel, Yashodhara V. Patil, Sabriyyah A. Ricketts, Leonardo S. Romero-Barajas, Laila H. Sareini, Channing S. Sesoko, Marcelio A. Shammami, Erin E. Sheardy, John R. Sherwood, Arren E. Simpson, Racha H. Tiba, Stephanie B. Conant, Jonathan S. Finkel, Jacob D. Kagey",
"short_author_list": "Sandoval et al",
"article_url": "https://mra.asm.org/content/9/20/e00160-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32409529"
},
{
"title": "Genome Sequences of 12 Phages That Infect Klebsiella pneumoniae",
"abstract": "Klebsiella pneumoniae is a pathogen responsible for significant proportions of nosocomial and health care-associated infections and is known to acquire multiple antibiotic resistance genes. Here, we announce the full genome sequences of 12 K. pneumoniae bacteriophages from samples collected in wastewater treatment facilities across the western United States.",
"full_author_list": "Trever L. Thurgood, Ruchira Sharma, Jackson J. Call, Joshua D. Chronis, Daniel D. Dawson, Zachary K. Finnegan, Kent W. Foster, Tyler Meek, Emily Potts, Michael R. Sirrine, Alex D. Atkinson, Jacob D. Fairholm, Yoga A. Handoko, Kai Li Ong, Olivia B. Tateoka, Daniel K. Arens, Liam Johnson, Jared L. Kruger, Emily Loertscher, Daniel W. Thompson, Jamison K. Walker, Richard A. Robison, Sherwood R. Casjens, Julianne H. Grose",
"short_author_list": "Thurgood et al",
"article_url": "https://mra.asm.org/content/9/16/e00024-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32299868"
},
{
"title": "Complete Genome Sequences of Cluster P1 and Cluster C1 Mycobacterium smegmatis Phages Jung and Ronan",
"abstract": "We present the complete genome sequences of Mycobacterium smegmatis phages Jung and Ronan, isolated from soil in Las Vegas, Nevada. The phages were isolated and annotated by students enrolled in a course for undergraduate research experience (CURE). Jung is a cluster P1 mycobacteriophage, while Ronan is in cluster C1.",
"full_author_list": "Richard Van, William Nie, Feruz Abdela, Bardia Eivazi, Dolores Kickbusch, Michael Finkle, Cody Cris, Matthew Rubinstein, Baylor Akavan, Mahdeed Raja, Jessica Vergara, Wilson Andrade, Abimael Barajas, Jocelyn Sanchez, Maria Duenas, Kurt Regner, Christy Strong and Philippos K. Tsourkas",
"short_author_list": "Van et al",
"article_url": "http://mra.asm.org/content/9/34/e00678-20",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2020",
"pubmed_id": "32816976"
},
{
"title": "Complete Genome Sequences of 12 B1 Cluster Mycobacteriophages, Gareth, JangoPhett, Kailash, MichaelPhcott, PhenghisKhan, Phleuron, Phergie, PhrankReynolds, PhrodoBaggins, Phunky, Vaticameos, and Virapocalypse.",
"abstract": "Twelve B1 cluster mycobacteriophages were isolated from soil samples collected in Philadelphia, PA, USA, using Mycobacterium smegmatis mc2 155 as a host, and were sequenced. The genome sequences range in size from 66,887 bp to 68,953 bp in length and have between 99 and 105 putative protein-coding genes.",
"full_author_list": "Apellido KA, Balchander D, Erlich MC, Gocal JK, Gocal WA, Haile S, Kang AK, Koduri S, Natrajan M, Parikh AA, Tata RK, Walor TA, Wong BM, Nako S, Tran T, Islam E, Mammen MP; Drexel University SEA-PHAGES annotators 2016; Drexel University SEA-PHAGES annotators 2017; Drexel University SEA-PHAGES annotators 2018, Ball SL, Bollivar DW, Butela KA, Pope WH, McDonald MT, Tang CA, Dalia RR, Smith KPW, Little JL, Moyer AE, Gurney SMR.",
"short_author_list": "Apellido KA et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "30834367"
},
{
"title": "Genome Sequences of Three Cluster C Mycobacteriophages, Bipolarisk, Bread, and FudgeTart",
"abstract": "Three mycobacteriophages, Bipolarisk, Bread, and FudgeTart, were isolated from enriched soil samples found in Crete, NE. All three phages are lytic, belong to subcluster C1, and infect Mycobacterium smegmatis mc2155. The structures of the three genomes are similar, with slight variations in gene number and content.",
"full_author_list": "Dane M. Bowder, Brandon W. Gannon, Kathryn J. Grint, Jason T. Iltz, Teryn M. Koch, Kaitlyn S. Mahnke, Brea D. Murnan, Alexandria M. Osborn, Danielle M. Schreiber, Grace L. Su, Jaime G. Troester, Erin L. Doyle",
"short_author_list": "Bowder et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31296672"
},
{
"title": "A Novel Genus of Actinobacterial Tectiviridae",
"abstract": "Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomyces phages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcus phage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.",
"full_author_list": "Steven M. Caruso, Tagide N. deCarvalho, Anthony Huynh, George Morcos, Nansen Kuo, Shabnam Parsa, and Ivan Erill",
"short_author_list": "Caruso et al.",
"article_url": "https://www.mdpi.com/1999-4915/11/12/1134/reprints",
"journal": "Viruses",
"journal_volume": "11",
"journal_issue": "1134",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31817897"
},
{
"title": "Genome Sequences of Mycobacteriophages Ebony and Holeinone",
"abstract": "Ebony and Holeinone represent the first mycobacteriophages isolated from Charlotte, NC, soil samples, using the host Mycobacterium smegmatis strain mc2155. Ebony has a 52,152-bp genome and showed similarity to other phages in the A11 subcluster. Holeinone has a 67,044-bp genome and showed similarity to other phages in the B2 subcluster.",
"full_author_list": "Jennifer Cook-Easterwood, Hailey Gase, Chioma Ngene, Joanna Katsanos",
"short_author_list": "Cook-Easterwood et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31147428"
},
{
"title": "Complete Genome Sequences of Nine Mycobacteriophages from New Zealand, Beatrix, Carthage, Daegal, Dulcie, Fancypants, Fenn, Inca, Naira, and Robyn",
"abstract": "Beatrix, Carthage, Daegal, Dulcie, Fancypants, Fenn, Inca, Naira, and Robyn are newly isolated bacteriophages capable of infecting Mycolicibacterium smegmatis mc2 155. We discovered, sequenced, and annotated these New Zealand bacteriophages. These phages illustrate that New Zealand harbors a selection of the highly diverse and distributed mycobacteriophage clusters found globally.",
"full_author_list": "C. G. Davies, J. K. Wojtus, C. E. R. Gilligan, S. F. Latu, T. J. Manning, C. E. Meyer, J. Nersesyan, R. I. Tennent, L. Oosthuizen, E. Palmer, A. F. M. Hoskin, J. Turnbull, J. A. Sweatman, N. Elliston-Boyes, C. J. Wallace, A. Baxter, Z. Borrie, J. S. Elder, O. Massey, A. Wong, O. K. Silander, N. E. Freed, H. L. Hendrickson",
"short_author_list": "Davies et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31097509"
},
{
"title": "Complete Genome Sequences of Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano",
"abstract": "Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano were isolated from soil using the host bacterium Mycobacterium smegmatis mc²155. Candle, Schatzie, and Sumter were discovered in Alabama and Waleliano in Maryland. The bacteriophages have been assigned clusters based on nucleotide similarity, as follows: Candle, R; Schatzie, J; Sumter, A1; and Waleliano, B4.",
"full_author_list": "Fast KM, Forrest BE, Granec GR, Larrimore JD, Morse AE, Ryan ED, Schellhammer PK, Keener TW, Sandel MW.",
"short_author_list": "Fast, KM et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/31346026",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31346026"
},
{
"title": "Genome Sequences of Cluster K Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley.",
"abstract": "Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley were isolated from soil using Mycobacterium smegmatis mc2155. Genomic analysis indicated that they belong to subclusters K1 and K5. Their genomic architectures are typical of cluster K mycobacteriophages, with most variability occurring on the right end of the genome sequence.",
"full_author_list": "Gaballa JM, Dabrian K, Desai R, Ngo R, Park D, Sakaji E, Sun Y, Tan B, Brinck M, Brobst O, Fernando R, Kim H, McCarthy S, Murphy M, Sarkis A, Sevier P, Singh A, Wu D, Wu MY, Ennis HA, Luhar R, Miller JE, Orchanian SB, Salbato AN, Alam S, Brenner L, Kailani Z, Laskow J, Ma X, Miikeda A, Nol-Bernardino P, Sukhina A, Walas N, Wei W, Do NP, Fournier CT, Kim CJ, Mosier SF, Pierson C1 Romero IG, Sanchez M, Sawyerr O, Wang J, Watanabe R, Wu S, Chen A, Kazane K, Kettoola Y, Goodwin EC, Lund AJ, Villella W, Williams D, Freise A, Moberg Parker",
"short_author_list": "Gaballa JM",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "30643892"
},
{
"title": "Genome Sequences of Arthrobacter sp. Phages Inspire2, Ronnie, Hunnie, DeWayne, CGermain, Copper, Azathoth, and Arby",
"abstract": "Eight siphoviral phages isolated from various soil types and locations in southwestern Pennsylvania using Arthrobacter sp. strain ATCC 21022 were sequenced. The phages all have relatively small genomes, with each genome containing 15,556 bp. All 8 phages are closely related to previously described cluster AN Arthrobacter phages (K. K. Klyczek, J. A. Bonilla, D. Jacobs-Sera, T. L. Adair, et al., PLoS One 12:e0180517, 2017, https://doi.org/10.1371/journal.pone.0180517; J. Y. Lee-Soety, S. Bhatt, T. L. Adair, J. A. Bonilla, et al., Genome Announc 5:e01092-17, 2017, https://doi.org/10.1128/genomeA.01092-17).",
"full_author_list": "Melinda Harrison, Matthew D. Mastropaolo, Andrew Conboy, Cabrini University SEA-PHAGES Annotators, Lisa McKernan, Robert Schmidt, Véronique A. Delesalle",
"short_author_list": "Harrison et al.",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31270200"
},
{
"title": "Complete Genome Sequences of Cluster F Mycobacteriophages EleanorGeorge, Mattes, and Spikelee",
"abstract": "EleanorGeorge, Mattes, and Spikelee are mycobacteriophages isolated from different soil samples using Mycobacterium smegmatis mc2155 as the host. Each was obtained using direct isolation techniques, purified, and then sequenced. Based on sequence similarity, all three belong to the F1 subcluster and are temperate phages.",
"full_author_list": "Christina Jacob, Yunia Alvarez, Cynthia Castro, Katherine Clarke, Linda Dantico, Bernadette J. Connors",
"short_author_list": "Jacob et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31395640"
},
{
"title": "Complete Genome Sequence of Bacteriophage Finny, Isolated from a Microbacterium foliorum Culture",
"abstract": "Actinobacteriophage Finny contains a circularly permuted 40,313-bp double-stranded DNA genome with 63 predicted protein-coding genes. Finny was directly isolated from a soil sample collected in New Braunfels, Texas, that was incubated with Microbacterium foliorum SEA B-24224. Finny is closely related to bacteriophages MCubed, Andromedas, ColaCorta, Eleri, and Sansa.",
"full_author_list": "Tiffany Lee, Michaela Aguirre, Shey Andrews, Kayla Bahr, Abigail Ballard, Matthew Bristerpostma, Faith Cox, Leah Dowell, David Kiker, Tiffany Lujan, Stacy Luka, Abbigal Ramirez, Rheaven Sandoval, Kenneth Underhill, Haze Murphy, Cecilia Cabrera, Dustin Edwards",
"short_author_list": "Lee et al",
"article_url": "https://mra.asm.org/content/8/40/e01039-19",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31582442"
},
{
"title": "Genome Sequences of Bacteriophages KaiHaiDragon and OneinaGillian, Isolated from Microbacterium foliorum in Riverside, California.",
"abstract": "KaiHaiDragon and OneinaGillian are two bacteriophages which have been recovered from soil samples using the bacterial host Microbacterium foliorum. Their genome lengths are 52,992 bp and 61,703 bp, with 91 and 104 predicted open reading frames, respectively. KaiHaiDragon belongs to cluster EC, and OneinaGillian is a member of cluster EG.",
"full_author_list": "Gillian Miller, Steven Tran, Rhiannon Abrahams, Daniel Bazan, Ethan Blaylock, Jessica Choi, Shannon Grewal, Elmira Hernandez, Daniel Kim, Kay Kim, Yumin Lee, Meagan Lopez, Rachel Specht, Nancy Kalaj, Arun Muthiah, Natasha Dean, Arturo Diaz",
"short_author_list": "Miller et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+Sequences+of+Bacteriophages+KaiHaiDragon+and+OneinaGillian%2C+Isolated+from+Microbacterium+foliorum+in+Riverside%2C+California",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "30975821"
},
{
"title": "Complete Genome Sequence of Cluster O Mycobacterium smegmatis Bacteriophage Ryadel.",
"abstract": "Mycobacteriophage Ryadel is a newly isolated cluster O Siphoviridae bacteriophage, characterized by an unusual prolate capsid, containing a 72,658-base-pair double-stranded DNA genome with 132 predicted protein-coding genes. Conserved among cluster O bacteriophages, the Ryadel genome contains 31 copies of a unique 17-bp sequence with dyad symmetry.",
"full_author_list": "Miller T, Bachhofer D, Cooper A, Doty J, Katuri J, Musgrave J, Palumbo A, Spann H, Stone A, Emmert K, Edwards J, Meik J, Pierce J, Edwards D.",
"short_author_list": "Miller et al.",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "30923246"
},
{
"title": "Complete Genome Sequences of Seven EA Cluster Microbacteriophages, Bustleton, MillyPhilly, Riyhil, Phriends, Pherbot, PrincePhergus, and TinSulphur",
"abstract": "Seven EA cluster microbacteriophages were isolated from soil collected around Philadelphia, PA, using the bacterial host Microbacterium foliorum. All of these phages have a highly conserved genome with regions of diversity localized to the 3′ end. In phage Phriends (EA1 cluster), this region contains an orpham gene with no known function.",
"full_author_list": "Anh M. Nguyen Quach, Amy E. Varghese, Kumal Siddiq, Isabella G. Pappano, Almas Thaha, Tracy A. Marcelis, Bora Feruku, Akhil Vindyala, Riyaz Mohamed, Kailee A. Johnson, Sayema Hakim, Shivashree Sekar, Pavithra Vinnakota, Nowrin H. Borsha, Ryneisha McKenzie, Sanya S. Ailani, Shruti Patel, Vincent A. Beggarly, Drexel University SEA-PHAGES annotators 2019, Matthew T. McDonald, Ritu R. Dalia, Svetlana Khakhina, Susan M. R. Gurney",
"short_author_list": "Nguyen Quach et al",
"article_url": "https://mra.asm.org/content/8/46/e01193-19",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31727713"
},
{
"title": "Complete Genome Sequence of Rhodococcus erythropolis Phage Shuman",
"abstract": "Shuman is a bacteriophage isolated in Nyack, New York, using Rhodococcus erythropolis NRRL B-1574 as a host. It is a member of cluster CA and has a genome length of 46,544 bp. Shuman contains 67 predicted protein-coding genes, 3 tRNA genes, and no transfer-messenger RNA (tmRNA) genes.",
"full_author_list": "Ponce Reyes S, Park PJ, Kaluka D, Washington JM.",
"short_author_list": "Reyes et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "30923242"
},
{
"title": "Complete Genome Sequences of Mycobacterium smegmatis Phages Chewbacca, Reptar3000, and Riparian, Isolated in Las Vegas, Nevada.",
"abstract": "Here, we present the complete genome sequences of Mycobacterium smegmatis phages Chewbacca, Reptar3000, and Riparian, isolated from soil in Las Vegas, NV. The phages were isolated and annotated by undergraduate students enrolled in the Phage Discovery course offered by the School of Life Sciences at the University of Nevada, Las Vegas.",
"full_author_list": "Salisbury A, Cassin E, Ayala-Pineda K, Barroga N, Cadiz V, Cisneros R, Fersini J, Jeanite T, Juste J, Ines J, Leyva G, Macalinao D, Muscelli S, Nhan S, Reyes GS, Rhoden H, Tan R, Torres E, Tran K, Uriarte-Valle G, Wallace C, Wong S, Regner K, Strong C, Tsourkas PK.",
"short_author_list": "Salisbury A et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "30746523"
},
{
"title": "Complete Genome Sequences of Mycobacterium smegmatis Phages NihilNomen and Carlyle, Isolated in Las Vegas, Nevada",
"abstract": "We present the complete genomes of the Mycobacterium smegmatis phages Carlyle and NihilNomen, isolated from soil in Las Vegas, Nevada. The phages were isolated and annotated by undergraduate students enrolled in the Phage Discovery course offered by the School of Life Sciences at the University of Nevada Las Vegas.",
"full_author_list": "Salisbury A, Doss R, Mehta A, Bhatti K, Dapra C, Huntsinger A, Rodriguez S, Yacek S, Sandberg R, Gildore A, Knudtson J, Tibayan F, Ohta T, Zafar N, Mercado G, Le A, Mekhaeel N, Willer J, Rodrich-Zuniga E, McFarland M, Regner K, Strong C, Tsourkas PK.",
"short_author_list": "Salisbury et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753266/",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31537662"
},
{
"title": "Complete Genome Sequences of Streptomyces lividans Bacteriophages Satis and JustBecause",
"abstract": "We present here the complete genomes of two Streptomyces bacteriophages, Satis and JustBecause. Both phages were isolated directly from soil samples collected in St. Louis, MO, and present with an unusual prolate head morphology and large genome lengths of over 180 kb.",
"full_author_list": "Kelly Hartigan, John Hudson Alarcon, Andrew Cao, Yongzhen Chen, Nicole Curnutt, Brooke Felsheim, Saransh Gothi, Lucia Grandison, Matthew McDermut, Kaeli-Skye Spight, Xuejing Xu, Kathleen Weston-Hafer, Christopher Shaffer",
"short_author_list": "Shaffer et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31395631"
},
{
"title": "Genome Sequence of Mycobacterium Phage LilHazelnut",
"abstract": "Here, we describe LilHazelnut, a novel mycobacteriophage that infects Mycobacterium smegmatis mc2155. LilHazelnut is a cluster Q phage that shares 99% nucleotide identity with phage Giles, is 53,746 bp in length, and has a G+C content of 67.5%. LilHazelnut is a temperate Siphoviridae virus, as is typical of cluster Q family members.",
"full_author_list": "Ryan A. Shanks, Ashley N. Hazel, William H. Jones, Miriam Segura-Totten",
"short_author_list": "Shanks et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31072888"
},
{
"title": "Genome Sequences of Six Cluster N Mycobacteriophages, Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob, Isolated on Mycobacterium smegmatis mc2 155",
"abstract": "The annotation of six cluster N Mycobacterium smegmatis phages (Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob) reveals regions of genomic diversity, particularly within the central region of the genome. The genome of Kevin1 includes two orphams (genes with no similarity to other phage genes), with one predicted to encode an AAA-ATPase.",
"full_author_list": "Russell A. Caratenuto, III, Grace O. Ciabattoni, Nicolas J. DesGranges, Cassidy L. Drost, Longhui Gao, Brianna Gipson, Nicholas C. Kahler, Nicole A. Kirven, Julia C. Melehani, Krishna Patel, Alecia B. Rokes, Ryan A. Seth, Matthew C. West, Alexa A. Alhout, Francis F. Akoto, Nicole Capogna, Netta Cudkevich, Lee H. Graham, Matthew S. Grapel, Maaz M. Haleem, Jamie B. Korenberg, Brooke P. Lichak, Lauren N. McKinley, Kourtney R. Mendello, Caitlin E. Murphy, Lauren M. Pyfer, Wascar A. Ramirez, Julia R. Reisner, Rachel H. Swope, Matthew J. Thoonkuzhy, Lauren A. Vargas, Croldy A. Veliz, Katherine R. Volpe, Kevin D. Zhang, Dylan Z. Faltine-Gonzalez, Caitlin M. Zuilkoski, Catherine M. Mageeney, Hamidu T. Mohammed, Margaret A. Kenna, Vassie C. Ware",
"short_author_list": "Ware et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2019",
"pubmed_id": "31147431"
},
{
"title": "Genome Sequences of Ilzat and Eleri, Two Phages Isolated Using Microbacterium foliorum NRRL B-24224.",
"abstract": "Bacteriophages Ilzat and Eleri are newly isolated Siphoviridae infecting Microbacterium foliorum NRRL B-24224. The phage genomes are similar in length, G+C content, and architecture and share 62.9% nucleotide sequence identity.",
"full_author_list": "Ali I, Jones AE, Mohamed A, Sivanathan V.",
"short_author_list": "Ali I, Jones AE, Mohamed A, Sivanathan V.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29650566"
},
{
"title": "Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages",
"abstract": "Bacteriophages are a major force in the evolution of bacteria due to their sheer abundance as well as their ability to infect and kill their hosts and to transfer genetic material. Bacteriophages that infect the Enterobacteriaceae family are of particular interest because this bacterial family contains dangerous animal and plant pathogens. Herein we report the isolation and characterization of two jumbo myovirus Erwinia phages, RisingSun and Joad, collected from apple trees. These two genomes are nearly identical with Joad harboring two additional putative gene products. Despite mass spectrometry data that support the putative annotation, 43% of their gene products have no significant BLASTP hit. These phages are also more closely related to Pseudomonas and Vibrio phages than to published Enterobacteriaceae phages. Of the 140 gene products with a BLASTP hit, 81% and 63% of the closest hits correspond to gene products from Pseudomonas and Vibrio phages, respectively. This relatedness may reflect their ecological niche, rather than the evolutionary history of their host. Despite the presence of over 800 Enterobacteriaceae phages on NCBI, the uniqueness of these two phages highlights the diversity of Enterobacteriaceae phages still to be discovered.",
"full_author_list": "Daniel K. Arens,T. Scott Brady,John L. Carter,Jenny A. Pape,David M. Robinson,Kerri A. Russell,Lyndsay A. Staley,Jason M. Stettler,Olivia B. Tateoka,Michelle H. Townsend,Kiara V. Whitley,Trevor M. Wienclaw,Taryn L. Williamson,Steven M. Johnson,Julianne H. Grose",
"short_author_list": "Arens et al",
"article_url": "https://doi.org/10.1371/journal.pone.0200202",
"journal": "PLoS One",
"journal_volume": "13(7): e0200202",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29979759"
},
{
"title": "Complete Genome Sequences of Six BI Cluster Streptomyces Bacteriophages, HotFries, Moozy, Rainydai, RavenPuff, Scap1, and SenditCS.",
"abstract": "Six double-stranded DNA Streptomyces bacteriophages, HotFries, Moozy, RavenPuff, Scap1, Rainydai, and SenditCS, were isolated using the phytopathogen Streptomyces scabiei as a host. These phages have been identified as Siphoviridae and members of cluster BI by genomic analysis.",
"full_author_list": "Blocker D, Koert M, Mattson C, Patel H, Patel P, Patel R, Paudel H; 2017 UMBC Phage Hunters, Erill I, Caruso SM.",
"short_author_list": "Blocker D et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "30533665"
},
{
"title": "Genome Sequences of Four Cluster P Mycobacteriophages",
"abstract": "Four bacteriophages infecting Mycobacterium smegmatis mc2155 (three belonging to subcluster P1 and one belonging to subcluster P2) were isolated from soil and sequenced. All four phages are similar in the left arm of their genomes, but the P2 phage differs in the right arm. All four genomes contain features of temperate phages.",
"full_author_list": "Doyle EL, Fillman CL, Reyna NS, Tobiason DM, Westholm DE, Askins JL, Backus BP, Baker AC, Ballard HS, Bisesi PJ, Bond L, Byrnes D, Carlstedt H, Dodson KS, Fallert MJ, Foster KJ, Games DN, Grams TR, Guild NA, Hurd A, Iwata N, Kepler CR, Krenzke LR, Luekens K, Lewis J, McEntee C, McGee JC, Nalley N3, Plymale RC, Prochaska J, Rogers RG, Schipper JB, Snyder K, Uhrich K, Vermillion CD, Vickers SK, Wenta MD, Yates TZ, Young CF, Stoner TH, Pope WH, Jacobs-Sera D, Garlena RA, Russell DA, Cresawn SG, Hatfull GF.",
"short_author_list": "Doyle et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29326199"
},
{
"title": "Complete Genome Sequence of Streptomyces Bacteriophage Abt2graduatex2",
"abstract": "The Streptomyces bacteriophage Abt2graduatex2 is a double-stranded DNA (dsDNA) Siphoviridae isolated from soil collected in Baltimore, MD, and harvested using Streptomyces griseus subsp. griseus. Abt2graduatex2, a cluster BG phage, encodes an HicA-like toxin.",
"full_author_list": "Ivan Erill, Steven M. Caruso, on behalf of the 2016 UMBC Phage Hunters",
"short_author_list": "Erill, Caruso, et al",
"article_url": "http://genomea.asm.org/content/6/3/e01480-17.full",
"journal": "Genome Announcements",
"journal_volume": "6",
"journal_issue": "3",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29348349"
},
{
"title": "Discovery and Biochemical Characterization of PlyP56, PlyN74, and PlyTB40-Bacillus Specific Endolysins.",
"abstract": "Three Bacillus bacteriophage-derived endolysins, designated PlyP56, PlyN74, and PlyTB40, were identified, cloned, purified, and characterized for their antimicrobial properties. Sequence alignment reveals these endolysins have an N-terminal enzymatically active domain (EAD) linked to a C-terminal cell wall binding domain (CBD). PlyP56 has a Peptidase_M15_4/VanY superfamily EAD with a conserved metal binding motif and displays biological dependence on divalent ions for activity. In contrast, PlyN74 and PlyTB40 have T7 lysozyme-type Amidase_2 and carboxypeptidase T-type Amidase_3 EADs, respectively, which are members of the MurNAc-LAA superfamily, but are not homologs and thus do not have a shared protein fold. All three endolysins contain similar SH3-family CBDs. Although minor host range differences were noted, all three endolysins show relatively broad antimicrobial activity against members of the Bacillus cereus sensu lato group with the highest lytic activity against B. cereus ATCC 4342. Characterization studies determined the optimal lytic activity for these enzymes was at physiological pH (pH 7.0–8.0), over a broad temperature range (4–55 °C), and at low concentrations of NaCl (<50 mM). Direct comparison of lytic activity shows the PlyP56 enzyme to be twice as effective at lysing the cell wall peptidoglycan as PlyN74 or PlyTB40, suggesting PlyP56 is a good candidate for further antimicrobial development as well as bioengineering studies.",
"full_author_list": "Etobayeva I, Linden SB, Alem F, Harb L, Rizkalla L, Mosier PD, Johnson AA, Temple L, Hakami RM, Nelson DC.",
"short_author_list": "Etobayeva et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977269/",
"journal": "Viruses",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29883383"
},
{
"title": "Genome Sequence of a Newly Isolated F2 Subcluster Mycobacteriophage from the Black Belt Geological Region of Western Alabama",
"abstract": "The bacteriophage Demsculpinboyz was discovered in a soil sample from the Black Belt region of Alabama using Mycobacterium smegmatis mc2155 as its host. The genome is 57,437 bp long and contains 116 protein-coding genes. It belongs to the F2 subcluster, which has only five other members.",
"full_author_list": "Fast KM, Keener T, Ali R, Butcher BM, Millwood JD, Odom T, Schellhammer PK, Ufomadu E, Sandel MW",
"short_author_list": "Fast KM et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/29371367",
"journal": "Genome Announcements",
"journal_volume": "6",
"journal_issue": "4",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29371367"
},
{
"title": "Complete Genome Sequences of Mycobacteriophages Kwksand96 and Cane17",
"abstract": "Bacteriophages Kwksand96 and Cane17 were isolated from Mycobacterium smegmatis mc2155. M. smegmatis is host to the highest number of phages analyzed from one species. Both mycobacteriophages were isolated from soil in west Alabama. Kwksand96 and Cane17 belong to subclusters B1 and C1, respectively, based on mycobacteriophage nucleotide sequence similarity.",
"full_author_list": "Fast KM, Keener TW, Castleberry S, Jones KD , Larrimore JD, Long CA, Newburn JT, Pritchett NC, Schellhammer PK, Sandel MW.",
"short_author_list": "Fast KM et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/30533760",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "30533760"
},
{
"title": "Eight Genome Sequences of Cluster BE1 Phages That Infect Streptomyces Species.",
"abstract": "Cluster BE1 Streptomyces bacteriophages belong to the Siphoviridae, with genome sizes over 130 kbp, and they contain direct terminal repeats of approximately 11 kbp. Eight newly isolated closely related cluster BE1 phages contain 43 to 48 tRNAs, one transfer-messenger RNA (tmRNA), and 216 to 236 predicted open reading frames (ORFs), but few of their genes are shared with other phages, including those infecting Streptomyces species.",
"full_author_list": "Hughes LE, Shaffer CD, Ware VC, Aguayo I, Aziz RM, Bhuiyan S, Bindert IS, Calovich-Benne CK, Chapman J, Donegan-Quick R, Farooq A, Garcia C, Graham LH, Green BY, Kenna MA, Kneeream ER, Laing CE, Mageeney CM, Meridew SN, Mikolon AR, Morgan RE, Nayek S, Olugbade ID, Pike KC, Schlegel LE, Shishido TC, Suresh T, Suri N, Weston Hafer K, Garlena RA, Russell DA, Cresawn SG, Pope WH, Jacobs-Sera D, Hatfull GF",
"short_author_list": "Hughes LE et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29326201"
},
{
"title": "Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage",
"abstract": "JangDynasty is a bacteriophage that infects Mycobacterium smegmatis mc2155. It has a genome length of 70,883 bp, with 124 predicted open reading frames (ORFs), 42 of which have known functions. JangDynasty belongs to cluster O, and like other cluster O phages, it is a siphovirus with a prolate capsid.",
"full_author_list": "Jang C, Kalaj N, Hwang B, Hughes L, Yang C, Pak T, Kim J, Han DY, Tedjakusnadi J, Fernandez N, Dean N, Muthiah A, Sutter NB, Diaz A",
"short_author_list": "Jang C et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/29798914",
"journal": "Genome Announcements",
"journal_volume": "6",
"journal_issue": "21",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29798914"
},
{
"title": "Complete Genome Sequences of Bacillus Phages Janet and OTooleKemple52.",
"abstract": "We report here the genome sequences of two novel Bacillus cereus group-infecting bacteriophages, Janet and OTooleKemple52. These bacteriophages are double-stranded DNA-containing Myoviridae isolated from soil samples. While their genomes share a high degree of sequence identity with one another, their host preferences are unique.",
"full_author_list": "Kent B, Raymond T, Mosier PD, Johnson AA; the 2016–2017 VCU Phage Hunters.",
"short_author_list": "Kent B et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29748396"
},
{
"title": "Complete Genome Sequences of 44 Arthrobacter Phages.",
"abstract": "We report here the complete genome sequences of 44 phages infecting Arthrobacter sp. strain ATCC 21022. These phages have double-stranded DNA genomes with sizes ranging from 15,680 to 70,707 bp and G+C contents from 45.1% to 68.5%. All three tail types (belonging to the families Siphoviridae, Myoviridae, and Podoviridae) are represented.",
"full_author_list": "Klyczek KK, Jacobs-Sera D, Adair TL, Adams SD, Ball SL, Benjamin RC, Bonilla JA, Breitenberger CA, Daniels CJ, Gaffney BL, Harrison M, Hughes LE, King RA, Krukonis GP, Lopez AJ, Monsen-Collar K, Pizzorno MC, Rinehart CA; SEA-PHAGES Program; PHIRE Program, Staples AK, Stowe EL, Garlena RA, Russell DA, Cresawn SG, Pope WH, Hatfull GF.",
"short_author_list": "Klyczek KK et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29437090"
},
{
"title": "Finding Some Good in an Invasive Species: Introduction and Assessment of a Novel CURE to Improve Experimental Design in Undergraduate Biology Classrooms.",
"abstract": "Reports such as Vision and Change in Undergraduate Biology Education call for integration of course-based undergraduate research experiences (CUREs) into biology curricula and less emphasis on \"cookbook\" laboratories. CUREs, often characterized by a single open-ended research question, allow students to develop hypotheses, design experiments, and collaborate with peers. Conversely, \"cookbook\" labs incentivize task completion and have pre-determined experimental outcomes. While research comparing CUREs and \"cookbook\" labs is growing, there are fewer comparisons among CUREs. Here, we present a novel CURE built around an invasive grass, Bromus inermis. We evaluated this CURE's effectiveness in improving students' understanding of the Vision and Change competency relating to the application of the scientific process through development and testing of hypotheses. We did so by comparing changes in pre- and posttest scores on the Experimental Design Ability Test (EDAT) between Brome CURE students and students in a concurrent CURE, SEA-PHAGES. While students in both CUREs showed improvements at the end of the semester, Brome CURE students showed a greater increase in EDAT scores than did SEA-PHAGES CURE students. Additionally, Brome CURE students had significantly higher gains in 6 of the 10 EDAT criteria. We conclude that the Brome CURE is an effective ecological parallel to the SEA-PHAGES CURE and can help students gain a meaningful understanding of Vision and Change competencies. Journal of Microbiology & Biology Education.",
"full_author_list": "Laungani R 1 , Tanner C 2 , Brooks TD 1 , Clement B 1 , Clouse M 1 , Doyle E 1 , Dworak S 3 , Elder B 1 , Marley K 1 , Schofield B 1 ",
"short_author_list": "Laungani R. et al",
"article_url": "",
"journal": "Journal of Microbiology & Biology Education ",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "PMID:29983845"
},
{
"title": "Complete Genome Sequences of HonestAbe, Anthony, and Taffo16, Three Cluster C Bacillus cereus Group Bacteriophages",
"abstract": "Three cluster C Myoviridae bacteriophages that infect Bacillus cereus group bacteria were isolated from soil collected in the mid-Atlantic region using B. thuringiensis subsp. kurstaki as a host. Bacillus phages HonestAbe, Anthony, and Taffo16 each shared 90% or higher average nucleotide identities within their subclusters.",
"full_author_list": "Martin Lee, Kayla M. Puglisi, UMBC STEM-BUILD Cohort 1, Ivan Erill, Steven M. Caruso",
"short_author_list": "Lee, Puglisi, et al",
"article_url": "http://genomea.asm.org/content/6/25/e00493-18",
"journal": "Genome Announcements",
"journal_volume": "6",
"journal_issue": "25",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29930035"
},
{
"title": "Genomic Sequence of Mycobacteriophage OKCentral2016",
"abstract": "OKCentral2016 is the first mycobacteriophage sequenced from Oklahoma soil using the bacterial host Mycobacterium smegmatis strain mc2155. OKCentral2016 has a double-stranded DNA genome composed of 50,072 bp, with 84 predicted coding genes and 1 tRNA sequence. This mycobacteriophage has sequence similarities to members of the A10 subcluster.",
"full_author_list": "Patton CJ, Kotturi H.",
"short_author_list": "Patton et al",
"article_url": "http://genomea.asm.org/content/6/8/e01208-17.abstract",
"journal": "Genome Announcements",
"journal_volume": "6",
"journal_issue": "8",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29472341"
},
{
"title": "Complete Genome Sequence of Cluster J Mycobacteriophage Superphikiman",
"abstract": "Mycobacteriophage Superphikiman is a cluster J bacteriophage which was isolated from soil collected in Philadelphia, PA. Superphikiman has a 109,799-bp genome with 239 predicted genes, including 2 tRNA genes.",
"full_author_list": "Pradhan P, Nako S, Tran T, Aluri LS, Anandarajan D, Betini N, Bhatt SD, Chengalvala S, Cox NE, Delvadia BP, Desai AS, Devaney AM, Doyle BK, Edgerton AO, Erlich MC, Fitzpatrick KC, Gajjar EA, Ganguly A, Gill RS, Good PM, Gupta N, Haddad LM, Han EJ, Jain S, Jiang A, Jurgielewicz AD, Kainth DK, Karam JM, Kodavatiganti M, Kriete SJ, MacDonald CE, Maret JP, Mathew AE, Natrajan M, Nishu NM, Patel N, Patel PD, Patel S, Patra K, Rai KK, Sarkar A, Shah P, Tata RK, Tawfik AH, Thuremella BT, Toma J, Veera S, Vemulapalli VK, Vidas TV, Vieira KS, Vijayakumar G, Walor TA, White CR, Wong BM, Zhao SL, Bollivar DW, McDonald MT, Dalia RR, Smith KPW, Little JL, Gurney SMR.",
"short_author_list": "Pradhan P et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/29437101?report=abstract",
"journal": "Genome Announcements",
"journal_volume": "6",
"journal_issue": "5",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "29437101"
},
{
"title": "Genome Sequences of Nine Erwinia amylovora Bacteriophages",
"abstract": "Erwinia amylovora is a plant pathogen belonging to the Enterobacteriaceae family, a family containing many plant and animal pathogens. Herein, we announce nine genome sequences of E. amylovora bacteriophages isolated from infected apple trees along the Wasatch Front in Utah.",
"full_author_list": "Sharma R, Berg JA, Beatty NJ, Choi MC, Cowger AE, Cozzens BJR, Duncan SG, Fajardo CP, Ferguson HP, Galbraith T, Herring JA, Hoj TR, Durrant JL, Hyde JR, Jensen GL, Ke SY, Killpack S, Kruger JL, Lawrence EEK, Nwosu IO, Tam TC, Thompson DW, Tueller JA, Ward MEH, Webb CJ, Wood ME, Yeates EL, Baltrus DA, Breakwell DP, Hope S, Grose JH.",
"short_author_list": "Sharma et al",
"article_url": "",
"journal": "Microbiology Resource Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "30533701"
},
{
"title": "Complete Genome Sequence of Cluster A1 Mycobacterium smegmatis Bacteriophage Arlo.",
"abstract": "Mycobacteriophage Arlo is a newly isolated Siphoviridae bacteriophage isolated from soil samples collected in Bluff Dale, Texas. Mycobacteriophage Arlo has a 52,960 base-pair double-stranded DNA genome that is predicted to contain 96 protein-coding genes. Mycobacteriophage Arlo is related to mycobacteriophage DD5 and other cluster A1 bacteriophages.",
"full_author_list": "Stewart B, Adams M, Fuentes M, Hanson L, Sandoval E, Tovar M, Trautman C, Willis B, Emmert K, Edwards J, Meik J, Pierce J, Edwards D.",
"short_author_list": "Stewart B et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2018",
"pubmed_id": "30533744"
},
{
"title": "Genome Sequences of Three Cluster AU Arthrobacter Phages, Caterpillar, Nightmare, and Teacup",
"abstract": "Caterpillar, Nightmare, and Teacup are cluster AU siphoviral phages isolated from enriched soil on Arthrobacter sp. strain ATCC 21022. These genomes are 58 kbp long with an average G+C content of 50%. Sequence analysis predicts 86 to 92 protein-coding genes, including a large number of small proteins with predicted transmembrane domains.",
"full_author_list": "Adair TL, Stowe E, Pizzorno MC, Krukonis G, Harrison M; Baylor University SEA-PHAGES; Bucknell University SEA-PHAGES; Cabrini University SEA-PHAGES, Cresawn SG, Garlena RA, Russell DA, Pope WH, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Adair et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "5",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29122860"
},
{
"title": "Complete Genome Sequences of Arthrobacter Phages Beans, Franzy, Jordan, Piccoletto, Shade, and Timinator.",
"abstract": "We report here the genome sequences of six newly isolated bacteriophages infecting Arthrobacter sp. ATCC 21022. All six have myoviral morphologies and have double-stranded DNA genomes with circularly permuted ends. The six phages are closely related with average nucleotide identities of 73.4 to 93.0% across genomes lengths of 49,797 to 51,347 bp.",
"full_author_list": "Adair TL, Bonilla JA, Klyczek K2, Lee-Soety JY, Rosas-Acosta G, Harrison M; Baylor University SEA-PHAGES; University of Wisconsin–River Falls SEA-PHAGES; Saint Joseph’s University Phage Safari; University of Texas at El Paso SEA-PHAGES; Cabrini University SEA-PHAGES, Bowman CA, Cresawn SG, Garlena RA, Russell DA, Pope WH8 Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Adair TL et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29097454"
},
{
"title": "Genome Sequences of Cluster K Mycobacteriophages DrHayes, Urkel, and SamuelLPlaqson",
"abstract": "Mycobacteriophages DrHayes, Urkel, and SamuelLPlaqson were isolated from soil samples in Spokane, WA, using Mycobacterium smegmatis mc2155 grown at room temperature. The three genomes differ by only a few nucleotides, are 60,526 bp long, have 97 predicted protein-coding genes and one tRNA gene, and are members of subcluster K1.",
"full_author_list": "Kirk R. Anders, Alex M. Murphy*, William F. Ettinger, Douglas Kempthorne, Charles Kittridge, Alex Kures, Sarah Lundgren, Jacob Masters, Rachel Noyes, Christina Winters, Perry Yazzolino, Kasandra Ziebert, Joseph Haydock, Stephen Hayes, Rebecca A. Garlena, Daniel A. Russell, Marianne K. Poxleitner, Ann-Scott H. Ettinger",
"short_author_list": "Anders et al",
"article_url": "http://genomea.asm.org/content/5/16/e01388-16.full",
"journal": "Genome Announcements",
"journal_volume": "5",
"journal_issue": "16",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28428316"
},
{
"title": "Genome Sequences of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, DarthP, Hammy, Krueger, LastHope, Peanam, PhelpsODU, Phrank, SirPhilip, Slimphazie, and Unicorn",
"abstract": "We report the genome sequences of 14 cluster K mycobacteriophages isolated using Mycobacterium smegmatis mc²155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites.",
"full_author_list": "Anders KR, Barekzi N, Best AA, Frederick GD, Mavrodi DV, Vazquez E; SEA-PHAGES, Amoh NYA, Baliraine FN, Buchser WJ, Cast TP, Chamberlain CE, Chung HM, D'Angelo WA, Farris CT, Fernandez-Martinez M, Fischman HD, Forsyth MH, Fortier AG, Gallo KF, Held GJ, Lomas MA, Maldonado-Vazquez NY, Moonsammy CH, Namboote P, Paudel S, Polley SM, Reyes GM, Rubin MR, Saha MS, Stukey J, Tobias TD, Garlena RA, Stoner TH, Cresawn SG, Jacobs-Sera D, Pope WH, Russell DA, Hatfull GF.",
"short_author_list": "Anders et al.",
"article_url": "https://mra.asm.org/content/5/16/e01388-16",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29217790"
},
{
"title": "Genome Sequences of 19 Rhodococcus erythropolis Cluster CA Phages",
"abstract": "We report the complete genome sequences of 19 cluster CA bacteriophages isolated from environmental samples using Rhodococcus erythropolis as a host. All of the phages are Siphoviridae, have similar genome lengths (46,314 to 46,985 bp) and G+C contents (58.5 to 58.8%), and share nucleotide sequence similarity.",
"full_author_list": "Bonilla, J. A., Isern, S., Findley, A. M., Klyczek, K. K., Michael, S. F., Saha, M. S., Buchser, W.J., Forsyth, M. H., Paudel, S., Gissendanner, C. R., Wiedemeier, A. M. D., Alonzo, F. L., University of Wisconsin-River Falls, SEA-PHAGES, Florida Gulf Coast University, SEA-PHAGES, University of Louisiana-Monroe, SEA-PHAGES, College of William and Mary SEA-PHAGES, Garlena, R. A., Russell, D. A., Pope, W. H., Cresawn, S. G., Jacobs-Sera, D., Hatfull, G. F.",
"short_author_list": "Bonilla et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29217789"
},
{
"title": "Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih.",
"abstract": "Seven mycobacteriophages from distinct geographical locations were isolated, using Mycobacterium smegmatis mc2155 as the host, and then purified and sequenced. All of the genomes are related to cluster A mycobacteriophages, BobSwaget and Lokk in subcluster A2; Fred313, KADY, Stagni, and StepMih in subcluster A3; and MyraDee in subcluster A18, the first phage to be assigned to that subcluster.",
"full_author_list": "Butela KA, Gurney SMR, Hendrickson HL, LeBlanc-Straceski JM, Zimmerman AM, Conant SB, Freed NE, Silander OK, Thomson JJ, Berkes CA, Bertolez C, Davies CG, Elinsky A, Hanlon AJ, Nersesyan J, Patel P, Sherwood J, Tieu Ngo T, Wisniewski KA, Yacoo K6 Arendse PM, Bowlen NW, Cunmulaj J, Downs JL, Ferrenberg CA, Gassman AE, Gilligan CER, Gorkiewicz E, Harness C, Huffman A, Jones C, Julien A, Kupic AE, Latu SF, Manning TJ, Maxwell D; Merrimack College SEA-PHAGES Annotators 2016, Meyer CE, Reardon M, Slaughter M, Swasey R, Tennent RI, Torres V, Waller T, Worcester RM, Yost BL, Cresawn SG, Garlena RA, Jacobs-Sera D, Pope WH, Russell DA9 Hatfull GF, Kagey JD.",
"short_author_list": "Butela KA et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29074662"
},
{
"title": "Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas",
"abstract": "We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly isolated from soil samples, using Mycobacterium smegmatis mc2155 as the host. Comparative genomic analyses with four previously described subcluster L3 phages reveal strong nucleotide similarity and gene conservation, with several large insertions/deletions near their right genome ends.",
"full_author_list": "Chung HM, D'Elia T, Ross JF, Alvarado SM, Brantley MC, Bricker LP, Butler CR, Crist C, Dane JM, Farran BW, Hobbs S, Lapak M, Lovell C, Ludergnani N, McMullen A, Mirza SA, Thrift N, Vaughan DP, Worley G, Ejikemeuwa A, Zaw M, Albritton CF, Bertrand SC, Chaudhry SS, Cheema VA, Do C, Do ML, Duong HM, El-Desoky DH, Green KM, Lee RN, Thornton LA, Vu JM, Zahra MN, Cresawn SG, Stoner TH, Garlena RA, Jacobs-Sera D, Pope WH, Russell DA, Hatfull GF",
"short_author_list": "Chung HM et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/29122864?report=abstract",
"journal": "Genome Announcements",
"journal_volume": "5",
"journal_issue": "45",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29122864"
},
{
"title": "Prophage-mediated defence against viral attack and viral counter-defence.",
"abstract": "Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host–virus dynamics, and counter-defence promotes phage co-evolution.",
"full_author_list": "Dedrick, R. M., Jacobs-Sera, D., Guerrero Bustamante, C. A., Garlena, R. A., Mavrich, T. N., Pope, W. H. , Reyes, J. C., Russell, D. A., Adair, T., Alvey, R., Bonilla, J. A., Bricker, J. S., Brown, B. R., Byrnes, D., Cresawn, S. G., Davis, W. B., Dickson, L. A., Edgington, N. P., Findley, A. M., Golebiewska, U., Grose, J. H., Hayes, C. F., Hughes, L. E., Hutchison, K. W., Isern, S., Johnson, A. A., Kenna, M. A., Klyczek, K. K, Mageeney, C. M., Michael, S. F., Molloy, S. D., Montgomery, M. T., Neitzel, J., Page, S. T., Pizzorno, M. C., Poxleitner, M. K., Rinehart, C. A., Robinson, C. J., Rubin, M. R., Teyim, J. N., Vazquez, E., Ware, V. C., Washington, J., and Hatfull, G. F. ",
"short_author_list": "Dedrick et al.",
"article_url": "https://www.ncbi.nlm.nih.gov/pubmed/28067906",
"journal": "Nature Microbiology",
"journal_volume": "2",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28067906"
},
{
"title": "Expression and evolutionary pattern of mycobacteriophage D29 and its tempeate close relatives",
"abstract": "BACKGROUND:\r\n\r\nMycobacteriophages are viruses that infect Mycobacterium hosts. A large collection of phages known to infect the same bacterial host strain - Mycobacterium smegmatis mc2155 - exhibit substantial diversity and characteristically mosaic architectures. The well-studied lytic mycobacteriophage D29 appears to be a deletion derivative of a putative temperate parent, although its parent has yet to be identified.\r\nRESULTS:\r\n\r\nHere we describe three newly-isolated temperate phages - Kerberos, Pomar16 and StarStuff - that are related to D29, and are predicted to be very close relatives of its putative temperate parent, revealing the repressor and additional genes that are lost in D29. Transcriptional profiles show the patterns of both lysogenic and lytic gene expression and identify highly-expressed, abundant, stable, small non-coding transcripts made from the Pleft early lytic promoter, and which are toxic to M. smegmatis.\r\nCONCLUSIONS:\r\n\r\nComparative genomics of phages D29, Kerberos, Pomar16 and StarStuff provide insights into bacteriophage evolution, and comparative transcriptomics identifies the pattern of lysogenic and lytic expression with unusual features including highly expressed, small, non-coding RNAs.",
"full_author_list": "Dedrick, R. M., Mavrich, T. N., Ng, W. L., and Hatfull, G. F. ",
"short_author_list": "Dedrick et al.",
"article_url": "",
"journal": "BMC Microbiology",
"journal_volume": "17",
"journal_issue": "",
"journal_pages": "225",
"pub_year": "2017",
"pubmed_id": "29197343"
},
{
"title": "Genome Sequences of Five Streptomyces Bacteriophages Forming Cluster BG",
"abstract": "Cluster BG of the actinobacteriophage was formed upon discovery of five novel bacteriophages isolated by enrichment from their host, Streptomyces griseus subsp. griseus strain ATCC 10137. Four members of this cluster (BabyGotBac, Maih, TP1605, and YDN12) share over 89% average nucleotide identity, while the other (Xkcd426) has only 72% similarity to other cluster members.",
"full_author_list": "Richard Donegan-Quick, Zane A. Gibbs, Patricia O. Amaku, Joshua T. Bernal, Dana A. M. Boyd, Angela R. Burr, Rainna E. Coelho, Akpedje S. Dossou, Ryan M. Henry, Mai Huynh, Thalia A. Kanani-Hendijani, Guillermina Martinez, Tianeaka O. McClendon-Moss, Sergio Orozco, Johnny M. San Martin, Kaitlyn E. Stoddart, Madison M. Stringer, Rachel L. Villegas, Subhayu Nayek, Nikita Suri, Rebecca A. Garlena, Daniel A. Russell, Lee E. Hughes",
"short_author_list": "Donegan-Quick et al",
"article_url": "http://genomea.asm.org/content/5/28/e00502-17.full?sid=6de2c6d6-1f99-4850-a0ba-bed93bbd0033",
"journal": "Genome Announcements",
"journal_volume": "5",
"journal_issue": "28",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28705962"
},
{
"title": "Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using Mycobacterium smegmatis mc2155.",
"abstract": "Mycobacteriophages Chancellor, Mitti, and Wintermute infect Mycobacterium smegmatis mc2155 and are closely related to phages Cheetobro and Fionnbharth in subcluster K4. Genome sizes range from 57,697 bp to 58,046 bp. Phages are predicted to be temperate and to infect the pathogen Mycobacterium tuberculosis.",
"full_author_list": "Edgington NP, Voshell SM, Ware VC, Akoto FF, Alhout AA, Atwal GJ, Balyozian JB, Cadieux ZA, Chop BM, Cresawn SG, Cudkevich N, Faltine-Gonzalez DZ, Garlena RA, Gilmer BJ, Graham LH, Grapel MS, Haleem MM, Jacobs-Sera D, Kenna MA, Khan MA, Klein TN, Korenberg JB, Lichak BP, Mageeney CM, McKinley LN, Mendello KR, Myers CM, Nguyen AT, Pasqualucci BA, Pope WH, Pyfer LM, Ramirez WA, Reisner JR, Russell DA, Sapao PA, Saux VC, Singh I, Stoner TH, Swope RH, Thoonkuzhy MJ, Walters ML, Vargas LA, Veliz CA, Zhang KD, Zuilkoski CM, Hatfull GF.",
"short_author_list": "Edgington NP et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29122858"
},
{
"title": "Bacillus cereus Group Bacteriophage Flapjack Genome Sequence",
"abstract": "The Bacillus cereus group bacteriophage Flapjack, a double-stranded DNA (dsDNA) Myoviridae isolate collected from soil collected in Washington, DC, is a member of cluster C3 and encodes an intramolecular chaperone-containing tail fiber protein previously found in Podoviridae and Siphoviridae but not annotated in the Myoviridae.",
"full_author_list": "Erill I, Caruso SM; 2016 UMBC Phage Hunters.",
"short_author_list": "Erill et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28774974"
},
{
"title": "Complete Genome Sequences of Three phi29-Like Bacillus cereus Group Podoviridae",
"abstract": "Three double-stranded DNA phi29-like Bacillus cereus group bacteriophages, BeachBum, Harambe, and SerPounce, were identified and characterized. BeachBum and Harambe are closely related but are remarkably different from previously identified phi29-like phages. SerPounce is substantially closer to other phi29-like phages, enabling the identification of its prohead RNA (pRNA) gene.",
"full_author_list": "Ivan Erill, Steven M. Caruso, on behalf of the 2016 UMBC Phage Hunters",
"short_author_list": "Erill, Caruso, et al",
"article_url": "http://genomea.asm.org/content/5/29/e00701-17",
"journal": "Genome Announcements",
"journal_volume": "5",
"journal_issue": "29",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "PMC5522947"
},
{
"title": "Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages",
"abstract": "Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages.",
"full_author_list": "Esplin IND, Berg JA, Sharma R, Allen RC, Arens DK, Ashcroft CR, Bairett SR, Beatty NJ, Bickmore M, Bloomfield TJ, Brady TS, Bybee RN, Carter JL, Choi MC, Duncan S, Fajardo CP, Foy BB, Fuhriman DA, Gibby PD, Grossarth SE, Harbaugh K, Harris N, Hilton JA, Hurst E, Hyde JR, Ingersoll K, Jacobson CM, James BD, Jarvis TM, Jaen-Anieves D, Jensen GL, Knabe BK, Kruger JL, Merrill BD, Pape JA, Payne Anderson AM, Payne DE, Peck MD, Pollock SV, Putnam MJ, Ransom EK, Ririe DB, Robinson DM, Rogers SL, Russell KA, Schoenhals JE, Shurtleff CA, Simister AR, Smith HG, Stephenson MB, Staley LA, Stettler JM, Stratton ML, Tateoka OB, Tatlow PJ, Taylor AS, Thompson SE, Townsend MH, Thurgood TL, Usher BK, Whitley KV, Ward AT, Ward MEH, Webb CJ, Wienclaw TM, Williamson TL, Wells MJ, Wright CK, Breakwell DP, Hope S, Grose JH.",
"short_author_list": "Esplin et al",
"article_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690319/",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29146842"
},
{
"title": "Genome Sequence of Mycobacterium Phage CrystalP.",
"abstract": "Mycobacteriophage CrystalP is a newly isolated phage infecting Mycobacterium smegmatis strain mc2155. CrystalP has a 76,483-bp genome and is predicted to contain 143 protein-coding and 2 tRNA genes, including repressor and integrase genes consistent with a temperate lifestyle. CrystalP is related to the mycobacteriophages Toto and Kostya and to other Cluster E phages.",
"full_author_list": "Fleischacker CL, Segura-Totten M; SEA-PHAGES 2016 Bioinformatics Workshop, Garlena RA, Jacobs-Sera D, Pope WH, Russell DA, Hatfull GF",
"short_author_list": "Fleischacker CL et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28705967"
},
{
"title": "An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning.",
"abstract": "Engaging undergraduate students in scientific research promises substantial benefits, but it is not accessible to all students and is rarely implemented early in college education, when it will have the greatest impact. An inclusive Research Education Community (iREC) provides a centralized scientific and administrative infrastructure enabling engagement of large numbers of students at different types of institutions. The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) is an iREC that promotes engagement and continued involvement in science among beginning undergraduate students. The SEA-PHAGES students show strong gains correlated with persistence relative to those in traditional laboratory courses regardless of academic, ethnic, gender, and socioeconomic profiles. This persistent involvement in science is reflected in key measures, including project ownership, scientific community values, science identity, and scientific networking.",
"full_author_list": "Hanauer DI, Graham MJ; SEA-PHAGES, Betancur L, Bobrownicki A, Cresawn SG, Garlena RA, Jacobs-Sera D, Kaufmann N, Pope WH, Russell DA, Jacobs WR Jr, Sivanathan V, Asai DJ, Hatfull GF.",
"short_author_list": "Hanauer et al.",
"article_url": "",
"journal": "Proc Natl Acad Sci U S A.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29208718"
},
{
"title": "Genome Sequences of Four Subcluster L2 Mycobacterium Phages, Finemlucis, Miley16, Wilder, and Zakai",
"abstract": "Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect Mycobacterium smegmatis mc2155 were isolated. The four phages are closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative protein-coding genes, including tyrosine integrases, cro, immunity repressors, and excise genes involved in the establishment of lysogeny.",
"full_author_list": "Herren CD, Peister A, Breton TS, Hill MS, Anderson MS, Chang AW, Klein SB, Thornton MM, Vars SJ, Wagner KE, Wiebe PL, Williams TG, Yanez CP, Ackles JM, Artis D, Brazier RJ, Bryant RJ, Callwood KO, Carter IH, DeBose CL, Edwards CD, Ezemba IC, Joaquin RR, Meghoo-Peddie ZM, Meghoo-Peddie ZG, Moore RW, Smith CE, Turner AJ, Vorters RL, Wider JJ, Krout LL, Comis MS, Davick MJ, Michaud EE, Shevenell BE, Stanley SE, Frank CI, Montgomery JR, Blumer LS, Doty JA, Smith-Caldas M, Pope WH, Cresawn SG, Russell DA, Garlena RA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Herren et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "5",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29146853"
},
{
"title": "Genome Sequences of Mycobacteriophages Kerberos, Pomar16, and StarStuff.",
"abstract": "We describe the genome sequences of three closely related mycobacteriophages, Kerberos, Pomar16, and StarStuff, isolated at similar times but from geographically distinct regions. All three genomes are similar to those of other subcluster A2 phages, such as L5 and D29, are temperate, and have siphoviral virion morphologies.",
"full_author_list": "Jacobs-Sera D, Catinas O, Fernandez-Martinez M, Garcia A, Garlena RA, Guerrero Bustamante CA, Larsen MH, Medellin RH, Melendez-Ortiz MY, Melendez-Rivera CM, Mercado-Andino AK, Mercado-Delgado AJ, Ortiz-Ortiz CP, Quesada-Gordillo AM3 Ramos JM, Rubin MR, Russell DA, Sadana RA, Saha S, Vazquez E, Villarreal D, Hatfull GF.",
"short_author_list": "Jacobs-Sera D et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28798169"
},
{
"title": "Genome Sequences of Subcluster K5 Mycobacteriophages AlleyCat, Edugator, and Guillsminger.",
"abstract": "Bacteriophages AlleyCat, Edugator, and Guillsminger were isolated on Mycobacterium smegmatis mc2155 from enriched soil samples. All are members of mycobacteriophage subcluster K5, with genomes of 62,112 to 63,344 bp. Each genome contains 92 to 99 predicted protein-coding genes and one tRNA. Guillsminger is the first mycobacteriophage to carry an IS1380 family transposon.",
"full_author_list": "King RA, Slowan-Pomeroy TM, Thomas JE, Ahmed T, Alexander KL, Biddle JM, Daniels MK1, Rowlett JR, Senay TE, Rinehart CA, Staples AK, Rowland NS, Gaffney BL, Emmons CB, Hauk MD, Nguyen RL, Naegele L, Strickland SS, Briggs LA, Rush AN, Saha S, Sadana R, Cresawn SG, Russell DA, Garlena RA, Pope WH, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "King RA et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29122861"
},
{
"title": "Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages.",
"abstract": "The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45-68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.",
"full_author_list": "Klyczek KK, Bonilla JA, Jacobs-Sera D, Adair TL, Afram P, Allen KG, Archambault ML, Aziz RM, Bagnasco FG, Ball SL, Barrett NA, Benjamin RC, Blasi CJ, Borst K, Braun MA, Broomell H, Brown CB, Brynell ZS, Bue AB, Burke SO, Casazza W, Cautela JA, Chen K, Chimalakonda NS, Chudoff D, Connor JA, Cross TS, Curtis KN, Dahlke JA, Deaton BM, Degroote SJ, DeNigris DM, DeRuff KC, Dolan M, Dunbar D, Egan MS, Evans DR, Fahnestock AK, Farooq A, Finn G, Fratus CR, Gaffney BL, Garlena RA, Garrigan KE, Gibbon BC, Goedde MA, Guerrero Bustamante CA, Harrison M, Hartwell MC, Heckman EL, Huang J, Hughes LE, Hyduchak KM, Jacob AE, Kaku M, Karstens AW, Kenna MA, Khetarpal S, King RA, Kobokovich AL, Kolev H, Konde SA, Kriese E, Lamey ME, Lantz CN, Lapin JS, Lawson TO, Lee IY, Lee SM, Lee-Soety JY, Lehmann EM, London SC, Lopez AJ, Lynch KC, Mageeney CM, Martynyuk T, Mathew KJ, Mavrich TN, McDaniel CM, McDonald H, McManus CJ, Medrano J, Mele FE, Menninger JE, Miller SN, Minick JE, Nabua CT, Napoli CK, Nkangabwa M, Oates EA, Ott CT, Pellerino SK, Pinamont WJ, Pirnie RT, Pizzorno MC, Plautz EJ, Pope WH, Pruett KM, Rickstrew G, Rimple PA, Rinehart CA, Robinson KM, Rose VA, Russell DA, Schick AM, Schlossman J, Schneider VM, Sells CA, Sieker JW, Silva MP, Silvi MM, Simon SE, Staples AK, Steed IL, Stowe EL, Stueven NA, Swartz PT, Sweet EA, Sweetman AT, Tender C, Terry K, Thomas C, Thomas DS, Thompson AR, Vanderveen L, Varma R, Vaught HL, Vo QD, Vonberg ZT, Ware VC, Warrad YM, Wathen KE, Weinstein JL, Wyper JF3, Yankauskas JR, Zhang C, Hatfull GF",
"short_author_list": "Klyczek KK et al.",
"article_url": "",
"journal": "PLoS One.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28715480"
},
{
"title": "Genome Sequences of 12 Cluster AN Arthrobacter Phages.",
"abstract": "Twelve siphoviral phages isolated using Arthrobacter sp. strain ATCC 21022 were sequenced. The phages all have relatively small genomes, ranging from 15,319 to 15,556 bp. All 12 phages are closely related to previously described cluster AN Arthrobacter phages.",
"full_author_list": "Lee-Soety JY, Bhatt S, Adair TL, Bonilla JA, Klyczek KK, Harrison M; Saint Joseph’s University SEA-PHAGES; Baylor University SEA-PHAGES; University of Wisconsin-River Falls SEA-PHAGES; Cabrini University SEA-PHAGES, Garlena RA, Bowman CA, Russell DA, Pope WH, Jacobs-Sera D, Cresawn SG, Hatfull GF.",
"short_author_list": "Lee-Soety JY et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29122859"
},
{
"title": "Bacteriophage evolution differs by host, lifestyle and genome",
"abstract": "Bacteriophages play key roles in microbial evolution1,2, marine nutrient cycling3 and human disease4. Phages are genetically diverse, and their genome architectures are characteristically mosaic, driven by horizontal gene transfer with other phages and host genomes5. As a consequence, phage evolution is complex and their genomes are composed of genes with distinct and varied evolutionary histories6,7. However, there are conflicting perspectives on the roles of mosaicism and the extent to which it generates a spectrum of genome diversity8 or genetically discrete populations9,10. Here, we show that bacteriophages evolve within two general evolutionary modes that differ in the extent of horizontal gene transfer by an order of magnitude. Temperate phages distribute into high and low gene flux modes, whereas lytic phages share only the lower gene flux mode. The evolutionary modes are also a function of the bacterial host and different proportions of temperate and lytic phages are distributed in either mode depending on the host phylum. Groups of genetically related phages fall into either the high or low gene flux modes, suggesting there are genetic as well as ecological drivers of horizontal gene transfer rates. Consequently, genome mosaicism varies depending on the host, lifestyle and genetic constitution of phages.",
"full_author_list": "Mavrich TN, Hatfull GF",
"short_author_list": "Mavrich TN, Hatfull GF",
"article_url": "",
"journal": "Nat Microbiol.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28692019"
},
{
"title": "Virus-host protein-protein interactions of mycobacteriophage Giles",
"abstract": "Mycobacteriophage are viruses that infect mycobacteria. More than 1,400 mycobacteriophage genomes have been sequenced, coding for over one hundred thousand proteins of unknown functions. Here we investigate mycobacteriophage Giles-host protein-protein interactions (PPIs) using yeast two-hybrid screening (Y2H). A total of 25 reproducible PPIs were found for a selected set of 10 Giles proteins, including a putative virion assembly protein (gp17), the phage integrase (gp29), the endolysin (gp31), the phage repressor (gp47), and six proteins of unknown function (gp34, gp35, gp54, gp56, gp64, and gp65). We note that overexpression of the proteins is toxic to M. smegmatis, although whether this toxicity and the associated changes in cellular morphology are related to the putative interactions revealed in the Y2H screen is unclear.",
"full_author_list": "Mehla J, Dedrick RM, Caufield JH, Wagemans J, Sakhawalkar N, Johnson A, Hatfull GF, Uetz P.",
"short_author_list": "Mehla et al.",
"article_url": "",
"journal": "Sci Rep",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29184079"
},
{
"title": "Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships",
"abstract": "The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are \"singletons\" with no closely related genomes. One group of six phages is closely related to Cluster A mycobacteriophages, but the other Gordonia phages are distant relatives and share only 10% of their genes with the mycobacteriophages. The Gordonia phage genomes vary in genome length (17.1 to 103.4 kb), percentage of GC content (47 to 68.8%), and genome architecture and contain a variety of features not seen in other phage genomes. Like the mycobacteriophages, the highly mosaic Gordonia phages demonstrate a spectrum of genetic relationships. We show this is a general property of bacteriophages and suggest that any barriers to genetic exchange are soft and readily violable.IMPORTANCE Despite the numerical dominance of bacteriophages in the biosphere, there is a dearth of complete genomic sequences. Current genomic information reveals that phages are highly diverse genomically and have mosaic architectures formed by extensive horizontal genetic exchange. Comparative analysis of 79 phages of Gordonia shows them to not only be highly diverse, but to present a spectrum of relatedness. Most are distantly related to phages of the phylogenetically proximal host Mycobacterium smegmatis, although one group of Gordonia phages is more closely related to mycobacteriophages than to the other Gordonia phages. Phage genome sequence space remains largely unexplored, but further isolation and genomic comparison of phages targeted at related groups of hosts promise to reveal pathways of bacteriophage evolution.",
"full_author_list": "Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, Russell DA, Warner MH; Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES), Hatfull GF",
"short_author_list": "Pope et al.",
"article_url": "",
"journal": "MBio.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28811342"
},
{
"title": "Complete Genome Sequences of 38 Gordonia sp. Bacteriophages.",
"abstract": "We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity.",
"full_author_list": "Pope WH, Montgomery MT, Bonilla JA, Dejong R, Garlena RA, Guerrero Bustamante C, Klyczek KK, Russell DA, Wertz JT, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28057748"
},
{
"title": "PhagesDB: the actinobacteriophage database",
"abstract": "The Actinobacteriophage Database (PhagesDB) is a comprehensive, interactive, database-backed website that collects and shares information related to the discovery, characterization and genomics of viruses that infect Actinobacterial hosts. To date, more than 8000 bacteriophages—including over 1600 with sequenced genomes—have been entered into the database. PhagesDB plays a crucial role in organizing the discoveries of phage biologists around the world—including students in the SEA-PHAGES program—and has been cited in over 50 peer-reviewed articles.",
"full_author_list": "Daniel A Russell Graham F Hatfull",
"short_author_list": "Russell et al",
"article_url": "",
"journal": "Bioinformatics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "28365761"
},
{
"title": "Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007",
"abstract": "We report here the genome sequences of three newly isolated phages that infect Mycobacterium smegmatis mc2155. Phages Findley, Hurricane, and TBond007 were discovered in geographically distinct locations and are related to cluster K mycobacteriophages, with Findley being similar to subcluster K2 phages and Hurricane and TBond007 being similar to subcluster K3 phages.",
"full_author_list": "Saha S, Yan W, Washington JM, Davis WB, Barbazuk WB, Medellin R, Mendez A, Ramos JR, Sadana R, Edmonds M, Feng G, Ilyas M, Kaiser J, Monroe SJ, Pham TV, Cresawn SG, Garlena RA, Stoner TH, Russell DA, Pope WH, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Saha S et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2017",
"pubmed_id": "29122862"
},
{
"title": "Paenibacillus larvae Phage Tripp Genome Has 378-Base-Pair Terminal Repeats",
"abstract": "Paenibacillus larvae bacteriophage Tripp was isolated from an American foulbrood diseased honey bee hive in North Carolina, USA. The 54,439-bp genome is 48.3% G+C, encodes 92 proteins, no tRNAs, and has 378-bp direct terminal repeats. It is currently unique in Genbank.",
"full_author_list": "J. Abraham, A.-C. Bousquet, E. Bruff, N. Carson, A. Clark, A. Connell, Z. Davis, J. Dums, C. Everington, A. Groth, N. Hawes, N. McArthur, C. McKenney, A. Oufkir, B. Pearce, S. Rampal, H. Rozier, J. Schaff, T. Slehria, S. Carson, E. S. Miller",
"short_author_list": "Abraham, Bousquet, Bruff, et al",
"article_url": "http://genomea.asm.org/content/4/1/e01498-15.long",
"journal": "Genome Announcements",
"journal_volume": "4",
"journal_issue": "1",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "26744371"
},
{
"title": "Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages.",
"abstract": "Brevibacillus laterosporus is a spore-forming bacterium that causes a secondary infection in beehives following European Foulbrood disease. To better understand the contributions of Brevibacillus bacteriophages to the evolution of their hosts, five novel phages (Jenst, Osiris, Powder, SecTim467, and Sundance) were isolated and characterized. When compared with the five Brevibacillus phages currently in NCBI, these phages were assigned to clusters based on whole genome and proteome synteny. Powder and Osiris, both myoviruses, were assigned to the previously described Jimmer-like cluster. SecTim467 and Jenst, both siphoviruses, formed a novel phage cluster. Sundance, a siphovirus, was assigned as a singleton phage along with the previously isolated singleton, Emery. In addition to characterizing the basic relationships between these phages, several genomic features were observed. A motif repeated throughout phages Jenst and SecTim467 was frequently upstream of genes predicted to function in DNA replication, nucleotide metabolism, and transcription, suggesting transcriptional co-regulation. In addition, paralogous gene pairs that encode a putative transcriptional regulator were identified in four Brevibacillus phages. These paralogs likely evolved to bind different DNA sequences due to variation at amino acid residues predicted to bind specific nucleotides. Finally, a putative transposable element was identified in SecTim467 and Sundance that carries genes homologous to those found in Brevibacillus chromosomes. Remnants of this transposable element were also identified in phage Jenst. These discoveries provide a greater understanding of the diversity of phages, their behavior, and their evolutionary relationships to one another and to their host. In addition, they provide a foundation with which further Brevibacillus phages can be compared.",
"full_author_list": "Berg JA, Merrill BD, Crockett JT, Esplin KP, Evans MR, Heaton KE, Hilton JA, Hyde JR, McBride MS, Schouten JT, Simister AR, Thurgood TL, Ward AT, Breakwell DP, Hope S, Grose JH.",
"short_author_list": "Berg JA et al.",
"article_url": "",
"journal": "PLoS One.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27304881"
},
{
"title": "Complete Genome Sequences of Five Bacteriophages That Infect Rhodobacter capsulatus.",
"abstract": "Five bacteriophages that infect the Rhodobacter capsulatus strain YW1 were isolated from stream water near Bloomington, Illinois, USA. Two distinct genome types are represented in the newly isolated bacteriophages. These genomes are different from other bacteriophage genomes previously described.",
"full_author_list": "Bollivar DW, Bernardoni B, Bockman MR, Miller B2, Russell DA, Delesalle VA, Krukonis GP, Hatfull GF, Cross MR, Szewczyk MM, Eppurath A.",
"short_author_list": "Bollivar DW et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27231352"
},
{
"title": "Rapid Verification of Terminators Using the pGR-Blue Plasmid and Golden Gate Assembly.",
"abstract": "The goal of this protocol is to allow for the rapid verification of bioinformatically identified terminators. Further, the plasmid (pGR-Blue) is designed specifically for this protocol and allows for the quantification of terminator efficiency. As a proof of concept, six terminators were bioinformatically identified in the mycobacteriophage Bernal13. Once identified, terminators were then made as oligonucleotides with the appropriate sticky ends and annealed together. Using Golden Gate Assembly (GGA), terminators were then cloned into pGR-Blue. Under visible light, false positive colonies appear blue and positively transformed colonies are white/yellow. After induction of an arabinose inducible promoter (pBad) with arabinose, colony strength can be determined by measuring the ratio of green fluorescent protein (GFP) produced to red fluorescent protein (RFP) produced. With pGR-Blue, the protocol can be completed in as little as three days and is ideal in an educational setting. Additionally, results show that this protocol is useful as a means for understanding in silico predictions of terminator efficiency related to the regulation of transcription.",
"full_author_list": "Bradshaw JC, Gongola AB, Reyna NS.",
"short_author_list": "Bradshaw JC, Gongola AB, Reyna NS.",
"article_url": "",
"journal": "J Vis Exp.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27167700"
},
{
"title": "Genome Sequence of Mycobacteriophage Cabrinians.",
"abstract": "Mycobacteriophage Cabrinians is a newly isolated phage capable of infecting both Mycobacterium phlei and Mycobacterium smegmatis and was recovered from a soil sample in New York City, NY. Cabrinians has a genome length of 56,669 bp, encodes 101 predicted proteins, and is a member of mycobacteriophages in cluster F.",
"full_author_list": "Chudoff D, Conboy A, Conboy D, Atoulelou M, Hasan S, Martinez A, Mastrando J, Roy R, Schmidt R, Sheed K, Smith J, Sperratore M, Struga R, Starr K, Suppi R, Uguru U, Terry K, Villafuerte R, Yuan V, Dunbar D.",
"short_author_list": "Chudoff D et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "26847904"
},
{
"title": "Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems.",
"abstract": "More than 180 individual phages infecting hosts in the phylum Actinobacteria have been sequenced and grouped into Cluster A because of their similar overall nucleotide sequences and genome architectures. These Cluster A phages are either temperate or derivatives of temperate parents, and most have an integration cassette near the centre of the genome containing an integrase gene and attP. However, about 20% of the phages lack an integration cassette, which is replaced by a 1.4 kbp segment with predicted partitioning functions, including plasmid-like parA and parB genes. Phage RedRock forms stable lysogens in Mycobacterium smegmatis in which the prophage replicates at 2.4 copies/chromosome and the partitioning system confers prophage maintenance. The parAB genes are expressed upon RedRock infection of M. smegmatis, but are downregulated once lysogeny is established by binding of RedRock ParB to parS-L, one of two centromere-like sites flanking the parAB genes. The RedRock parS-L and parS-R sites are composed of eight directly repeated copies of an 8 bp motif that is recognized by ParB. The actinobacteriophage parABS cassettes span considerable sequence diversity and specificity, providing a suite of tools for use in mycobacterial genetics.",
"full_author_list": "Dedrick RM, Mavrich TN, Ng WL, Cervantes Reyes JC, Olm MR, Rush RE, Jacobs-Sera D, Russell DA, Hatfull GF.",
"short_author_list": "Dedrick et al.",
"article_url": "",
"journal": "Mol Microbiol.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27146086"
},
{
"title": "Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes.",
"abstract": "The presence of tRNA genes in bacteriophages has been explained on the basis of codon usage (tRNA genes are retained in the phage genome if they correspond to codons more common in the phage than in its host) or amino acid usage (independent of codon, the amino acid corresponding to the retained tRNA gene is more common in the phage genome than in the bacterial host). The existence of a large database of sequenced mycobacteriophages, isolated on the common host Mycobacterium smegmatis, allows us to test the above hypotheses as well as explore other hypotheses for the presence of tRNA genes. Our analyses suggest that amino acid rather than codon usage better explains the presence of tRNA genes in mycobacteriophages. However, closely related phages that differ in the presence of tRNA genes in their genomes are capable of lysing the common bacterial host and do not differ in codon or amino acid usage. This suggests that the benefits of having tRNA genes may be associated with either growth in the host or the ability to infect more hosts (i.e., host range) rather than simply infecting a particular host.",
"full_author_list": "Delesalle VA, Tanke NT, Vill AC, Krukonis GP.",
"short_author_list": "Delesalle VA, Tanke NT, Vill AC, Krukonis GP.",
"article_url": "",
"journal": "Bacteriophage.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27738556"
},
{
"title": "Genome Sequence of Bacillus cereus Group Phage SalinJah",
"abstract": "The double-stranded DNA (dsDNA) Myoviridae Bacillus cereus group bacteriophage SalinJah was isolated from soil collected in Gyeonggi-do, South Korea. SalinJah, a cluster C phage with a broad host range, suggests the need to create a new subcluster with SalinJah and Helga as founding members.",
"full_author_list": "Ivan Erill, Steven M. Caruso, on behalf of the 2015 UMBC Phage Hunters",
"short_author_list": "Erill, Caruso, et al",
"article_url": "http://genomea.asm.org/content/4/5/e00953-16.long",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27688335"
},
{
"title": "A Measure of College Student Persistence in the Sciences (PITS).",
"abstract": "Curricular changes that promote undergraduate persistence in science, technology, engineering, and mathematics (STEM) disciplines are likely associated with particular student psychological outcomes, and tools are needed that effectively assess these developments. Here, we describe the theoretical basis, psychometric properties, and predictive abilities of the Persistence in the Sciences (PITS) assessment survey designed to measure these in course-based research experiences (CREs). The survey is constructed from existing psychological assessment instruments, incorporating a six-factor structure consisting of project ownership (emotion and content), self-efficacy, science identity, scientific community values, and networking, and is supported by a partial confirmatory factor analysis. The survey has strong internal consistency (Cronbach's alpha: α = 0.96) and was validated using standard simple and multiple regression analyses. The regression analyses demonstrated that the factors of the PITS survey were significant predictors of the intent to become a research scientist and, as such, potentially valid for the measurement of persistence in the sciences. The PITS survey provides an effective method for measuring the psychological outcomes of undergraduate research experiences relevant to persistence in STEM and offers an approach to the development and validation of more sophisticated assessment tools that recognize the specificities of the type of educational opportunities embedded in a CRE.",
"full_author_list": "Hanauer DI, Graham MJ, Hatfull GF.",
"short_author_list": "Hanauer DI, Graham MJ, Hatfull GF.",
"article_url": "",
"journal": "CBE—Life Sciences Education",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27810869"
},
{
"title": "Complete Genome Sequences of 61 Mycobacteriophages.",
"abstract": "Mycobacteriophages-viruses of mycobacteria-provide insights into viral diversity and evolution as well as numerous tools for genetic dissection of Mycobacterium tuberculosis Here we report the complete genome sequences of 61 mycobacteriophages newly isolated from environmental samples using Mycobacterium smegmatis mc(2)155 that expand our understanding of phage diversity.",
"full_author_list": "Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) Program; KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) Mycobacterial Genetics Course; University of California–Los Angeles Research Immersion Laboratory in Virology; Phage Hunters Integrating Research and Education (PHIRE) Program.",
"short_author_list": "Hatfull GF et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27389257"
},
{
"title": "Genome Sequence of Mycobacterium Phage Waterfoul.",
"abstract": "Waterfoul is a newly isolated temperate siphovirus of Mycobacterium smegmatis mc2155. It was identified as a member of the K5 cluster of Mycobacterium phages and has a 61,248-bp genome with 95 predicted genes.",
"full_author_list": "Jackson PN, Embry EK, Johnson CO, Watson TL, Weast SK, DeGraw CJ, Douglas JR, Sellers JM, D'Angelo WA, Mavrodi DV.",
"short_author_list": "Jackson PN et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27856585"
},
{
"title": "Mycobacteriophages as Incubators for Intein Dissemination and Evolution.",
"abstract": "Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific. Strikingly, despite this phage specificity, inteins localize to functional motifs shared with bacteria, such that intein-containing genes have similar roles, like hydrolase activity and nucleic acid binding, indicating a global commonality among intein-hosting proteins. Additionally, there are multiple insertion points within active centers, implying independent invasion events, with regulatory implications. Several phage inteins were shown to be splicing competent and to encode functional homing endonucleases, important for mobility. Further, bioinformatic analysis supports the potential for phages as facilitators of intein movement among mycobacteria and related genera. Analysis of catalytic intein residues finds the highly conserved penultimate histidine inconsistently maintained among mycobacteriophages. Biochemical characterization of a noncanonical phage intein shows that this residue influences precursor accumulation, suggesting that splicing has been tuned in phages to modulate generation of important proteins. Together, this work expands our understanding of phage-based intein dissemination and evolution and implies that phages provide a context for evolution of splicing-based regulation.\r\n\r\nIMPORTANCE:\r\nInteins are mobile protein splicing elements found in critical genes across all domains of life. Mycobacterial inteins are of particular interest because of their occurrence in pathogenic species, such as Mycobacterium tuberculosis and Mycobacterium leprae, which harbor inteins in important proteins. We have discovered a similarity in activities of intein-containing proteins among mycobacteriophages and their intein-rich actinobacterial hosts, with implications for both posttranslational regulation by inteins and phages participating in horizontal intein transfer. Our demonstration of multiple insertion points within active centers of phage proteins implies independent invasion events, indicating the importance of intein maintenance at specific functional sites. The variable conservation of a catalytic splicing residue, leading to profoundly altered splicing rates, points to the regulatory potential of inteins and to mycobacteriophages playing a role in intein evolution. Collectively, these results suggest inteins as posttranslational regulators and mycobacteriophages as both vehicles for intein distribution and incubators for intein evolution.",
"full_author_list": "Kelley DS, Lennon CW; SEA-PHAGES, Belfort M, Novikova O.",
"short_author_list": "Kelley DS, Lennon CW; SEA-PHAGES, Belfort M, Novikova O.",
"article_url": "",
"journal": "MBio.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27703073"
},
{
"title": "Genome Sequences of Streptomyces Phages Amela and Verse",
"abstract": "Amela and Verse are two Streptomyces phages isolated by enrichment on Streptomyces venezuelae (ATCC 10712) from two different soil samples. Amela has a genome length of 49,452, with 75 genes. Verse has a genome length of 49,483, with 75 genes. Both belong to the BD3 subcluster of Actinobacteriophage.",
"full_author_list": "Layton SR, Hemenway RM, Munyoki CM, Barnes EB, Barnett SE, Bond AM, Narvaez JM, Sirisakd CD, Smith BR, Swain J, Syed O, Bowman CA, Russell DA, Bhuiyan S, Donegan-Quick R, Benjamin RC, Hughes LE.",
"short_author_list": "Layton et al",
"article_url": "http://genomea.asm.org/content/4/1/e01589-15",
"journal": "Genome Announcements",
"journal_volume": "4",
"journal_issue": "1",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "26893416"
},
{
"title": "Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies",
"abstract": "BACKGROUND:\r\nPhage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes.\r\n\r\nRESULTS:\r\nThe original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome.\r\n\r\nCONCLUSIONS:\r\nUsing available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure.",
"full_author_list": "Merrill BD, Ward AT1, Grose JH, Hope S.",
"short_author_list": "Merrill BD, Ward AT1, Grose JH, Hope S.",
"article_url": "",
"journal": "BMC Genomics.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27561606"
},
{
"title": "Genome Sequences of Newly Isolated Mycobacteriophages Forming Cluster S.",
"abstract": "We describe the genomes of two mycobacteriophages, MosMoris and Gattaca, newly isolated on Mycobacterium smegmatis The two phages are very similar to each other, differing in 61 single nucleotide polymorphisms and six small insertion/deletions. Both have extensive nucleotide sequence similarity to mycobacteriophage Marvin and together form cluster S.",
"full_author_list": "Mills ML, Bragg J, Bruce A, Dehn A, Drouin J, Hefner M, Katon D, McHugh D, Zeba F, Bowman CA, Cresawn SG, Jacobs-Sera D, Russell DA, Pope WH, Hatfull GF, Dunbar DA, Zegers GP, Page ST.",
"short_author_list": "Mills ML et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27688332"
},
{
"title": "Genome Sequences of Gordonia Phages Bowser and Schwabeltier.",
"abstract": "Gordonia phages Bowser and Schwabeltier are newly isolated phages infecting Gordonia terrae 3612. Bowser and Schwabeltier have similar siphoviral morphologies and their genomes are related to each other, but not to other phages. Their lysis cassettes are atypically situated among virion tail genes, and Bowser encodes two tyrosine integrases.",
"full_author_list": "Montgomery MT, Pope WH, Arnold ZM, Basina A, Iyer AM, Stoner TH, Kasturiarachi NS, Pressimone CA, Schiebel JG, Furbee EC, Grubb SR, Warner MH, Garlena RA, Russell DA, Jacobs-Sera D1, Hatfull GF.",
"short_author_list": "Montgomery MT et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27516498"
},
{
"title": "Genome Sequences of Gordonia terrae Bacteriophages Phinally and Vivi2.",
"abstract": "Bacteriophages Phinally and Vivi2 were isolated from soil from Pittsburgh, Pennsylvania, USA, using host Gordonia terrae 3612. The Phinally and Vivi2 genomes are 59,265 bp and 59,337 bp, respectively, and share sequence similarity with each other and with GTE6. Fewer than 25% of the 87 to 89 putative genes have predictable functions.",
"full_author_list": "Pope W, Anderson KC, Arora C, Bortz ME, Burnet G, Conover DH, D'Incau GM, Ghobrial JA, Jonas AL, Migdal EJ, Rote NL, German BA, McDonnell JE, Mezghani N, Schafer CE, Thompson PK, Ulbrich MC, Yu VJ, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27540050"
},
{
"title": "Genome Sequence of Gordonia Phage Emalyn.",
"abstract": "Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages.",
"full_author_list": "Pope WH, Guido MJ, Iyengar P, Nigra JT, Serbin MB, Kasturiarachi NS, Pressimone CA, Schiebel JG, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27516499"
},
{
"title": "Genome Sequence of Gordonia Phage BetterKatz.",
"abstract": "BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz's genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages.",
"full_author_list": "Pope WH, Berryman EN, Forrest KM, McHale L, Wertz AT, Zhuang Z, Kasturiarachi NS, Pressimone CA, Schiebel JG, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27516497"
},
{
"title": "Genome Sequences of Gordonia Bacteriophages Obliviate, UmaThurman, and Guacamole.",
"abstract": "We describe three newly isolated phages-Obliviate, UmaThurman, and Guacamole-that infect Gordonia terrae 3612. The three genomes are related to one another but are not closely related to other previously sequenced phages or prophages. The three phages are predicted to use integration-dependent immunity systems as described in several mycobacteriophages.",
"full_author_list": "Pope WH, Akbar AF, Ayers TN, Belohoubek SG, Chung CF, Hartman AC, Kayiti T, Kessler CM2 Koman PI, Kotovskiy GA, Morgan TM, Rohac RM, Silva GM, Willis CE 3rd, Milliken KA, Shedlock KA, Stanton AC, Toner CL, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27365348"
},
{
"title": "Genome Sequences of Gordonia Phages BaxterFox, Kita, Nymphadora, and Yeezy.",
"abstract": "Gordonia phages BaxterFox, Kita, Nymphadora, and Yeezy are newly characterized phages of Gordonia terrae, isolated from soil samples in Pittsburgh, Pennsylvania. These phages have genome lengths between 50,346 and 53,717 bp, and encode on average 84 predicted proteins. All have G+C content of 66.6%.",
"full_author_list": "Pope WH, Bandla S, Colbert AK, Eichinger FG, Gamburg MB, Horiates SG, Jamison JM, Julian DR, Moore WA, Murthy P, Powell MC, Smith SV, Mezghani N, Milliken KA, Thompson PK, Toner CL, Ulbrich MC, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27516501"
},
{
"title": "Genome Sequence of Gordonia Phage Yvonnetastic.",
"abstract": "Gordonia bacteriophage Yvonnetastic was isolated from soil in Pittsburgh, PA, using Gordonia terrae 3612 as a host. Yvonnetastic has siphoviral morphology and a genome of 98,136 bp, with 198 predicted protein-coding genes and five tRNA genes. Yvonnetastic does not share substantial sequence similarity with other sequenced bacteriophage genomes.",
"full_author_list": "Pope WH, Bandyopadhyay A, Carlton ML, Kane MT, Panchal NJ, Pham YC, Reynolds ZJ, Sapienza MS, German BA, McDonnell JE, Schafer CE, Yu VJ, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27389265"
},
{
"title": "Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha.",
"abstract": "Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia terrae 3612. Both have siphoviral morphologies with isometric heads and long tails (500 nm). The genomes are 75,380 bp long and closely related, and the tape measure genes (9 kbp) are among the largest to be identified.",
"full_author_list": "Pope WH, Benczkowski MS, Green DE, Hwang M, Kennedy B, Kocak B, Kruczek E, Lin L, Moretti ML, Onelangsy FL, Mezghani N, Milliken KA, Toner CL, Thompson PK, Ulbrich MC, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27340062"
},
{
"title": "Genome Sequences of Gordonia Phages Hotorobo, Woes, and Monty.",
"abstract": "Hotorobo, Woes, and Monty are newly isolated bacteriophages of Gordonia terrae 3612. The three phages are related, and their genomes are similarly sized (76,972 bp, 73,752 bp, and 75,680 bp for Hotorobo, Woes, and Monty, respectively) and organized. They have extremely long tails and among the longest tape measure protein genes described to date.",
"full_author_list": "Pope WH, Davis JP, O'Shea S, Pfeiffer AC, Rich AN, Xue JC, Shedlock KA, Stanton AC, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27516500"
},
{
"title": "Genome Sequence of Gordonia Bacteriophage Lucky10.",
"abstract": "Lucky10 is a newly isolated phage of Gordonia terrae 3612 that was recovered from a soil sample in Pittsburgh, PA. Lucky10 has siphoviral morphology and a double-stranded DNA (dsDNA) genome of 42,979 bp, with 70 predicted protein-coding genes. Lucky10 shows little similarity to previously reported Gordonia phages.",
"full_author_list": "Pope WH, Brown AK, Fisher DJ, Okwiya NH, Savage KA, German BA, McDonnell JE, Schafer CE, Yu VJ, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27365346"
},
{
"title": "Genome Sequences of Gordonia terrae Phages Attis and SoilAssassin.",
"abstract": "Attis and SoilAssassin are two closely related bacteriophages isolated on Gordonia terrae 3612 from separate soil samples in Pittsburgh, PA. The Attis and SoilAssassin genomes are 47,881 bp and 47,880 bp, respectively, and have 74 predicted protein-coding genes, including toxin-antitoxin systems, but no tRNAs.",
"full_author_list": "Pope WH, Biery DN, Huff ZT, Huynh AB, McFadden WM, Mouat JS, Schneiderman S, Song H, Szpak LE, Umbaugh MS, German BA, McDonnell JE, Mezghani N, Schafer CE, Thompson PK, Ulbrich MC, Yu VJ, Furbee EC, Grubb SR, Warner MH, Montgomery MT, Garlena RA, Russell DA, Jacobs-Sera D, Hatfull GF.",
"short_author_list": "Pope WH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27365347"
},
{
"title": "Genome Sequence of Mycobacteriophage ErnieJ.",
"abstract": "ErnieJ, a cluster C mycobacteriophage that infects Mycobacterium smegmatis mc2155, was recovered from soil in Washington, DC. Its genome is 153,243 bp in size and encodes 227 predicted proteins, 30 tRNAs, and one transfer-messenger RNA (tmRNA). Ten percent of the predicted proteins have homologs in phages that infect nonmycobacterial Actinobacteria.",
"full_author_list": "Robinson CJ, London-Thomas LY, Dickson LA, Clinton TA, Baig H, Bute M, Fahad M, Farrakhan K, Grady N, Guthrie NE, Hafid R, Harvey J, Hunnicutt K, Larsen VL, McDuffie T, McGee EN, Pailin JY, Peacock B, Thomas A, Anderson WA.",
"short_author_list": "Robinson CJ et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27881532"
},
{
"title": "Complete Genome Sequence of Gordonia terrae 3612",
"abstract": "Here, we report the complete genome sequence of Gordonia terrae 3612, also known by the strain designations ATCC 25594, NRRL B-16283, and NBRC 100016. The genome sequence reveals it to be free of prophage and clustered regularly interspaced short palindromic repeats (CRISPRs), and it is an effective host for the isolation and characterization of Gordonia bacteriophages.",
"full_author_list": "Russell DA, Guerrero Bustamante CA, Garlena RA, Hatfull GF.",
"short_author_list": "Russell DA et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27688316"
},
{
"title": "Complete Genome Sequence of Arthrobacter sp. ATCC 21022, a Host for Bacteriophage Discovery.",
"abstract": "We report the complete genome sequence ofArthrobactersp. ATCC 21022, a strain maintained by ATCC and a commonly used host for bacteriophage isolation and genomic analysis. The strain is prophage-free and CRISPR-free but codes for two predicted restriction-modification systems.",
"full_author_list": "Russell DA, Hatfull GF.",
"short_author_list": "Russell DA, Hatfull GF.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27013048"
},
{
"title": "Genomic characterization and comparison of seven Myoviridae bacteriophage infecting <em>Bacillus thuringiensis</em>",
"abstract": "Bacillus thuringiensis Kurstaki, a bacterium that is a source of biopesticides and a safe simulant for pathogenic Bacillus species, was used to isolate seven unique bacteriophages. The phage genomes were sequenced and ranged in size from 158,100 to 163,019bp encoding 290-299 genes, and the GC content of ~38% was similar to that of the host bacterium. All phages had terminal repeats 2-3kb long. Three of the phages encoded tRNAs and three contained a self-splicing intron in the DNA polymerase gene. They were categorized as a single cluster (>60% nucleotide conservation) containing three subclusters (>80% nucleotide conservation), supported by genomic synteny and phylogenetic analysis. Considering the published genomes of phages that infect the genus Bacillus and noting the ability of many of the Bacillus cereus group phages to infect multiple species, a clustering system based on gene content is proposed. ",
"full_author_list": "Sauder A.B., Quinn M.R., Brouillette A., Caruso S., Cresawn S., Erill I., Lewis L., Loesser-Casey K., Pate M., Scott C., Stockwell S., Temple L.",
"short_author_list": "Sauder et al",
"article_url": "http://www.sciencedirect.com/science/article/pii/S0042682215005334",
"journal": "Virology",
"journal_volume": "489",
"journal_issue": "",
"journal_pages": "243-251",
"pub_year": "2016",
"pubmed_id": "26773385"
},
{
"title": "Scaling Up: Adapting a Phage-Hunting Course to Increase Participation of First-Year Students in Research.",
"abstract": "Authentic research experiences are valuable components of effective undergraduate education. Research experiences during the first years of college are especially critical to increase persistence in science, technology, engineering, and mathematics fields. The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) model provides a high-impact research experience to first-year students but is usually available to a limited number of students, and its implementation is costly in faculty time and laboratory space. To offer a research experience to all students taking introductory biology at Gonzaga University (n = 350/yr), we modified the traditional two-semester SEA-PHAGES course by streamlining the first-semester Phage Discovery lab and integrating the second SEA-PHAGES semester into other courses in the biology curriculum. Because most students in the introductory course are not biology majors, the Phage Discovery semester may be their only encounter with research. To discover whether students benefit from the first semester alone, we assessed the effects of the one-semester Phage Discovery course on students' understanding of course content. Specifically, students showed improvement in knowledge of bacteriophages, lab math skills, and understanding experimental design and interpretation. They also reported learning gains and benefits comparable with other course-based research experiences. Responses to open-ended questions suggest that students experienced this course as a true undergraduate research experience.",
"full_author_list": "Staub NL, Poxleitner M, Braley A, Smith-Flores H, Pribbenow CM, Jaworski L, Lopatto D, Anders KR.",
"short_author_list": "Staub NL et al",
"article_url": "",
"journal": "CBE—Life Sciences Education",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2016",
"pubmed_id": "27146160"
},
{
"title": "Genome Sequences of Six <em>Paenibacillus larvae</em> Siphoviridae Phages",
"abstract": "Six sequenced and annotated genomes of Paenibacillus larvae phages isolated from the combs of American foulbrood-diseased beehives are 37 to 45 kbp and have approximately 42% G+C content and 60 to 74 protein-coding genes. Phage Lily is most divergent from Diva, Rani, Redbud, Shelly, and Sitara.",
"full_author_list": "Carson S, Bruff E, DeFoor W, Dums J, Groth A, Hatfield T, Iyer A, Joshi K, McAdams S, Miles D, Miller D, Oufkir A, Raynor B, Riley S, Roland S, Rozier H, Talley S, Miller ES.",
"short_author_list": "Carson et al",
"article_url": "http://genomea.asm.org/content/3/3/e00101-15.long",
"journal": "Genome Announcements",
"journal_volume": "3",
"journal_issue": "3",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "26089405"
},
{
"title": "Comparative genomics of Cluster O mycobacteriophages",
"abstract": "Mycobacteriophages - viruses of mycobacterial hosts - are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages - Corndog, Catdawg, Dylan, Firecracker, and YungJamal - designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange.",
"full_author_list": "Cresawn SG, Pope WH, Jacobs-Sera D, Bowman CA, Russell DA, Dedrick RM, Adair T, Anders KR, Ball S, Bollivar D, Breitenberger C, Burnett SH, Butela K, Byrnes D, Carzo S, Cornely KA, Cross T, Daniels RL, Dunbar D, Findley AM, Gissendanner CR, Golebiewska UP, Hartzog GA, Hatherill JR, Hughes LE, Jalloh CS, De Los Santos C, Ekanem K, Khambule SL, King RA, King-Smith C, Klyczek K, Krukonis GP, Laing C, Lapin JS, Lopez AJ, Mkhwanazi SM, Molloy SD, Moran D, Munsamy V, Pacey E, Plymale R, Poxleitner M, Reyna N, Schildbach JF, Stukey J, Taylor SE, Ware VC, Wellmann AL, Westholm D, Wodarski D, Zajko M, Zikalala TS, Hendrix RW, Hatfull GF",
"short_author_list": "Cresawn SG, Pope WH, Jacobs-Sera D, Bowman CA, et al",
"article_url": "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118725",
"journal": "PLoS One",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "25742016"
},
{
"title": "An optimized enrichment technique for the isolation of Arthrobacter bacteriophage species from soil sample isolates.",
"abstract": "Bacteriophage isolation from environmental samples has been performed for decades using principles set forth by pioneers in microbiology. The isolation of phages infecting Arthrobacter hosts has been limited, perhaps due to the low success rate of many previous isolation techniques, resulting in an underrepresented group of Arthrobacter phages available for study. The enrichment technique described here, unlike many others, uses a filtered extract free of contaminating bacteria as the base for indicator bacteria growth, Arthrobacter sp. KY3901, specifically. By first removing soil bacteria the target phages are not hindered by competition with native soil bacteria present in initial soil samples. This enrichment method has resulted in dozens of unique phages from several different soil types and even produced different types of phages from the same enriched soil sample isolate. The use of this procedure can be expanded to most nutrient rich aerobic media for the isolation of phages in a vast diversity of interesting host bacteria.",
"full_author_list": "Cross T, Schoff C, Chudoff D, Graves L, Broomell H, Terry K, Farina J, Correa A, Shade D, Dunbar D.",
"short_author_list": "Cross T et al.",
"article_url": "",
"journal": "J Vis Exp.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "25938576"
},
{
"title": "Complete Genome Sequence of Bacillus cereus Group Phage TsarBomba",
"abstract": "The Bacillus cereus group bacteriophage TsarBomba, a double-stranded DNA Myoviridae, was isolated from soil collected in Saratov, Russia. TsarBomba was found to be similar to Bacillus phages BCP78 and BCU4, and to have a wide host range among Bacillus cereus group species.",
"full_author_list": "Ivan Erill, Steven M. Caruso, on behalf of the 2014 UMBC Phage Hunters",
"short_author_list": "Erill, Caruso, et al",
"article_url": "http://genomea.asm.org/content/3/5/e01178-15.full",
"journal": "Genome Announcements",
"journal_volume": "3",
"journal_issue": "5",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "26472830"
},
{
"title": "Genome Sequences of Two Bacillus cereus Group Bacteriophages, Eyuki and AvesoBmore",
"abstract": "The genomes of two double-stranded DNA (dsDNA) bacteriophages isolated on Bacillus thuringiensis show similarity to previously sequenced phages and provide evidence of the mosaicism of phage genomes.",
"full_author_list": "Ivan Erill, Steven M. Caruso, on behalf of the 2013 UMBC Phage Hunters",
"short_author_list": "Erill, Caruso, et al",
"article_url": "http://genomea.asm.org/content/3/5/e01199-15.full",
"journal": "Genome Announcements",
"journal_volume": "3",
"journal_issue": "5",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "26472840"
},
{
"title": "Transcriptomic Characterization of an Infection of Mycobacterium smegmatis by the Cluster A4 Mycobacteriophage Kampy.",
"abstract": "The mycobacteriophages, phages that infect the genus Mycobacterium, display profound genetic diversity and widespread geographical distribution, and possess significant medical and ecological importance. However, most of the majority of functions of mycobacteriophage proteins and the identity of most genetic regulatory elements remain unknown. We characterized the gene expression profile of Kampy, a cluster A4 mycobacteriophage, during infection of its host, Mycobacterium smegmatis, using RNA-Seq and mass spectrometry. We show that mycobacteriophage Kampy transcription occurs in roughly two phases, an early phase consisting of genes for metabolism, DNA synthesis, and gene regulation, and a late phase consisting of structural genes and lysis genes. Additionally, we identify the earliest genes transcribed during infection, along with several other possible regulatory units not obvious from inspection of Kampy's genomic structure. The transcriptional profile of Kampy appears similar to that of mycobacteriophage TM4 but unlike that of mycobacteriophage Giles, a result which further expands our understanding of the diversity of mycobacteriophage gene expression programs during infection.",
"full_author_list": "Halleran A, Clamons S, Saha M",
"short_author_list": "Halleran et al.",
"article_url": "",
"journal": "PLos One",
"journal_volume": "10",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "26513661"
},
{
"title": "Measuring Networking as an Outcome Variable in Undergraduate Research Experiences.",
"abstract": "he aim of this paper is to propose, present, and validate a simple survey instrument to measure student conversational networking. The tool consists of five items that cover personal and professional social networks, and its basic principle is the self-reporting of degrees of conversation, with a range of specific discussion partners. The networking instrument was validated in three studies. The basic psychometric characteristics of the scales were established by conducting a factor analysis and evaluating internal consistency using Cronbach's alpha. The second study used a known-groups comparison and involved comparing outcomes for networking scales between two different undergraduate laboratory courses (one involving a specific effort to enhance networking). The final study looked at potential relationships between specific networking items and the established psychosocial variable of project ownership through a series of binary logistic regressions. Overall, the data from the three studies indicate that the networking scales have high internal consistency (α = 0.88), consist of a unitary dimension, can significantly differentiate between research experiences with low and high networking designs, and are related to project ownership scales. The ramifications of the networking instrument for student retention, the enhancement of public scientific literacy, and the differentiation of laboratory courses are discussed.",
"full_author_list": "Hanauer DI, Hatfull G.",
"short_author_list": "Hanauer DI, Hatfull G.",
"article_url": "",
"journal": "CBE—Life Sciences Education",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "26538387"
},
{
"title": "The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins",
"abstract": "Mycobacteriophages are viruses that infect mycobacterial hosts and are prevalent in the environment. Nearly 700 mycobacteriophage genomes have been completely sequenced, revealing considerable diversity and genetic novelty. Here, we have determined the protein complement of mycobacteriophage Giles by mass spectrometry and mapped its genome-wide protein interactome to help elucidate the roles of its 77 predicted proteins, 50% of which have no known function. About 22,000 individual yeast two-hybrid (Y2H) tests with four different Y2H vectors, followed by filtering and retest screens, resulted in 324 reproducible protein-protein interactions, including 171 (136 nonredundant) high-confidence interactions. The complete set of high-confidence interactions among Giles proteins reveals new mechanistic details and predicts functions for unknown proteins. The Giles interactome is the first for any mycobacteriophage and one of just five known phage interactomes so far. Our results will help in understanding mycobacteriophage biology and aid in development of new genetic and therapeutic tools to understand Mycobacterium tuberculosis.\r\nIMPORTANCE:\r\n\r\nMycobacterium tuberculosis causes over 9 million new cases of tuberculosis each year. Mycobacteriophages, viruses of mycobacterial hosts, hold considerable potential to understand phage diversity, evolution, and mycobacterial biology, aiding in the development of therapeutic tools to control mycobacterial infections. The mycobacteriophage Giles protein-protein interaction network allows us to predict functions for unknown proteins and shed light on major biological processes in phage biology. For example, Giles gp76, a protein of unknown function, is found to associate with phage packaging and maturation. The functions of mycobacteriophage-derived proteins may suggest novel therapeutic approaches for tuberculosis. Our ORFeome clone set of Giles proteins and the interactome data will be useful resources for phage interactomics",
"full_author_list": "Mehla J, Dedrick RM, Caufield JH, Siefring R, Mair M, Johnson A, Hatfull GF, Uetz P",
"short_author_list": "Mehla et al.",
"article_url": "",
"journal": "J Bacteriol",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": ""
},
{
"title": "Genome Sequences of Five Additional Brevibacillus laterosporus Bacteriophages.",
"abstract": "Brevibacillus laterosporus has been isolated from many different environments, including beehives, and produces compounds that are toxic to many organisms. Five B. laterosporus phages have been isolated previously. Here, we announce five additional phages that infect this bacterium, including the first B. laterosporus siphoviruses to be discovered.",
"full_author_list": "Merrill BD, Berg JA, Graves KA, Ward AT, Hilton JA, Wake BN, Grose JH, Breakwell DP1 Burnett SH.",
"short_author_list": "Merrill BD et al",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "26494658"
},
{
"title": "Genome sequence of Mycobacteriophage Momo",
"abstract": "Momo is a newly discovered phage of Mycobacterium smegmatis mc(2)155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages.",
"full_author_list": "Pope WH, Bina EA, Brahme IS, Hill AB, Himmelstein PH, Hunsicker SM, Ish AR, Le TS, Martin MM, Moscinski CN, Shetty SA, Swierzewski T, Iyengar VB, Kim H, Schafer CE, Grubb SR, Warner MH, Bowman CA, Russell DA, Hatfull GF.",
"short_author_list": "Pope WH et al",
"article_url": "http://genomea.asm.org/content/3/3/e00601-15.long",
"journal": "Genome Announcements",
"journal_volume": "2015 Jun 18;3(3)",
"journal_issue": "",
"journal_pages": "e00601-15",
"pub_year": "2015",
"pubmed_id": "26089415"
},
{
"title": "Genome sequences of Mycobacteriophages Luchador and Nerujay",
"abstract": "Luchador and Nerujay are two newly isolated mycobacteriophages recovered from soil samples using Mycobacterium smegmatis. Their genomes are 53,387 bp and 53,455 bp long and have 96 and 97 predicted open reading frames, respectively. Nerujay is related to subcluster A1 phages, and Luchador represents a new subcluster, A14.",
"full_author_list": "Pope WH, Ahmed T, Drobitch MK, Early DR, Eljamri S, Kasturiarachi NS, Klonicki EF, Manjooran DT, Ní Chochlain AN, Puglionesi AO, Rajakumar V, Shindle KA, Tran MT, Brown BR, Churilla BM, Cohen KL, Wilkes KE, Grubb SR, Warner MH, Bowman CA, Russell DA, Hatfull GF",
"short_author_list": "Pope WH et al",
"article_url": "http://genomea.asm.org/content/3/3/e00599-15.long",
"journal": "Genome Announcements",
"journal_volume": "2015 Jun 18;3(3",
"journal_issue": "",
"journal_pages": "pii: e00599-15",
"pub_year": "2015",
"pubmed_id": "26089414"
},
{
"title": "Genome sequence of Mycobacteriophage Phayonce",
"abstract": "Mycobacteriophage Phayonce is a newly isolated phage recovered from a soil sample in Pittsburgh, PA, using Mycobacterium smegmatis mc(2)155 as a host. Phayonce's genome is 49,203 bp long and contains 77 protein-coding genes, 23 of them having predicted functions. Phayonce shares a strong similarity in nucleotide sequence with phages of cluster P.",
"full_author_list": "Pope WH, Jacobetz E, Johnson CA, Kihle BL, Sobeski MA, Werner MB, Adkins NL, Kramer ZJ, Montgomery MT, Grubb SR, Warner MH, Bowman CA, Russell DA, Hatfull GF.",
"short_author_list": "Pope WH et al",
"article_url": "http://genomea.asm.org/content/3/3/e00598-15.long",
"journal": "Genome Announcements",
"journal_volume": "2015 Jun 18;3(3)",
"journal_issue": "",
"journal_pages": "e00598-15",
"pub_year": "2015",
"pubmed_id": "26089413"
},
{
"title": "Genome sequence of a newly isolated mycobacteriophage, ShedlockHolmes",
"abstract": "Mycobacteriophage ShedlockHolmes is a newly isolated phage infecting Mycobacterium smegmatis mc(2)155. It has a 61,081-bp genome containing 99 predicted protein-coding genes and one tRNA gene. ShedlockHolmes is closely related to mycobacteriophages Pixie, Keshu, and MacnCheese and is a new member of subcluster K3.",
"full_author_list": "Pope WH, Carter JT, Dasher KL, Haynberg MC, Reddi A, Shedlock KA, Lapin JS, Prout AK, Grubb SR, Warner MH, Bowman CA, Russell DA, Hatfull GF.",
"short_author_list": "Pope WH et al",
"article_url": "http://genomea.asm.org/content/3/3/e00597-15.long",
"journal": "Genome Announcements",
"journal_volume": "2015 Jun 18;3(3)",
"journal_issue": "",
"journal_pages": "e00597-15",
"pub_year": "2015",
"pubmed_id": "26089412"
},
{
"title": "Genome sequence of Mycobacteriophage Mindy",
"abstract": "Mycobacteriophage Mindy is a newly isolated phage of Mycobacterium smegmatis, recovered from a soil sample in Pittsburgh, Pennsylvania, USA. Mindy has a genome length of 75,796 bp, encodes 147 predicted proteins and two tRNAs, and is closely related to mycobacteriophages in cluster E.",
"full_author_list": "Pope WH, Bernstein NI, Fasolas CS, Mezghani N, Pressimone CA, Selvakumar P, Stanton AC, Lapin JS, Prout AK, Grubb SR, Warner MH, Bowman CA, Russell DA, Hatfull GF.",
"short_author_list": "Pope WH et al",
"article_url": "http://genomea.asm.org/content/3/3/e00596-15.long",
"journal": "Genome Announcements",
"journal_volume": "2015 Jun 18;3(3)",
"journal_issue": "",
"journal_pages": "e00596-15",
"pub_year": "2015",
"pubmed_id": "26089411"
},
{
"title": "Genome Sequences of Cluster G Mycobacteriophages Cambiare, FlagStaff, and MOOREtheMARYer.",
"abstract": "Mycobacteriophages Cambiare, FlagStaff, and MOOREtheMARYer are newly isolated phages of Mycobacterium smegmatis mc(2) 155 recovered from soil samples in Pittsburgh, PA. All three genomes are closely related to cluster G mycobacteriophages but differ sufficiently in nucleotide sequence and gene content to warrant division of cluster G into several subclusters.",
"full_author_list": "Pope WH, Augustine DA, Carroll DC, Duncan JC, Harwi KM, Howry R, Jagessar B, Lum BA, Meinert JW, Migliozzi JS, Milliken KA, Mitchell CJ, Nalatwad AS, Orlandini KC, Rhein MJ, Saravanan V, Seese BA, Schiebel JG, Thomas KB, Adkins NL, Cohen KL, Iyengar VB, Kim H, Kramer ZJ, Montgomery MT, Schafer CE, Wilkes KE, Grubb SR, Warner MH, Bowman CA, Russell DA, Hatfull GF",
"short_author_list": "Pope WH et al",
"article_url": "http://genomea.asm.org/content/3/3/e00595-15.long",
"journal": "Genome Announcements",
"journal_volume": "2015 Jun 18;3(3)",
"journal_issue": "",
"journal_pages": "00595-15",
"pub_year": "2015",
"pubmed_id": "26089410"
},
{
"title": "Genome Sequences of Mycobacteriophages AlanGrant, Baee, Corofin, OrangeOswald, and Vincenzo, New Members of Cluster B.",
"abstract": "AlanGrant, Baee, Corofin, OrangeOswald, and Vincenzo are newly isolated phages of Mycobacterium smegmatis mc(2)155 discovered in Pittsburgh, Pennsylvania, USA. All five phages share nucleotide similarity with cluster B mycobacteriophages but span considerable diversity with Corofin and OrangeOswald in subcluster B3, AlanGrant and Vincenzo in subcluster B4, and Baee in subcluster B5.",
"full_author_list": "Pope WH, Carbonara ME, Cioffi HM, Cruz T, Dang BQ, Doyle AN, Fan OH, Gallagher M, Gentile GM, German BA, Farrell ME, Gerwig M, Hunter KL, Lefever VE, Marfisi NA, McDonnell JE, Monga JK, Quiroz KG, Pong AC, Rimple PA, Situ M, Sohnen PC, Stockinger AN, Thompson PK, Torchio NM, Toner CL, Ulbrich MC, Vohra NI, Zakir A, Adkins NL, Brown BR, Churilla BM, Kramer ZJ, Lapin JS, Montgomery MT, Prout AK, Grubb SR, Warner MH, Bowman CA, Russell DA, Hatfull GF.",
"short_author_list": "Pope WH et al",
"article_url": "http://genomea.asm.org/content/3/3/e00586-15.long",
"journal": "Genome Announcements",
"journal_volume": "2015 Jun 18;3(3)",
"journal_issue": "",
"journal_pages": "e00586-15",
"pub_year": "2015",
"pubmed_id": "26089409"
},
{
"title": "Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity",
"abstract": "The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. ",
"full_author_list": "Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science; Phage Hunters Integrating Research and Education; Mycobacterial Genetics Course",
"short_author_list": "Pope, Bowman, Russell, et al",
"article_url": "http://elifesciences.org/content/4/e06416",
"journal": "eLIFE",
"journal_volume": "4",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "25919952"
},
{
"title": "Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages.",
"abstract": "Background The genomic sequences of mycobacteriophages, phages infecting mycobacterial hosts, are diverse and mosaic. Mycobacteriophages often share little nucleotide similarity, but most of them have been grouped into lettered clusters and further into subclusters. Traditionally, mycobacteriophage genomes are analyzed based on sequence alignment or knowledge of gene content. However, these approaches are computationally expensive and can be ineffective for significantly diverged sequences. As an alternative to alignment-based genome analysis, we evaluated tetranucleotide usage in mycobacteriophage genomes. These methods make it easier to characterize features of the mycobacteriophage population at many scales. Description We computed tetranucleotide usage deviation (TUD), the ratio of observed counts of 4-mers in a genome to the expected count under a null model. TUD values are comparable between members of a phage subcluster and distinct between subclusters. With few exceptions, neighbor joining phylogenetic trees and hierarchical clustering dendrograms constructed using TUD values place phages in a monophyletic clade with members of the same subcluster. Regions in a genome with exceptional TUD values can point to interesting features of genomic architecture. Finally, we found that subcluster B3 mycobacteriophages contain significantly overrepresented 4-mers and 6-mers that are atypical of phage genomes. Conclusions Statistics based on tetranucleotide usage support established clustering of mycobacteriophages and can uncover interesting relationships within and between sequenced phage genomes. These methods are efficient to compute and do not require sequence alignment or knowledge of gene content. The code to download mycobacteriophage genome sequences and reproduce our analysis is freely available at https://github.com/bsiranosian/tango_final.",
"full_author_list": "Siranosian B, Perera S, Williams E, Ye C, de Graffenried C, Shank P.",
"short_author_list": "Siranosian B. et al.",
"article_url": "",
"journal": "F1000Res.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2015",
"pubmed_id": "27134721"
},
{
"title": "A web-based restriction endonuclease tool for mycobacteriophage cluster prediction",
"abstract": "A recent explosion in the amount of genomic data has revealed a large genetic diversity in the bacteriophages that infect Mycobacterium smegmatis. In an effort to assess the novelty of newly described mycobacteriophage isolates and provide a preliminary determination of their probable cluster assignment prior to full genome sequencing, we have developed a systematic approach that relies on restriction endonuclease analysis. We demonstrate that a web-based tool, the Phage Enzyme Tool (or PET), is capable of rapidly facilitating this analysis and exhibits reliability in the putative placement of mycobacteriophages into specific clusters of previously sequenced phages. We propose that this tool represents a useful analytical step in the initial study of phage genomes and that this tool will increase the efficiency of phage genome characterization and enhance the educational activities involving mycobacteriophage discovery.",
"full_author_list": "Gissendanner CR, Wiedemeier AM, Wiedemeier PD, Minton RL, Bhuiyan S, Harmson JS, Findley AM",
"short_author_list": "Gissendanner CR et al",
"article_url": "http://onlinelibrary.wiley.com/doi/10.1002/jobm.201300860/abstract",
"journal": "Journal of Basic Microbiology",
"journal_volume": "Oct 54",
"journal_issue": "10",
"journal_pages": "1140-5",
"pub_year": "2014",
"pubmed_id": "24740689"
},
{
"title": "Genome Sequences of Three Novel Bacillus cereus Bacteriophages.",
"abstract": "The Bacillus cereus group is an assemblage of highly related firmicute bacteria that cause a variety of diseases in animals, including insects and humans. We announce three high-quality, complete genome sequences of bacteriophages we isolated from soil samples taken at the bases of fruit trees in Utah County, Utah. While two of the phages (Shanette and JL) are highly related myoviruses, the bacteriophage Basilisk is a siphovirus.",
"full_author_list": "Grose JH, Jensen JD, Merrill BD, Fisher JN, Burnett SH, Breakwell DP.",
"short_author_list": "Grose JH et al.",
"article_url": "",
"journal": "Genome Announcements",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2014",
"pubmed_id": "24459255"
},
{
"title": "The genomes, proteomes, and structures of three novel phages that infect the Bacillus cereus group and carry putative virulence factors",
"abstract": "This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to well-characterized phages suggested that JL and Shanette were members of the family Myoviridae, which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T=9 icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus, B. anthracis, and B. thuringiensis. This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. Importance: The Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus, B. anthracis, and B. thuringiensis. Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species.",
"full_author_list": "Grose JH, Belnap DM, Jensen JD, Mathis AD, Prince JT, Merrill BD, Burnett SH, Breakwell DP",
"short_author_list": "Grose JH, et al",
"article_url": "http://jvi.asm.org/content/88/20/11846.long",
"journal": "Journal of Virology",
"journal_volume": "Oct 88",
"journal_issue": "20",
"journal_pages": "11846-60",
"pub_year": "2014",
"pubmed_id": "25100842"
},
{
"title": "Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity",
"abstract": "The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains.\r\nRESULTS:\r\nWhole genome nucleotide and proteome comparison of the 93 extant Bacillus phages revealed 12 distinct clusters, 28 subclusters and 14 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member of the group. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,922 protein families (phams) of which only 951 (19%) had a predicted function. In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains.\r\nCONCLUSIONS:\r\nThis analysis provides a basis for understanding and characterizing Bacillus phages and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.",
"full_author_list": "Grose JH, Jensen GL, Burnett SH, Breakwell DP",
"short_author_list": "Grose JH, et al",
"article_url": "http://www.biomedcentral.com/1471-2164/15/855",
"journal": "BMC Genomics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2014",
"pubmed_id": "25280881"
},
{
"title": "A broadly implementable research course in phage discovery and genomics for first-year undergraduate students",
"abstract": "Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.\r\nIMPORTANCE:\r\nEngagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.",
"full_author_list": "Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy JJ, Denver DR, Dunbar D, Elgin SC, Findley AM, Gissendanner CR, Golebiewska UP, Guild N, Hartzog GA, Grillo WH, Hollowell GP, Hughes LE, Johnson A, King RA, Lewis LO, Li W, Rosenzweig F, Rubin MR, Saha MS, Sandoz J, Shaffer CD, Taylor B, Temple L, Vazquez E, Ware VC, Barker LP, Bradley KW, Jacobs-Sera D, Pope WH, Russell DA, Cresawn SG, Lopatto D, Bailey CP, Hatfull GF.\r\n",
"short_author_list": "Jordan TC et al",
"article_url": "http://mbio.asm.org/content/5/1/e01051-13.full#ref-31",
"journal": "mBio",
"journal_volume": "Feb 4, 5",
"journal_issue": "1",
"journal_pages": "e01051-13",
"pub_year": "2014",
"pubmed_id": "24496795"
},
{
"title": "Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages",
"abstract": "Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages.\r\nRESULTS:\r\nP. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium, respectively.\r\nCONCLUSIONS:\r\nThis paper represents the first comparison of phage genomes in the Paenibacillus genus and the first organization of P. larvae phages based on sequence and structure. This analysis provides an important contribution to the field of bacteriophage genomics by serving as a foundation on which to build an understanding of the natural predators of P. larvae.",
"full_author_list": "Merrill BD, Grose JH, Breakwell DP, Burnett SH",
"short_author_list": "Merrill BD et al",
"article_url": "http://www.biomedcentral.com/1471-2164/15/745",
"journal": "BMC Genomics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2014",
"pubmed_id": "25174730"
},
{
"title": "Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repetoires of tRNA isotypes",
"abstract": "Genomic analysis of a large set of phages infecting the common host Mycobacterium smegmatis mc(2)155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode. Importance: The bacteriophage population is vast, dynamic, and old and plays a central role in bacterial pathogenicity. We know surprisingly little about the genetic diversity of the phage population, although metagenomic and phage genome sequencing indicates that it is great. Probing the depth of genetic diversity of phages of a common host, Mycobacterium smegmatis, provides a higher resolution of the phage population and how it has evolved. Three new phages constituting a new cluster M further expand the diversity of the mycobacteriophages and introduce novel features. As such, they provide insights into phage genome architecture, virion structure, and gene regulation at the transcriptional and translational levels.",
"full_author_list": "Pope WH, Anders KR, Baird M, Bowman CA, Boyle MM, Broussard GW, Chow T, Clase KL, Cooper S, Cornely KA, DeJong RJ, Delesalle VA, Deng L, Dunbar D, Edgington NP, Ferreira CM, Weston Hafer K, Hartzog GA, Hatherill JR, Hughes LE, Ipapo K, Krukonis GP, Meier CG, Monti DL, Olm MR, Page ST, Peebles CL, Rinehart CA, Rubin MR, Russell DA, Sanders ER, Schoer M, Shaffer CD, Wherley J, Vazquez E, Yuan H, Zhang D, Cresawn SG, Jacobs-Sera D, Hendrix RW, Hatfull GF.\r\n",
"short_author_list": "Pope WH et al",
"article_url": "http://jvi.asm.org/content/88/5/2461.long",
"journal": "Journal of Virology",
"journal_volume": "Mar 88",
"journal_issue": "5",
"journal_pages": "2461-80",
"pub_year": "2014",
"pubmed_id": "24335314"
},
{
"title": "Genomics and proteomics of mycobacteriophage Patience, an accidental tourist in the mycobacterium neighborhood",
"abstract": "Newly emerging human viruses such as Ebola virus, severe acute respiratory syndrome (SARS) virus, and HIV likely originate within an extant population of viruses in nonhuman hosts and acquire the ability to infect and cause disease in humans. Although several mechanisms preventing viral infection of particular hosts have been described, the mechanisms and constraints on viral host expansion are ill defined. We describe here mycobacteriophage Patience, a newly isolated phage recovered using Mycobacterium smegmatis mc(2)155 as a host. Patience has genomic features distinct from its M. smegmatis host, including a much lower GC content (50.3% versus 67.4%) and an abundance of codons that are rarely used in M. smegmatis. Nonetheless, it propagates well in M. smegmatis, and we demonstrate the use of mass spectrometry to show expression of over 75% of the predicted proteins, to identify new genes, to refine the genome annotation, and to estimate protein abundance. We propose that Patience evolved primarily among lower-GC hosts and that the disparities between its genomic profile and that of M. smegmatis presented only a minimal barrier to host expansion. Rapid adaptions to its new host include recent acquisition of higher-GC genes, expression of out-of-frame proteins within predicted genes, and codon selection among highly expressed genes toward the translational apparatus of its new host.\r\nIMPORTANCE:\r\nThe mycobacteriophage Patience genome has a notably lower GC content (50.3%) than its Mycobacterium smegmatis host (67.4%) and has markedly different codon usage biases. The viral genome has an abundance of codons that are rare in the host and are decoded by wobble tRNA pairing, although the phage grows well and expression of most of the genes is detected by mass spectrometry. Patience thus has the genomic profile of a virus that evolved primarily in one type of host genetic landscape (moderate-GC bacteria) but has found its way into a distinctly different high-GC environment. Although Patience genes are ill matched to the host expression apparatus, this is of little functional consequence and has not evidently imposed a barrier to migration across the microbial landscape. Interestingly, comparison of expression levels and codon usage profiles reveals evidence of codon selection as the genome evolves and adapts to its new environment.",
"full_author_list": "Pope WH, Jacobs-Sera D, Russell DA, Rubin DH, Kajee A, Msibi ZN, Larsen MH, Jacobs WR Jr, Lawrence JG, Hendrix RW, Hatfull GF.",
"short_author_list": "Pope WH, Jacobs-Sera D, Russell DA, Rubin DH, Kajee A, Msibi",
"article_url": "http://mbio.asm.org/content/5/6/e02145-14",
"journal": "mBio",
"journal_volume": "5",
"journal_issue": "6",
"journal_pages": "pii: e02145-14",
"pub_year": "2014",
"pubmed_id": "25467442"
},
{
"title": "Switches, Switches, Every Where, In Any Drop We Drink",
"abstract": "In this issue, Broussard et al. (2013) report genetic switches that regulate cell fate selection; a recombinase attachment site is embedded within a repressor coding sequence, such that integration truncates a proteolysis domain, stabilizing the repressor and setting the switch.",
"full_author_list": "Bonnet J, Endy D.",
"short_author_list": "Bonnet J, Endy D.",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/?term=23352244%5Buid%5D",
"journal": "Molecular Cell",
"journal_volume": "49",
"journal_issue": "2",
"journal_pages": "232-3",
"pub_year": "2013",
"pubmed_id": "23352244"
},
{
"title": "Genome sequences of five b1 subcluster mycobacteriophages",
"abstract": "Mycobacteriophages infect members of the Mycobacterium genus in the phylum Actinobacteria and exhibit remarkable diversity. Genome analysis groups the thousands of known mycobacteriophages into clusters, of which the B1 subcluster is currently the third most populous. We report the complete genome sequences of five additional members of the B1 subcluster.",
"full_author_list": "Breakwell DP, Barrus EZ, Benedict AB, Brighton AK, Fisher JN, Gardner AV, Kartchner BJ, Ladle KC, Lunt BL, Merrill BD, Morrell JD, Burnett SH, Grose JH.",
"short_author_list": "Breakwell et al",
"article_url": "http://genomea.asm.org/content/1/6/e00968-13.long",
"journal": "Genome Announcements",
"journal_volume": "1",
"journal_issue": "6",
"journal_pages": "",
"pub_year": "2013",
"pubmed_id": "24285667"
},
{
"title": " Integration-Dependent Bacteriophage Immunity Provides Insights into the Evolution of Genetic Switches",
"abstract": "Genetic switches are critical components of developmental circuits. Because temperate bacteriophages are vastly abundant and greatly diverse, they are rich resources for understanding the mechanisms and evolution of switches and the molecular control of genetic circuitry. Here, we describe a new class of small, compact, and simple switches that use site-specific recombination as the key decision point. The phage attachment site attP is located within the phage repressor gene such that chromosomal integration results in removal of a C-terminal tag that destabilizes the virally encoded form of the repressor. Integration thus not only confers prophage stability but also is a requirement for lysogenic establishment. The variety of these self-contained integration-dependent immunity systems in different genomic contexts suggests that these represent ancestral states in switch evolution from which more-complex switches have evolved. They also provide a powerful toolkit for building synthetic biological circuits.",
"full_author_list": "Broussard GW, Oldfield LM, Villanueva VM, Lunt BL, Shine EE, Hatfull GF.",
"short_author_list": "Broussard GW et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/?term=23246436",
"journal": "Molecular Cell",
"journal_volume": "49",
"journal_issue": "2",
"journal_pages": "237-48",
"pub_year": "2013",
"pubmed_id": "23246436"
},
{
"title": "Complete genome sequences of 63 mycobacteriophages",
"abstract": "Mycobacteriophages are viruses that infect mycobacterial hosts. The current collection of sequenced mycobacteriophages-all isolated on a single host strain, Mycobacterium smegmatis mc(2)155, reveals substantial genetic diversity. The complete genome sequences of 63 newly isolated mycobacteriophages expand the resolution of our understanding of phage diversity.",
"full_author_list": "Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) Program; KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) Mycobacterial Genetics Course; University of California—Los Angeles Research Immersion Laboratory in Virology; Phage Hunters Integrating Research and Education (PHIRE) Program",
"short_author_list": "Hatfull et al",
"article_url": "http://genomea.asm.org/content/1/6/e00847-13.long",
"journal": "Genome Announcements",
"journal_volume": "1",
"journal_issue": "6",
"journal_pages": "",
"pub_year": "2013",
"pubmed_id": "24285655"
},
{
"title": "Genomic characterization of six novel Bacillus pumilus bacteriophages",
"abstract": "Twenty-eight bacteriophages infecting the local host Bacillus pumilus BL-8 were isolated, purified, and characterized. Nine genomes were sequenced, of which six were annotated and are the first of this host submitted to the public record. The 28 phages were divided into two groups by sequence and morphological similarity, yielding 27 cluster BpA phages and 1 cluster BpB phage, which is a BL-8 prophage. Most of the BpA phages have a host range restricted to distantly related strains, B. pumilus and B. simplex, reflecting the complexities of Bacillus taxonomy. Despite isolation over wide geographic and temporal space, the six cluster BpA phages share most of their 23 functionally annotated protein features and show a high degree of sequence similarity, which is unique among phages of the Bacillus genera. This is the first report of B. pumilus phages since 1981.",
"full_author_list": "Lorenz L, Lins B, Barrett J, Montgomery A, Trapani S, Schindler A, Christie GE, Cresawn SG, Temple L",
"short_author_list": "Lorenz L, et al",
"article_url": "http://www.sciencedirect.com/science/article/pii/S0042682213004066",
"journal": "Virology",
"journal_volume": "Sept 444",
"journal_issue": "1-2",
"journal_pages": "374-83",
"pub_year": "2013",
"pubmed_id": "23906709"
},
{
"title": "Cluster J mycobacteriophages:intron splicing in capsid and tail genes",
"abstract": "Bacteriophages isolated on Mycobacterium smegmatis mc(2)155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution. ",
"full_author_list": "Pope WH, Jacobs-Sera D, Best AA, Broussard GW, Connerly PL, Dedrick RM, Kremer TA, Offner S, Ogiefo AH, Pizzorno MC, Rockenbach K, Russell DA, Stowe EL, Stukey J, Thibault SA, Conway JF, Hendrix RW, Hatfull GF.",
"short_author_list": "Pope, WH et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/23874930",
"journal": "PLoS One",
"journal_volume": "8",
"journal_issue": "7",
"journal_pages": "e69273",
"pub_year": "2013",
"pubmed_id": "23874930"
},
{
"title": "Phage cluster relationships identified through single gene analysis",
"abstract": "Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved.\r\nRESULTS:\r\nA single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages.\r\nCONCLUSIONS:\r\nTMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.",
"full_author_list": "Smith KC, Castro-Nallar E, Fisher JN, Breakwell DP, Grose JH, Burnett SH.",
"short_author_list": "Smith KC et al",
"article_url": "http://www.biomedcentral.com/1471-2164/14/410",
"journal": "BMC Genomics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2013",
"pubmed_id": "23777341"
},
{
"title": "Rewritable digital data storage in live cells via engineered control of recombination directionality.",
"abstract": "The use of synthetic biological systems in research, healthcare, and manufacturing often requires autonomous history-dependent behavior and therefore some form of engineered biological memory. For example, the study or reprogramming of aging, cancer, or development would benefit from genetically encoded counters capable of recording up to several hundred cell division or differentiation events. Although genetic material itself provides a natural data storage medium, tools that allow researchers to reliably and reversibly write information to DNA in vivo are lacking. Here, we demonstrate a rewriteable recombinase addressable data (RAD) module that reliably stores digital information within a chromosome. RAD modules use serine integrase and excisionase functions adapted from bacteriophage to invert and restore specific DNA sequences. Our core RAD memory element is capable of passive information storage in the absence of heterologous gene expression for over 100 cell divisions and can be switched repeatedly without performance degradation, as is required to support combinatorial data storage. We also demonstrate how programmed stochasticity in RAD system performance arising from bidirectional recombination can be achieved and tuned by varying the synthesis and degradation rates of recombinase proteins. The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems.",
"full_author_list": "Bonnet J, Subsoontorn P, Endy D.",
"short_author_list": "Bonnet J, Subsoontorn P, Endy D.",
"article_url": "http://www.pnas.org/content/early/2012/05/14/1202344109.full.pdf",
"journal": "Proceedings of the National Academy of Sciences of the United States of America",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2012",
"pubmed_id": "22615351"
},
{
"title": "The Rewards and Challenges of Undergraduate Peer Mentoring in Course-based Research: Student Perspectives from a Liberal Arts Institution.",
"abstract": "A growing movement in higher education seeks to integrate authentic research experiences for students in traditional laboratory settings (Lopatto, 2010). These “course-based research” models have been successfully employed at several institutions (Boomer & Dutton, 2002; Brodl, 2005; Caruso, Sandoz, & Kelsey, 2009; Drew & Triplett, 2008; Elwess & Latourelle, 2004; Howard & Mislowski, 2005; Ronsheim, Pregnall, Schwarz, Schlessman, & Raley-Susman, 2009; Shaffer et al., 2010; Harrison, Dunbar, Ratmansky, Boyd, & Lopatto, 2011). Students report that their engagement in course-based research has enabled them to think like scientists, tackle new experimental methods with confidence, persevere in the data collection process, and approach coursework in other science courses with renewed enthusiasm. These benefits build upon those gains acquired through traditional undergraduate research in the sciences: competencies in research design, hypothesis formation, data collection and analysis, computing, and information literacy (Laursen, Hunter, Seymour, & Thiry, 2010; Bauer & Bennett, 2003; Hathaway, Nagda, & Gregerman, 2002; Hunter, Laursen, & Seymour, 2007; Kardash, 2000; Kremer & Bringle, 1990; Lopatto, 2004; Rauckhorst, Czaja, & Magolda, 2001; Russell, Hancock, & McCullough, 2007; Seymour, Hunter, Laursen, & DeAntoni, 2004). Course-based research is primed for implementation in an increasing number of colleges and universities, but the initiative faces challenges at institutions of higher education in order to balance the needs of students with staffing and funding shortages.",
"full_author_list": "Dunbar, David & Harrison, Melinda & Mageeney, Catherine & Catagnus, Christopher & Cimo, Amy & Beckowski, Catherine & Ratmansky, Linda",
"short_author_list": "Dunbar et al",
"article_url": "https://www.elon.edu/u/academics/undergraduate-research/purm/wp-content/uploads/sites/923/2019/06/PURM-1.2-Dunbar-et-al1.pdf",
"journal": "Perspectives on Undergraduate Research and Mentoring",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2012",
"pubmed_id": ""
},
{
"title": "Complete genome sequences of 138 mycobacteriophages",
"abstract": "Bacteriophages are the most numerous biological entities in the biosphere, and although their genetic diversity is high, it remains ill defined. Mycobacteriophages-the viruses of mycobacterial hosts-provide insights into this diversity as well as tools for manipulating Mycobacterium tuberculosis. We report here the complete genome sequences of 138 new mycobacteriophages, which-together with the 83 mycobacteriophages previously reported-represent the largest collection of phages known to infect a single common host, Mycobacterium smegmatis mc(2) 155.",
"full_author_list": "Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program; KwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students; Phage Hunters Integrating Research and Education Program",
"short_author_list": "Hatfull et al",
"article_url": "http://jvi.asm.org/content/86/4/2382.long",
"journal": "Journal of Virology",
"journal_volume": "86",
"journal_issue": "4",
"journal_pages": "2382-4",
"pub_year": "2012",
"pubmed_id": "22282335"
},
{
"title": "The secret lives of mycobacteriophages.",
"abstract": "The study of mycobacteriophages provides insights into viral diversity and evolution, as well as the genetics and physiology of their pathogenic hosts. Genomic characterization of 80 mycobacteriophages reveals a high degree of genetic diversity and an especially rich reservoir of interesting genes. These include a vast number of genes of unknown function that do not match known database entries and many genes whose functions can be predicted but which are not typically found as components of phage genomes. Thus many mysteries surround these genomes, such as why the genes are there, what do they do, how are they expressed and regulated, how do they influence the physiology of the host bacterium, and what forces of evolution directed them to their genomic homes? Although the genetic diversity and novelty of these phages is full of intrigue, it is a godsend for the mycobacterial geneticist, presenting an abundantly rich toolbox that can be exploited to devise new and effective ways for understanding the genetics and physiology of human tuberculosis. As the number of sequenced genomes continues to grow, their mysteries continue to thicken, and the time has come to learn more about the secret lives of mycobacteriophages.\r\n\r\nPubMed Link: http://www.ncbi.nlm.nih.gov/pubmed/22420855",
"full_author_list": "Hatfull, Graham F.",
"short_author_list": "Hatfull, GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/22420855",
"journal": "Advances in Virus Research",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "179-288",
"pub_year": "2012",
"pubmed_id": "22420855"
},
{
"title": "On the nature of mycobacteriophage diversity and host preference",
"abstract": "The complete genome sequences of over 220 mycobacteriophages reveal them to be highly diverse, with numerous types sharing little or no nucleotide sequence identity with each other. We have determined the preferences of these phages for Mycobacterium tuberculosis and for other strains of Mycobacterium smegmatis, and find there is a correlation between genome type (cluster, subcluster, singleton) and host range. For many of the phages, expansion of host range occurs at relatively high frequencies, and we describe several examples in which host constraints occur at early stages of infection (adsorption or DNA injection), and phages have the ability to expand their host range through mutations in tail genes. We present a model in which phage diversity is a function of both the ability of phages to rapidly adapt to new hosts and the richness of the diversity of the bacterial population from which those phages are isolated.",
"full_author_list": "Jacobs-Sera D, Marinelli LJ, Bowman C, Broussard GW, Guerrero Bustamante C, Boyle MM, Petrova ZO, Dedrick RM, Pope WH; Science Education Alliance Phage Hunters Advancing Genomics And Evolutionary Science Sea-Phages Program, Modlin RL, Hendrix RW, Hatfull GF.",
"short_author_list": "Jacobs-Sera, D., et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/23084079",
"journal": "Virology",
"journal_volume": "434",
"journal_issue": "2",
"journal_pages": "187-201",
"pub_year": "2012",
"pubmed_id": "23084079"
},
{
"title": "Mycobacteriophage Marvin: a new singleton phage with an unusual genome organization.",
"abstract": "Mycobacteriophages represent a genetically diverse group of viruses that infect mycobacterial hosts. Although more than 80 genomes have been sequenced, these still poorly represent the likely diversity of the broader population of phages that can infect the host, Mycobacterium smegmatis mc(2)155. We describe here a newly discovered phage, Marvin, which is a singleton phage, having no previously identified close relatives. The 65,100-bp genome contains 107 predicted protein-coding genes arranged in a noncanonical genomic architecture in which a subset of the minor tail protein genes are displaced about 20 kbp from their typical location, situated among nonstructural genes anticipated to be expressed early in lytic growth. Marvin is not temperate, and stable lysogens cannot be recovered from infections, although the presence of a putative xis gene suggests that Marvin could be a relatively recent derivative of a temperate parent. The Marvin genome is replete with novel genes not present in other mycobacteriophage genomes, and although most are of unknown function, the presence of amidoligase and glutamine amidotransferase genes suggests intriguing possibilities for the interactions of Marvin with its mycobacterial hosts.",
"full_author_list": "Mageeney C, Pope WH, Harrison M, Moran D, Cross T, Jacobs-Sera D, Hendrix RW, Dunbar D, Hatfull GF.",
"short_author_list": "Mageeney C, et al.",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/22357284",
"journal": "Journal of Virology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2012",
"pubmed_id": "22357284"
},
{
"title": "The evolution of the tape measure protein: units, duplications and losses.",
"abstract": "Abstract\r\n\r\n\r\nBACKGROUND: \r\n\r\nA large family of viruses that infect bacteria, called phages, is characterized by long tails used to inject DNA into their victims' cells. The tape measure protein got its name because the length of the corresponding gene is proportional to the length of the phage's tail: a fact shown by actually copying or splicing out parts of DNA in exemplar species. A natural question is whether there exist units for these tape measures, and if different tape measures have different units and lengths. Such units would allow us to retrace the evolution of tape measure proteins using their duplication/loss history. The vast number of sequenced phages genomes allows us to attack this problem with a comparative genomics approach.\r\n\r\nRESULTS: \r\n\r\nHere we describe a subset of phages whose tape measure proteins contain variable numbers of an 11 amino acids sequence repeat, aligned with sequence similarity, structural properties, and simple arithmetics. This subset provides a unique opportunity for the combinatorial study of phage evolution, without the added uncertainties of multiple alignments, which are trivial in this case, or of protein functions, that are well established. We give a heuristic that reconstructs the duplication history of these sequences, using divergent strains to discriminate between mutations that occurred before and after speciation, or lineage divergence. The heuristic is based on an efficient algorithm that gives an exhaustive enumeration of all possible parsimonious reconstructions of the duplication/speciation history of a single nucleotide. Finally, we present a method that allows, when possible, to discriminate between duplication and loss events.\r\n\r\nCONCLUSIONS: \r\n\r\nEstablishing the evolutionary history of viruses is difficult, in part due to extensive recombinations and gene transfers, and high mutation rates that often erase detectable similarity between homologous genes. In this paper, we introduce new tools to address this problem.\r\n",
"full_author_list": "Belcaid M, Bergeron A, Poisson G.",
"short_author_list": "Belcaid M, Bergeron A, Poisson G.",
"article_url": "",
"journal": "BMC Bioinformatics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2011",
"pubmed_id": "22151602"
},
{
"title": "Phamerator: a bioinformatic tool for comparative bacteriophage genomics.",
"abstract": "BACKGROUND:\r\nBacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.\r\nRESULTS:\r\nWe describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange.\r\nCONCLUSIONS:\r\nPhamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.",
"full_author_list": "Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfu",
"short_author_list": "Cresawn SG, et al.",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/21991981",
"journal": "BMC Bioinformatics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2011",
"pubmed_id": "21991981"
},
{
"title": "Genomic and Functional Analyses of Rhodococcus equi Phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7",
"abstract": "The isolation and results of genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiDocB7, ReqiPine5, and ReqiPoco6 (hereafter referred to as Pepy6, DocB7, Pine5, and Poco6, respectively) are reported. Two phages, Pepy6 and Poco6, more than 75% identical, exhibited genome organization and protein sequence likeness to Lactococcus lactis phage 1706 and clostridial prophage elements. An unusually high fraction, 27%, of Pepy6 and Poco6 proteins were predicted to possess at least one transmembrane domain, a value much higher than the average of 8.5% transmembrane domain-containing proteins determined from a data set of 36,324 phage protein entries. Genome organization and protein sequence comparisons place phage Pine5 as the first nonmycobacteriophage member of the large Rosebush cluster. DocB7, which had the broadest host range among the four isolates, was not closely related to any phage or prophage in the database, and only 23 of 105 predicted encoded proteins could be assigned a functional annotation. Because of the relationship of Rhodococcus to Mycobacterium, it was anticipated that these phages should exhibit some of the features characteristic of mycobacteriophages. Traits that were identified as shared by the Rhodococcus phages and mycobacteriophages include the prevalent long-tailed morphology and the presence of genes encoding LysB-like mycolate-hydrolyzing lysis proteins. Application of DocB7 lysates to soils amended with a host strain of R. equi reduced recoverable bacterial CFU, suggesting that phage may be useful in limiting R. equi load in the environment while foals are susceptible to infection.",
"full_author_list": "E. J. Summer, M. Liu, J. J. Gill, M. Grant, T. N. Chan-Cortes, L. Ferguson, C. Janes, K. Lange, M. Bertoli, C. Moore, R. C. Orchard, N. D. Cohen, and R. Young",
"short_author_list": "E. J. Summer et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020559/",
"journal": "Applied and Environmental Microbiology",
"journal_volume": "77",
"journal_issue": "2",
"journal_pages": "669-683",
"pub_year": "2011",
"pubmed_id": "PMC3020559"
},
{
"title": "Classroom-based science research at the introductory level: changes in career choices and attitude",
"abstract": "Our study, focused on classroom-based research at the introductory level and using the Phage Genomics course as the model, shows evidence that first-year students doing research learn the process of science as well as how scientists practice science. A preliminary but notable outcome of our work, which is based on a small sample, is the change in student interest in considering different career choices such as graduate education and science in general. This is particularly notable, as previous research has described research internships as clarifying or confirming rather than changing undergraduates' decisions to pursue graduate education. We hypothesize that our results differ from previous studies of the impact of engaging in research because the students in our study are still in the early stages of their undergraduate careers. Our work builds upon the classroom-based research movement and should be viewed as encouraging to the Vision and Change in Undergraduate Biology Education movement advocated by the American Association for the Advancement of Science, the National Science Foundation, and other undergraduate education stakeholders.",
"full_author_list": "Harrison M, Dunbar D, Ratmansky L, Boyd K, Lopatto D",
"short_author_list": "Harrison, Dunbar, Ratmansky, et al",
"article_url": "http://www.lifescied.org/content/10/3/279.long",
"journal": "CBE—Life Sciences Education",
"journal_volume": "10",
"journal_issue": "3",
"journal_pages": "279-286",
"pub_year": "2011",
"pubmed_id": "21885824"
},
{
"title": "Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution",
"abstract": "Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.",
"full_author_list": "Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, Anderson MD, Anderson AG, Ang AA, Ares M Jr, Barber AJ, Barker LP, Barrett JM, Barshop WD, Bauerle CM, Bayles IM, Belfield KL, Best AA, Borjon A Jr, Bowman CA, Boyer CA, Bradley KW, Bradley VA, Broadway LN, Budwal K, Busby KN, Campbell IW, Campbell AM, Carey A, Caruso SM, Chew RD, Cockburn CL, Cohen LB, Corajod JM, Cresawn SG, Davis KR, Deng L, Denver DR, Dixon BR, Ekram S, Elgin SC, Engelsen AE, English BE, Erb ML, Estrada C, Filliger LZ, Findley AM, Forbes L, Forsyth MH, Fox TM, Fritz MJ, Garcia R, George ZD, Georges AE, Gissendanner CR, Goff S, Goldstein R, Gordon KC, Green RD, Guerra SL, Guiney-Olsen KR, Guiza BG, Haghighat L, Hagopian GV, Harmon CJ, Harmson JS, Hartzog GA, Harvey SE, He S, He KJ, Healy KE, Higinbotham ER, Hildebrandt EN, Ho JH, Hogan GM, Hohenstein VG, Holz NA, Huang VJ, Hufford EL, Hynes PM, Jackson AS, Jansen EC, Jarvik J, Jasinto PG, Jordan TC, Kasza T, Katelyn MA, Kelsey JS, Kerrigan LA, Khaw D, Kim J, Knutter JZ, Ko CC, Larkin GV, Laroche JR, Latif A, Leuba KD, Leuba SI, Lewis LO, Loesser-Casey KE, Long CA, Lopez AJ, Lowery N, Lu TQ, Mac V, Masters IR, McCloud JJ, McDonough MJ, Medenbach AJ, Menon A, Miller R, Morgan BK, Ng PC, Nguyen E, Nguyen KT, Nguyen ET, Nicholson KM, Parnell LA, Peirce CE, Perz AM, Peterson LJ, Pferdehirt RE, Philip SV, Pogliano K, Pogliano J, Polley T, Puopolo EJ, Rabinowitz HS, Resiss MJ, Rhyan CN, Robinson YM, Rodriguez LL, Rose AC, Rubin JD, Ruby JA, Saha MS, Sandoz JW, Savitskaya J, Schipper DJ, Schnitzler CE, Schott AR, Segal JB, Shaffer CD, Sheldon KE, Shepard EM, Shepardson JW, Shroff MK, Simmons JM, Simms EF, Simpson BM, Sinclair KM, Sjoholm RL, Slette IJ, Spaulding BC, Straub CL, Stukey J, Sughrue T, Tang TY, Tatyana LM, Taylor SB, Taylor BJ, Temple LM, Thompson JV, Tokarz MP, Trapani SE, Troum AP, Tsay J, Tubbs AT, Walton JM, Wang DH, Wang H, Warner JR, Weisser EG, Wendler SC, Weston-Hafer KA, Whelan HM, Williamson KE, Willis AN, Wirtshafter HS, Wong TW, Wu P, Yang Y, Yee BC, Zaidins DA, Zhang B, Zúniga MY, Hendrix RW, Hatfull GF.",
"short_author_list": "Pope WH et al",
"article_url": "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016329",
"journal": "PLoSOne",
"journal_volume": "6",
"journal_issue": "1",
"journal_pages": "e16329",
"pub_year": "2011",
"pubmed_id": "21298013"
},
{
"title": "Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4",
"abstract": "Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them--with the exception of TM4--form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.",
"full_author_list": "Pope WH, Ferreira CM, Jacobs-Sera D, Benjamin RC, Davis AJ, DeJong RJ, Elgin SC, Guilfoile FR, Forsyth MH, Harris AD, Harvey SE, Hughes LE, Hynes PM, Jackson AS, Jalal MD, MacMurray EA, Manley CM, McDonough MJ, Mosier JL, Osterbann LJ, Rabinowitz HS, Rhyan CN, Russell DA, Saha MS, Shaffer CD, Simon SE, Sims EF, Tovar IG, Weisser EG, Wertz JT, Weston-Hafer KA, Williamson KE, Zhang B, Cresawn SG, Jain P, Piuri M, Jacobs WR Jr, Hendrix RW, Hatfull GF.",
"short_author_list": "Pope WH, Ferreira CM, Jacobs-Sera D, et al",
"article_url": "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026750",
"journal": "PLoS One",
"journal_volume": "6",
"journal_issue": "10",
"journal_pages": "",
"pub_year": "2011",
"pubmed_id": "22053209"
},
{
"title": "The phage-host arms race: shaping the evolution of microbes.",
"abstract": "Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. Here, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.",
"full_author_list": "Stern A, Sorek R.",
"short_author_list": "Stern A, Sorek R.",
"article_url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3274958/",
"journal": "Bioessays. ",
"journal_volume": "33",
"journal_issue": "1",
"journal_pages": "43-51",
"pub_year": "2011",
"pubmed_id": " 20979102 "
},
{
"title": "A method for rapid genetic integration into plasmodium falciparum utilizing mycobacteriophage Bxb1 integrase.",
"abstract": "Genetic manipulation of the human malaria parasite Plasmodium falciparum has presented substantial challenges for research efforts aimed at better understanding the complex biology of this highly virulent organism. The development of methods to perform gene disruption, allelic replacement or transgene expression has provided important insights into the function of parasite genes. However, genomic integration studies have been hindered by low transfection and recombination efficiencies, and are complicated by the propensity of this parasite to maintain episomal replicating plasmids. We have developed a fast and efficient site-specific system of integrative recombination into the P. falciparum genome, which is catalyzed by the mycobacteriophage Bxb1 serine integrase. This system has the advantage of providing greater genetic and phenotypic homogeneity within transgenic lines as compared to earlier methods based on episomal replication of plasmids. Herein, we present this methodology.",
"full_author_list": "Sophie H Adjalley, Marcus C S Lee, David A Fidock",
"short_author_list": "Adjalley SH, Lee MC, Fidock DA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20676977",
"journal": "Methods in molecular biology (Clifton, N.J.)",
"journal_volume": "634",
"journal_issue": "",
"journal_pages": "87-100",
"pub_year": "2010",
"pubmed_id": "20676977"
},
{
"title": "Regions and residues of an asymmetric operator DNA interacting with the monomeric repressor of temperate mycobacteriophage L1.",
"abstract": "Previously, the repressor protein of mycobacteriophage L1 bound to two operator DNAs with dissimilar affinity. Surprisingly, the putative operator consensus sequence, 5'GGTGGa/cTGTCAAG, lacks the dyad symmetry reported for the repressor binding operators of lambda and related phages. To gain insight into the structure of the L1 repressor-asymmetric operator DNA complex, we have performed various in vitro experiments. A dimethyl sulfate protection assay revealed that five guanine bases, mostly distributed in the two adjacent major grooves of the 13 bp operator DNA helix, participate in repressor binding. Hydroxyl radical footprinting demonstrated that interaction between the repressor and operator DNA is asymmetric in nature and occurs primarily through one face of the DNA helix. Genetic studies not only confirmed the results of the dimethyl sulfate protection assay but also indicated that other bases in the 13 bp operator DNA are critical for repressor binding. Interestingly, repressor that weakly induced bending in the asymmetric operator DNA interacted with this operator as a monomer. The tertiary structure of the L1 repressor-operator DNA complex therefore appears to be distinct from those of the lambdoid phages even though the number of repressor molecules per operator site closely matched that of the lambda phage system.",
"full_author_list": "Amitava Bandhu, Tridib Ganguly, Biswanath Jana, Rajkrishna Mondal, Subrata Sau",
"short_author_list": "Bandhu A et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20377203",
"journal": "Biochemistry",
"journal_volume": "49",
"journal_issue": "19",
"journal_pages": "4235-43",
"pub_year": "2010",
"pubmed_id": "20377203"
},
{
"title": "The Deinococcus radiodurans Snf2 intein caught in the act: detection of the Class 3 intein signature Block F branched intermediate.",
"abstract": "Inteins are the protein equivalent of introns. They are remarkable and robust single turnover enzymes that splice out of precursor proteins during post-translational maturation of the host protein (extein). The Deinococcus radiodurans Snf2 intein is the second member of the recently discovered Class 3 subfamily of inteins to be characterized. Class 3 inteins have a unique sequence signature: (a) they start with residues other than the standard Class 1 Cys, Ser or Thr, (b) have a noncontiguous, centrally located Trp/Cys/Thr triplet, and (c) all but one have Ser or Thr at the start of the C-extein instead of the more common Cys. We previously proposed that Class 3 inteins splice by a variation in the standard intein-mediated protein splicing mechanism that includes a novel initiating step leading to the formation of a previously unrecognized branched intermediate. In this mechanism defined with the Class 3 prototypic Mycobacteriophage Bethlehem DnaB intein, the triplet Cys attacks the peptide bond at the N-terminal splice junction to form the class specific branched intermediate after which the N-extein is transferred to the side chain of the Ser, Thr, or Cys at the C-terminal splice junction to form the standard intein branched intermediate. Analysis of the Deinococcus radiodurans Snf2 intein confirms this splicing mechanism. Moreover, the Class 3 specific Block F branched intermediate was isolated, providing the first direct proof of its existence.",
"full_author_list": "Lear E Brace, Maurice W Southworth, Kazuo Tori, Michelle L Cushing, Francine Perler",
"short_author_list": "Brace LE et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20521254",
"journal": "Protein science : a publication of the Protein Society",
"journal_volume": "19",
"journal_issue": "8",
"journal_pages": "1525-33",
"pub_year": "2010",
"pubmed_id": "20521254"
},
{
"title": "The mycobacteriophage Ms6 encodes a chaperone-like protein involved in the endolysin delivery to the peptidoglycan.",
"abstract": "Like most double-stranded (ds) DNA phages, mycobacteriophage Ms6 uses the holin-endolysin system to achieve lysis of its host. In addition to endolysin (lysA) and holin (hol) genes, Ms6 encodes three accessory lysis proteins. In this study we investigated the lysis function of Gp1, which is encoded by the gp1 gene that lies immediately upstream of lysA. Escherichia coli lysis was observed after coexpression of LysA and Gp1 in the absence of Ms6 holin. Gp1 does not belong to the holin class of proteins, and we provide evidence that it shares several characteristics with molecular chaperones. We show that Gp1 interacts with LysA, and that this interaction is necessary for LysA delivery to its target. In addition, PhoA fusions showed that, in Mycobacterium smegmatis, LysA is exported to the extracytoplasmic environment in the presence of Gp1. We also show that Gp1 is necessary for efficient M. smegmatis lysis, as Ms6 gp1 deletion results in host lysis defects. We propose that delivery of Ms6 endolysin to the murein layer is assisted by Gp1, a chaperone-like protein, in a holin-independent manner.",
"full_author_list": "Maria João Catalão, Filipa Gil, José Moniz-Pereira, Madalena Pimentel",
"short_author_list": "Catalão MJ et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20545844",
"journal": "Molecular microbiology",
"journal_volume": "77",
"journal_issue": "3",
"journal_pages": "672-86",
"pub_year": "2010",
"pubmed_id": "20545844"
},
{
"title": "Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections",
"abstract": "Antibiotic-resistant bacteria threaten life worldwide. Although new antibiotics are scarce, the use of bacteriophages, viruses that infect bacteria, is rarely proposed as a means of offsetting this shortage. Doubt also remains widespread about the efficacy of phage therapy despite recent encouraging results. Using a bioluminescent Pseudomonas aeruginosa strain, we monitored and quantified the efficacy of a bacteriophage treatment in mice during acute lung infection. Bacteriophage treatment not only was effective in saving animals from lethal infection, but also was able to prevent lung infection when given 24 h before bacterial infection, thereby extending the potential use of bacteriophages as therapeutic agents to combat bacterial lung infection.",
"full_author_list": "Debarbieux L, Leduc D, Maura D, Morello E, Criscuolo A, Grossi O, Balloy V, Touqui L.\r\n",
"short_author_list": "Debarbieux L, Leduc D, Maura D, Morello E, Criscuolo A, Gros",
"article_url": "",
"journal": "The Journal of Infectious Diseases",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2010",
"pubmed_id": "20196657"
},
{
"title": "Rapid assessment of the viability of Mycobacterium avium subsp. paratuberculosis cells after heat treatment, using an optimized phage amplification assay.",
"abstract": "Thermal inactivation experiments were carried out to assess the utility of a recently optimized phage amplification assay to accurately enumerate viable Mycobacterium avium subsp. paratuberculosis cells in milk. Ultra-heat-treated (UHT) whole milk was spiked with large numbers of M. avium subsp. paratuberculosis organisms (10(6) to 10(7) CFU/ml) and dispensed in 100-microl aliquots in thin-walled 200-microl PCR tubes. A Primus 96 advanced thermal cycler (Peqlab, Erlangen, Germany) was used to achieve the following time and temperature treatments: (i) 63 degrees C for 3, 6, and 9 min; (ii) 68 degrees C for 20, 40, and 60 s; and (iii) 72 degrees C for 5, 10, 15, and 25 s. After thermal stress, the number of surviving M. avium subsp. paratuberculosis cells was assessed by both phage amplification assay and culture on Herrold's egg yolk medium (HEYM). A high correlation between PFU/ml and CFU/ml counts was observed for both unheated (r(2) = 0.943) and heated (r(2) = 0.971) M. avium subsp. paratuberculosis cells. D and z values obtained using the two types of counts were not significantly different (P > 0.05). The D(68 degrees C), mean D(63 degrees C), and D(72 degrees C) for four M. avium subsp. paratuberculosis strains were 81.8, 9.8, and 4.2 s, respectively, yielding a mean z value of 6.9 degrees C. Complete inactivation of 10(6) to 10(7) CFU of M. avium subsp. paratuberculosis/ml milk was not observed for any of the time-temperature combinations studied; 5.2- to 6.6-log(10) reductions in numbers were achieved depending on the temperature and time. Nonlinear thermal inactivation kinetics were consistently observed for this bacterium. This study confirms that the optimized phage assay can be employed in place of conventional culture on HEYM to speed up the acquisition of results (48 h instead of a minimum of 6 weeks) for inactivation experiments involving M. avium subsp. paratuberculosis-spiked samples.",
"full_author_list": "Antonio Foddai, Christopher T Elliott, Irene R Grant",
"short_author_list": "Foddai A, Elliott CT, Grant IR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20097817",
"journal": "Applied and environmental microbiology",
"journal_volume": "76",
"journal_issue": "6",
"journal_pages": "1777-82",
"pub_year": "2010",
"pubmed_id": "20097817"
},
{
"title": "Mycobacteriophage Ms6 LysB specifically targets the outer membrane of Mycobacterium smegmatis.",
"abstract": "LysB, a mycobacteriophage Ms6-encoded protein, was previously identified as a lipolytic enzyme able to hydrolyse the ester bond in lipase and esterase substrates. In the present work, we show that LysB can hydrolyse lipids containing mycolic acids from the outer membrane of the mycobacterial cell wall. LysB was shown to hydrolyse the mycolic acids from the mycolyl-arabinogalactan-peptidoglycan complex where the mycolates of the inner leaflet of the outer membrane are covalently attached to an arabinosyl head group. In addition, treatment of the extractable lipids from Mycobacterium smegmatis, Mycobacterium bovis BCG and Mycobacterium tuberculosis H37Ra with LysB showed that trehalose 6,6'-dimycolate (TDM), a trehalose diester of two mycolic acid molecules, was hydrolysed by the enzyme. We have also determined the structures of the mycolic acid molecules that form the M. smegmatis TDM. The identification of a phage-encoded enzyme that targets the outer membrane of the mycobacterial cell wall enhances our understanding of the mechanism of mycobacteriophage lysis.",
"full_author_list": "Filipa Gil, Anna E Grzegorzewicz, Maria João Catalão, João Vital, Michael R McNeil, Madalena Pimentel",
"short_author_list": "Gil F et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20093291",
"journal": "Microbiology (Reading, England)",
"journal_volume": "156",
"journal_issue": "Pt 5",
"journal_pages": "1497-504",
"pub_year": "2010",
"pubmed_id": "20093291"
},
{
"title": "Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size",
"abstract": "Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.",
"full_author_list": "Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, Hoyte NN, Bowman CA, Tantoco AT, Paladin EC, Myers MS, Smith AL, Grace MS, Pham TT, O'Brien MB, Vogelsberger AM, Hryckowian AJ, Wynalek JL, Donis-Keller H, Bogel MW, Peebles CL, Cresawn SG, Hendrix RW.",
"short_author_list": "Hatfull et al.",
"article_url": "",
"journal": "J Mol Biol.",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2010",
"pubmed_id": "20064525"
},
{
"title": "Mycobacteriophages: Genes and Genomes.",
"abstract": "Viruses are powerful tools for investigating and manipulating their hosts, but the enormous size and amazing genetic diversity of the bacteriophage population have emerged as something of a surprise. In light of the evident importance of mycobacteria to human health-especially Mycobacterium tuberculosis, which causes tuberculosis-and the difficulties that have plagued their genetic manipulation, mycobacteriophages are especially appealing subjects for discovery, genomic characterization, and manipulation. With more than 70 complete genome sequences available, the mycobacteriophages have provided a wealth of information on the diversity of phages that infect a common bacterial host, revealed the pervasively mosaic nature of phage genome architectures, and identified a huge number of genes of unknown function. Mycobacteriophages have provided key tools for tuberculosis genetics, and new methods for simple construction of mycobacteriophage recombinants will facilitate postgenomic explorations into mycobacteriophage biology. Expected final online publication date for the Annual Review of Microbiology Volume 64 is September 08, 2010. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.",
"full_author_list": "Hatfull GF",
"short_author_list": "Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20528690",
"journal": "Annual Review of Microbiology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2010",
"pubmed_id": "20528690"
},
{
"title": "Mycobacteriophages: Genes and Genomes",
"abstract": "Viruses are powerful tools for investigating and manipulating their hosts, but the enormous size and amazing genetic diversity of the bacte- riophage population have emerged as something of a surprise. In light of the evident importance of mycobacteria to human health—especially Mycobacterium tuberculosis, which causes tuberculosis—and the difficul- ties that have plagued their genetic manipulation, mycobacteriophages are especially appealing subjects for discovery, genomic characteriza- tion, and manipulation. With more than 70 complete genome sequences available, the mycobacteriophages have provided a wealth of informa- tion on the diversity of phages that infect a common bacterial host, revealed the pervasively mosaic nature of phage genome architectures, and identified a huge number of genes of unknown function. My- cobacteriophages have provided key tools for tuberculosis genetics, and new methods for simple construction of mycobacteriophage recombi- nants will facilitate postgenomic explorations into mycobacteriophage biology.",
"full_author_list": "Hatfull GF",
"short_author_list": "Hatfull GF",
"article_url": "",
"journal": "Annual Review of Microbiology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2010",
"pubmed_id": ""
},
{
"title": "Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size.",
"abstract": "Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.",
"full_author_list": "Graham F Hatfull, Deborah Jacobs-Sera, Jeffrey G Lawrence, Welkin H Pope, Daniel A Russell, Ching-Chung Ko, Rebecca J Weber, Manisha C Patel, Katherine L Germane, Robert H Edgar, Natasha N Hoyte, Charles A Bowman, Anthony T Tantoco, Elizabeth C Paladin, Marlana S Myers, Alexis L Smith, Molly S Grace, Thuy T Pham, Matthew B O'Brien, Amy M Vogelsberger, Andrew J Hryckowian, Jessica L Wynalek, Helen Donis-Keller, Matt W Bogel, Craig L Peebles, Steven G Cresawn, Roger W Hendrix",
"short_author_list": "Hatfull GF et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20064525",
"journal": "Journal of molecular biology",
"journal_volume": "397",
"journal_issue": "1",
"journal_pages": "119-43",
"pub_year": "2010",
"pubmed_id": "20064525"
},
{
"title": "Cloning and expression of a mureinolytic enzyme from the mycobacteriophage TM4.",
"abstract": "Abstract In this study, we describe the characterization, cloning, expression and purification of the lysin A gene of the mycobacteriophage TM4. The gene TM4_gp29 (gp29) is a 1644-bp gene that codes for a 58.6-kDa protein and contains peptidoglycan recognition protein, Zn-binding and amidase catalytic domains. The gene was cloned into Escherichia coli using the 'His-Tag' pQE60 vector. After affinity chromatography-mediated purification, the protein was concentrated and visualized using sodium dodecyl sulphate polyacrylamide gel electrophoresis. Evidence of peptidoglycan-degrading activity was observed initially by a chloroform assay and later by conventional zymogram analysis.",
"full_author_list": "Marine Henry, Máire Begley, Horst Neve, Fiona Maher, Reynolds Paul Ross, Olivia McAuliffe, Aidan Coffey, Jim M O'Mahony",
"short_author_list": "Henry M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20727013",
"journal": "FEMS microbiology letters",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2010",
"pubmed_id": "20727013"
},
{
"title": "In silico analysis of Ardmore, a novel mycobacteriophage isolated from soil.",
"abstract": "Ardmore is a novel mycobacteriophage isolated from a soil sample collected in County Waterford, Ireland. The genome of this phage has been fully sequenced and is composed of 52,141 bp of linear double stranded DNA with a GC content of 61.49%. 88 ORFs were identified of which 34 were assigned predicted functions based on their homology to previously characterised proteins, their location in the genome, computer-predicted structural characteristics or presence of conserved motifs in their sequence. The Ardmore genome appears highly similar to mycobacteriophages Fruitloop and Tweety with BLASTn analysis showing 87% and 80% identity respectively. A predicted beta-lactamase gene was detected in the sequence, and an unusual +1 frameshift event for the translation of tail genes was also observed.",
"full_author_list": "Marine Henry, Orla O'Sullivan, Roy D Sleator, Aidan Coffey, R Paul Ross, Olivia McAuliffe, Jim M O'Mahony",
"short_author_list": "Henry M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20064590",
"journal": "Gene",
"journal_volume": "453",
"journal_issue": "1-2",
"journal_pages": "9-23",
"pub_year": "2010",
"pubmed_id": "20064590"
},
{
"title": "[Expression and purification of lysin B in mycobacteriophage D29 and analysis of its enzymatic properties]",
"abstract": "LysinB (LysB) in mycobacteriophage D29 was cloned and expressed and its enzymatic properties were analysed. The lysB gene was amplified by PCR from mycobacteriophage D29 genomic DNA and inserted into pET22b vector. The constructed recombinant plasmid was transformed into Escherichia coli BL21(DE3) to express fusion protein, which was purified by Ni-NTA column and enzymatic activity detected. The results showed that expression plasmid pET22b-lysB was constructed successfully. Highly purified recombination protein (His-LysB) was obtained 33.2 mg from 1 L LB culture medium. A screening for His-LysB activity on esterase and lipase substrates confirmed the lipolytic activity. With p-nitrophenyl butyrate as substrate, the thermal stability of the enzyme was poor when the temperature was above 30 degrees C. The enzyme exhibited higher stability at pH 5.0-9.5. The optimum temperature and pH for the lipolytic activity of His-LysB were 23 degrees C and 7.5 respectively. Under the optimum conditions, the specific activity of His-LysB was 1.3 U/mg. Zn2+, CU2+, Mg2+, Mn2+ and phenylmethane sulfonyl fruoride severely inhibited the lipolytic activity of His-LysB. The result provides a new option for tuberculosis drug research and development.",
"full_author_list": "Lili Hou, Limei Hao, Jiancheng Qi, Ge Yang",
"short_author_list": "Hou L et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20575441",
"journal": "Sheng wu gong cheng xue bao = Chinese journal of biotechnology",
"journal_volume": "26",
"journal_issue": "4",
"journal_pages": "517-22",
"pub_year": "2010",
"pubmed_id": "20575441"
},
{
"title": "Taking phage integration to the next level as a genetic tool for mycobacteria.",
"abstract": "Genes must be stably integrated into bacterial chromosomes for complementation of gene deletion mutants in animal infection experiments or to express antigens in vaccine strains. However, with currently available vectors it is cumbersome to create multiple, stable, unmarked chromosomal integrations in mycobacteria. Here, we have constructed a novel integration vector for mycobacteria that enables expression of genes from a cassette protected from transcriptional interference by bi-directional transcriptional terminators proven to be highly efficient in in vitro transcription termination assays. Removal of the integrase gene by a site-specific recombinase, easily identifiable by loss of a backbone reporter gene, stabilizes the integration cassette and makes this vector ideally suitable for infection experiments. This integration vector can be easily adapted to different mycobacteriophage attachment sites (attB) due to its modular design. Integration of a gfp expression cassette at the L5, Giles and Ms6 attB sites in the chromosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis yielded identical gfp expression levels, indicating that none of these sites are compromised for gene expression. The copy number of pAL5000-based extrachromosomal plasmids is 23 in M. smegmatis as determined by quantitative real-time PCR and accounts for the previously observed drastic reduction of gene expression upon integration of plasmids into the chromosome of mycobacteria. Gfp expression and fluorescence of M. smegmatis and M. tuberculosis strains with multiple integrations of gfp increased concomitantly with the copy number demonstrating that these vectors can be used to generate stronger phenotypes and/or to analyze several genes simultaneously in vivo.",
"full_author_list": "Jason Huff, Agata Czyz, Robert Landick, Michael Niederweis",
"short_author_list": "Huff J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20692326",
"journal": "Gene",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2010",
"pubmed_id": "20692326"
},
{
"title": "Insights into the function of the WhiB-like protein of mycobacteriophage TM4--a transcriptional inhibitor of WhiB2.",
"abstract": "WhiB-like proteins of actinomycetes are known to co-ordinate iron-sulfur (Fe-S) clusters and are believed to have regulatory functions in many essential bacterial processes. The systematic determination of the genome sequences of mycobacteriophages has revealed the presence of several whiB-like genes in these viruses. Here we focussed on the WhiB-like protein of mycobacteriophage TM4, WhiBTM4. We provide evidence that this viral protein is capable of co-ordinating a Fe-S cluster. The UV-visible absorption spectra obtained from freshly purified and reconstituted WhiBTM4 were consistent with the presence of an oxygen sensitive [2Fe-2S] cluster. Expression of WhiBTM4 in the mycobacterial host led to hindered septation resembling a WhiB2 knockout phenotype whereas basal expression of WhiBTM4 led to superinfection exclusion. The quantification of mRNA-levels during phage infection showed that whiBTM4 is a highly transcribed early phage gene and a dominant negative regulator of WhiB2. Strikingly, both apo-WhiB2 of Mycobacterium tuberculosis and apo-WhiBTM4 were capable of binding to the conserved promoter region upstream of the whiB2 gene indicating that WhiB2 regulates its own synthesis which is inhibited in the presence of WhiBTM4. Thus, we provide substantial evidence supporting the hypothesis of viral and bacterial WhiB proteins being important Fe-S containing transcriptional regulators with DNA-binding capability.",
"full_author_list": "Jan Rybniker, Angela Nowag, Edeltraud van Gumpel, Nicole Nissen, Nirmal Robinson, Georg Plum, Pia Hartmann",
"short_author_list": "Rybniker J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20545868",
"journal": "Molecular microbiology",
"journal_volume": "77",
"journal_issue": "3",
"journal_pages": "642-57",
"pub_year": "2010",
"pubmed_id": "20545868"
},
{
"title": "Validation of a modified method for Bxb1 mycobacteriophage integrase-mediated recombination in Plasmodium falciparum by localization of the H-protein of the glycine cleavage complex to the mitochondrion.",
"abstract": "The glycine cleavage complex (GCV) is a potential source of the one carbon donor 5,10-methylene-tetrahydrofolate (5,10-CH(2)-THF) in the malaria parasite Plasmodium falciparum. One carbon (C1) donor units are necessary for amino acid and nucleotide biosynthesis, and for the initiation of mitochondrial and plastid translation. In other organisms, GCV activity is closely coordinated with the activity of serine hydroxymethyltransferase (SHMT) enzymes. P. falciparum contains cytosolic and mitochondrial SHMT isoforms, and thus, the subcellular location of the GCV is an important indicator of its role in malaria metabolism. To determine the subcellular localization of the GCV, we used a modified version of the published method for mycobacteriophage integrase-mediated recombination in P. falciparum to generate cell lines containing one of the component proteins of the GCV, the H-protein, fused to GFP. Here, we demonstrate that this modification results in rapid generation of chromosomally integrated transgenic parasites, and we show that the H-protein localizes to the mitochondrion.",
"full_author_list": "Maroya D Spalding, Marina Allary, John R Gallagher, Sean T Prigge",
"short_author_list": "Spalding MD et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20403390",
"journal": "Molecular and biochemical parasitology",
"journal_volume": "172",
"journal_issue": "2",
"journal_pages": "156-60",
"pub_year": "2010",
"pubmed_id": "20403390"
},
{
"title": "Genomics and bioinformatics in undergraduate curricula: Contexts for hybrid laboratory/lecture courses for entering and advanced science students",
"abstract": "Emerging interest in genomics in the scientific community prompted biologists at James Madison University to create two courses at different levels to modernize the biology curriculum. The courses are hybrids of classroom and laboratory experiences. An upper level class uses raw sequence of a genome (plasmid or virus) as the subject on which to base the experience of genomic analysis. Students also learn bioinformatics and software programs needed to support a project linking structure and function in proteins and showing evolutionary relatedness of similar genes. An optional entry-level course taken in addition to the required first-year curriculum and sponsored in part by the Howard Hughes Medical Institute, engages first year students in a primary research project. In the first semester, they isolate and characterize novel bacteriophages that infect soil bacteria. In the second semester, these young scientists annotate the genes on one or more of the unique viruses they discovered. These courses are demanding but exciting for both faculty and students and should be accessible to any interested faculty member.",
"full_author_list": "Temple L, Cresawn SG, Monroe JD.",
"short_author_list": "Temple L, Cresawn SG, Monroe JD.",
"article_url": "",
"journal": "Biochemistry and Molecular Biology Education",
"journal_volume": "38",
"journal_issue": "1",
"journal_pages": "23-8",
"pub_year": "2010",
"pubmed_id": "21567786"
},
{
"title": "Splicing of the mycobacteriophage Bethlehem DnaB intein: identification of a new mechanistic class of inteins that contain an obligate block F nucleophile.",
"abstract": "Inteins are single turnover enzymes that splice out of protein precursors during maturation of the host protein (extein). The Cys or Ser at the N terminus of most inteins initiates a four-step protein splicing reaction by forming a (thio)ester bond at the N-terminal splice junction. Several recently identified inteins cannot perform this acyl rearrangement because they do not begin with Cys, Thr, or Ser. This study analyzes one of these, the mycobacteriophage Bethlehem DnaB intein, which we describe here as the prototype for a new class of inteins based on sequence comparisons, reactivity, and mechanism. These Class 3 inteins are characterized by a non-nucleophilic N-terminal residue that co-varies with a non-contiguous Trp, Cys, Thr triplet (WCT) and a Thr or Ser as the first C-extein residue. Several mechanistic differences were observed when compared with standard inteins or previously studied atypical KlbA Ala(1) inteins: (a) cleavage at the N-terminal splice junction in the absence of all standard N- and C-terminal splice junction nucleophiles, (b) activation of the N-terminal splice junction by a variant Block B motif that includes the WCT triplet Trp, (c) decay of the branched intermediate by thiols or Cys despite an ester linkage at the C-extein branch point, and (d) an absolute requirement for the WCT triplet Block F Cys. Based on biochemical data and confirmed by molecular modeling, we propose roles for these newly identified conserved residues, a novel protein splicing mechanism that includes a second branched intermediate, and an intein classification with three mechanistic categories.",
"full_author_list": "Kazuo Tori, Bareket Dassa, Margaret A Johnson, Maurice W Southworth, Lear E Brace, Yoshizumi Ishino, Shmuel Pietrokovski, Francine B Perler",
"short_author_list": "Tori K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19940146",
"journal": "The Journal of biological chemistry",
"journal_volume": "285",
"journal_issue": "4",
"journal_pages": "2515-26",
"pub_year": "2010",
"pubmed_id": "19940146"
},
{
"title": "Antagonistic effects Na+ and Mg2+ on the structure, function, and stability of mycobacteriophage L1 repressor.",
"abstract": "Temperate mycobacteriophage L1 encodes an unusual repressor (CI) for regulating its lytic-lysogenic switching and, in contrast to the repressors of most temperate phages, it binds to multiple asymmetric operator DNAs. Here, ions like Na(+), Cl(-), and acetate(-) ions were demonstrated to facilitate the optimal binding of CI to cognate operator DNA, whereas K(+), Li(+), NH4(+), Mg(2+), carbonate(2-), and citrate(3-) ions significantly affected its operator binding activity. Of these ions, Mg(2+) unfolded CI most severely at room temperature and, compared to Mg(2+), Na(+) provided improved thermal stability to CI. Furthermore, the intrinsic tryptophan fluorescence of CI was changed notably upon replacing Na(+) with Mg(2+) and these opposing effects of Mg(2+) and Na(+) were also noticed in their actions on the C-terminal fragment (CTD) of CI. Taken together, Na(+) appeared to be more appropriate than Mg(2+) for maintaining the biologically active conformation of CI needed for its optimal binding to operator DNA.",
"full_author_list": "Amitava Bandhu, Tridib Ganguly, Palas K Chanda, Malabika Das, Biswanath Jana, Gopal Chakrabarti, Subrata Sau",
"short_author_list": "Bandhu A et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19470244",
"journal": "BMB reports",
"journal_volume": "42",
"journal_issue": "5",
"journal_pages": "293-8",
"pub_year": "2009",
"pubmed_id": "19470244"
},
{
"title": "Non-STEM undergraduates become enthusiastic phage-hunters",
"abstract": "To increase science literacy and appreciation among nonscience majors, we offered a course in which 20 non-STEM (science, technology, engineering, math) undergraduates participated in a unique, two-semester research experience. Each student isolated and characterized his or her own bacteriophage from soil samples. One bacteriophage was selected for sequencing and together, the class annotated the genome of the newly sequenced bacteriophage. The class produced a group poster and gave PowerPoint presentations, and one student presented the joint work at a science symposium",
"full_author_list": "Caruso SM, Sandoz J, Kelsey J.",
"short_author_list": "Caruso SM1, Sandoz J, Kelsey J.",
"article_url": "http://www.lifescied.org/content/8/4/278.long",
"journal": "CBE—Life Sciences Education",
"journal_volume": "Winter 8",
"journal_issue": "4",
"journal_pages": "278-82",
"pub_year": "2009",
"pubmed_id": "19952096"
},
{
"title": "Defects in glycopeptidolipid biosynthesis confer phage I3 resistance in Mycobacterium smegmatis.",
"abstract": "Mycobacteriophages have played an important role in the development of genetic tools and diagnostics for pathogenic mycobacteria, including Mycobacterium tuberculosis. However, despite the isolation of numerous phages that infect mycobacteria, the mechanisms of mycobacteriophage infection remain poorly understood, and knowledge about phage receptors is minimal. In an effort to identify the receptor for phage I3, we screened a library of Mycobacterium smegmatis transposon mutants for phage-resistant strains. All four phage I3-resistant mutants isolated were found to have transposon insertions in genes located in a cluster involved in the biosynthesis of the cell-wall-associated glycopeptidolipid (GPL), and consequently the mutants did not synthesize GPLs. The loss of GPLs correlated specifically with phage I3 resistance, as all mutants retained sensitivity to two other mycobacteriophages: D29 and Bxz1. In order to define the minimal receptor for phage I3, we then tested the phage sensitivity of previously described GPL-deficient mutants of M. smegmatis that accumulate biosynthesis intermediates of GPLs. The results indicated that, while the removal of most sugar residues from the fatty acyl tetrapeptide (FATP) core of GPL did not affect sensitivity to phage I3, a single methylated rhamnose, transferred by the rhamnosyltransferase Gtf2 to the FATP core, was critical for phage binding.",
"full_author_list": "Jiemin Chen, Jordan Kriakov, Albel Singh, William R Jacobs, Gurdyal S Besra, Apoorva Bhatt",
"short_author_list": "Chen J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19744987",
"journal": "Microbiology (Reading, England)",
"journal_volume": "155",
"journal_issue": "Pt 12",
"journal_pages": "4050-7",
"pub_year": "2009",
"pubmed_id": "19744987"
},
{
"title": "Comparison of the performances of two in-house rapid methods for antitubercular drug susceptibility testing.",
"abstract": "Resistance to rifampin (rifampicin), isoniazid, and streptomycin of 69 Mycobacterium tuberculosis isolates was analyzed by an in-house method based on mycobacteriophage D29 and a colorimetric micromethod. Both methods showed sensitivity and specificity values ranging from 93% to 100%. These simple methods offer an option for drug resistance assessment of M. tuberculosis.",
"full_author_list": "Agustina I de la Iglesia, Emma J Stella, Héctor R Morbidoni",
"short_author_list": "de la Iglesia AI, Stella EJ, Morbidoni HR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19015333",
"journal": "Antimicrobial agents and chemotherapy",
"journal_volume": "53",
"journal_issue": "2",
"journal_pages": "808-10",
"pub_year": "2009",
"pubmed_id": "19015333"
},
{
"title": "Optimization of a phage amplification assay to permit accurate enumeration of viable Mycobacterium avium subsp. paratuberculosis cells.",
"abstract": "A commercially available phage amplification assay, FASTPlaqueTB (Biotec Laboratories, Ipswich, United Kingdom), when used according to the manufacturer's instructions, does not permit accurate enumeration of Mycobacterium avium subsp. paratuberculosis. The aim of this study was to optimize the phage amplification assay conditions to permit accurate quantification of viable M. avium subsp. paratuberculosis cells. The burst time for M. avium subsp. paratuberculosis was initially determined to inform decisions about optimal incubation time before plating, and then other test parameters were altered to evaluate how the correlation between plaque and colony counts was affected. The D29 mycobacteriophage replicates more slowly in M. avium subsp. paratuberculosis than in Mycobacterium smegmatis (used to optimize the commercial test originally), and the mean burst time for four M. avium subsp. paratuberulosis strains was 210 +/- 36.8 min at 37 degrees C compared to 63 +/- 17.5 min for M. smegmatis mc(2) 155. To achieve 100% correlation between plaque and colony counts, the optimized phage assay includes the following: (i) resuspension of the samples to be tested in Middlebrook 7H9 broth containing 10% oleic acid-albumin-dextrose-catalase and 2 mM calcium chloride, followed by overnight incubation at 37 degrees C before performance of the phage assay; (ii) a 2-h incubation of the sample with D29 mycobacteriophage before viricide treatment; and (iii) a further 90-min incubation after viricide treatment and neutralization up to the burst time (total incubation time, 210 min) before plating with M. smegmatis mc(2) 155 in 7H9 agar. The optimized phage amplification assay was able to detect 1 to 10 CFU/ml of M. avium subsp. paratuberculosis in spiked milk or broth within 48 h, as demonstrated by the results of several blind trials.",
"full_author_list": "Antonio Foddai, Christopher T Elliott, Irene R Grant",
"short_author_list": "Foddai A, Elliott CT, Grant IR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19395561",
"journal": "Applied and environmental microbiology",
"journal_volume": "75",
"journal_issue": "12",
"journal_pages": "3896-902",
"pub_year": "2009",
"pubmed_id": "19395561"
},
{
"title": "The mycobacteriophage D29 gene 65 encodes an early-expressed protein that functions as a structure-specific nuclease.",
"abstract": "The genomes of mycobacteriophages of the L5 family, which includes the lytic phage D29, contain several genes putatively linked to DNA synthesis. One such gene is 65, which encodes a protein belonging to the RecA/DnaB helicase superfamily. In this study a recombinant version of the mycobacteriophage D29 gp65 was functionally characterized. The results indicated that it is not a helicase as predicted but an exonuclease that removes 3' arms from forked structures in an ATP-dependent manner. The gp65 exonuclease acts progressively from the 3' end, until the fork junction is reached. As it goes past, its progress is stalled over a stretch of seven to eight nucleotides immediately downstream of the junction. It efficiently acts on forked structures with single stranded arms. It also acts upon 5' and 3' flaps, though with somewhat relaxed specificity, but not on double-stranded forks. Sequence comparison revealed the presence of a KNRXG motif in the C-terminal half of the protein. This is a conserved element found in the RadA/Sms family of DNA repair proteins. A mutation (R203G) in this motif led to complete loss of nuclease activity. This indicated that KNRXG plays an important role in the nuclease function of not only gp65, but possibly other RadA/Sms family proteins as well. This is the first characterization of a bacteriophage-derived RadA/Sms class protein. Given its mode of action, it is very likely that gp65 is involved in processing branched replication intermediates formed during the replication of phage DNA.",
"full_author_list": "Nabanita Giri, Priyanka Bhowmik, Bidisha Bhattacharya, Mahashweta Mitra, Sujoy K Das Gupta",
"short_author_list": "Giri N et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19028888",
"journal": "Journal of bacteriology",
"journal_volume": "191",
"journal_issue": "3",
"journal_pages": "959-67",
"pub_year": "2009",
"pubmed_id": "19028888"
},
{
"title": "Synonymous codon usage analysis of thirty two mycobacteriophage genomes.",
"abstract": "Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.",
"full_author_list": "Sameer Hassan, Vasantha Mahalingam, Vanaja Kumar",
"short_author_list": "Hassan S, Mahalingam V, Kumar V",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20150956",
"journal": "Advances in bioinformatics",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "316936",
"pub_year": "2009",
"pubmed_id": "20150956"
},
{
"title": "Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction",
"abstract": "Translational initiation region of bacteriophage T4 gene 25 contains three potential Shine and Dalgarno sequences: SD1, SD2 and SD3. Mutational analysis has predicted that an mRNA stem-loop structure may include SD1 and SD2, bringing the most typical sequence SD3, GAGG, to the initiation codon. Here, we report physical evidence demonstrating that previously predicted mRNA stem-loop structure indeed exists in vivo during gene 25 expression in T4-infected Escherichia coli cells. The second mRNA stem-loop structure is identified 14 nucleotides upstream of the stem-loop I, while the SD3 sequence, as well as the start codon of the gene, are proved to be within an unfolded stretch of mRNA. Phylogenetic comparison of 38 T4-like phages reveals that the T-even and some pseudoT-even phages evolve a similar structural strategy for the translation initiation of 25, while pseudoT-even, schizoT-even and exoT-even phages use an alternative mRNA arrangement. Taken together, the results indicate that a specific mRNA fold forms the split ribosome binding site at the gene 26-25 intercistronic junction, which is highly competent in the translational initiation. We conclude that this ribosome binding site has evolved after T-even diverged from other T4-like phages. Additionally, we determine that the SD sequence GAGG is most widespread in T4.\r\n",
"full_author_list": "Malys N, Nivinskas R.\r\n",
"short_author_list": "Malys N, Nivinskas R.",
"article_url": "",
"journal": "Molecular Microbiology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2009",
"pubmed_id": "19708923"
},
{
"title": "Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase.",
"abstract": "Mycobacteriophages encounter a unique problem among phages of Gram-positive bacteria, in that lysis must not only degrade the peptidoglycan layer but also circumvent a mycolic acid-rich outer membrane covalently attached to the arabinogalactan-peptidoglycan complex. Mycobacteriophages accomplish this by producing two lysis enzymes, Lysin A (LysA) that hydrolyses peptidoglycan, and Lysin B (LysB), a novel mycolylarabinogalactan esterase, that cleaves the mycolylarabinogalactan bond to release free mycolic acids. The D29 LysB structure shows an alpha/beta hydrolase organization with a catalytic triad common to cutinases, but which contains an additional four-helix domain implicated in the binding of lipid substrates. Whereas LysA is essential for mycobacterial lysis, a Giles DeltalysB mutant mycobacteriophage is viable, but defective in the normal timing, progression and completion of host cell lysis. We propose that LysB facilitates lysis by compromising the integrity of the mycobacterial outer membrane linkage to the arabinogalactan-peptidoglycan layer.",
"full_author_list": "Kimberly Payne, Qingan Sun, James Sacchettini, Graham F Hatfull",
"short_author_list": "Payne K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19555454",
"journal": "Molecular microbiology",
"journal_volume": "73",
"journal_issue": "3",
"journal_pages": "367-81",
"pub_year": "2009",
"pubmed_id": "19555454"
},
{
"title": "Fluoromycobacteriophages for rapid, specific, and sensitive antibiotic susceptibility testing of Mycobacterium tuberculosis.",
"abstract": "Rapid antibiotic susceptibility testing of Mycobacterium tuberculosis is of paramount importance as multiple- and extensively-drug resistant strains of M. tuberculosis emerge and spread. We describe here a virus-based assay in which fluoromycobacteriophages are used to deliver a GFP or ZsYellow fluorescent marker gene to M. tuberculosis, which can then be monitored by fluorescent detection approaches including fluorescent microscopy and flow cytometry. Pre-clinical evaluations show that addition of either Rifampicin or Streptomycin at the time of phage addition obliterates fluorescence in susceptible cells but not in isogenic resistant bacteria enabling drug sensitivity determination in less than 24 hours. Detection requires no substrate addition, fewer than 100 cells can be identified, and resistant bacteria can be detected within mixed populations. Fluorescence withstands fixation by paraformaldehyde providing enhanced biosafety for testing MDR-TB and XDR-TB infections.",
"full_author_list": "Mariana Piuri, William R Jacobs, Graham F Hatfull",
"short_author_list": "Piuri M, Jacobs WR, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19300517",
"journal": "PloS one",
"journal_volume": "4",
"journal_issue": "3",
"journal_pages": "e4870",
"pub_year": "2009",
"pubmed_id": "19300517"
},
{
"title": "Transfer, stable maintenance and expression of the mycolactone polyketide megasynthase mls genes in a recombination-impaired Mycobacterium marinum.",
"abstract": "The human pathogen Mycobacterium ulcerans produces a polyketide metabolite called mycolactone with potent immunomodulatory activity. M. ulcerans strain Agy99 has a 174 kb plasmid called pMUM001 with three large genes (mlsA1, 51 kb; mlsA2, 7.2 kb; mlsB, 43 kb) that encode type I polyketide synthases (PKS) required for the biosynthesis of mycolactone, as demonstrated by transposon mutagenesis. However, there have been no reports of transfer of the mls locus to another mycobacterium to demonstrate that these genes are sufficient for mycolactone production because in addition to their large size, the mls genes contain a high level of internal sequence repetition, such that the entire 102 kb locus is composed of only 9.5 kb of unique DNA. The combination of their large size and lack of stability during laboratory passage makes them a challenging prospect for transfer to a more rapidly growing and genetically tractable host. Here we describe the construction of two bacterial artificial chromosome Escherichia coli/Mycobacterium shuttle vectors, one based on the pMUM001 origin of replication bearing mlsB, and the other based on the mycobacteriophage L5 integrase, bearing mlsA1 and mlsA2. The combination of these two constructs permitted the two-step transfer of the entire 174 kb pMUM001 plasmid to Mycobacterium marinum, a rapidly growing non-mycolactone-producing mycobacterium that is a close genetic relative of M. ulcerans. To improve the stability of the mls locus in M. marinum, recA was inactivated by insertion of a hygromycin-resistance gene using double-crossover allelic exchange. As expected, the DeltarecA mutant displayed increased susceptibility to UV killing and a decreased frequency of homologous recombination. Southern hybridization and RT-PCR confirmed the stable transfer and expression of the mls genes in both wild-type M. marinum and the recA mutant. However, neither mycolactone nor its predicted precursor metabolites were detected in either strain. These experiments show that it is possible to successfully manipulate and stably transfer the large mls genes, but that other bacterial host factors appear to be required to facilitate mycolactone production.",
"full_author_list": "Jessica L Porter, Nicholas J Tobias, Hui Hong, Kellie L Tuck, Grant A Jenkin, Timothy P Stinear",
"short_author_list": "Porter JL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19383681",
"journal": "Microbiology (Reading, England)",
"journal_volume": "155",
"journal_issue": "Pt 6",
"journal_pages": "1923-33",
"pub_year": "2009",
"pubmed_id": "19383681"
},
{
"title": "Clinical evaluation of the mycobacteriophage-based assay in rapid detection of Mycobacterium tuberculosis in respiratory specimens.",
"abstract": "CONTEXT: Search for a cost-effective, rapid and accurate test has renewed interest in mycobacteriophage as a tool in the diagnosis of tuberculosis (TB). There has been no reported data on the performance of phage assay in a high burden, low-resource setting like Kanpur city, India. AIMS: To assess the sensitivity and specificity of the FASTPlaque TB kit ability to impact the bacillary load in the phage assay and its performance in the sputum smear sample negative cases. MATERIALS AND METHODS: The study involved a cross-sectional blinded assessment of phage assay using the FASTPlaque TB kit on 68 suspected cases of pulmonary TB against sputum smear microscopy by Ziehl-Neilsen staining and culture by the LJ method. RESULTS: The sensitivity, specificity and positive and negative predictive values of the phage assay were 90.7, 96, 97.5 and 85.7%, respectively. The assay was negative in all the five specimens growing mycobacteria other than TB. The sensitivity of the phage assay tended to decrease with the bacillary load. Of the smear-negative cases, three were false negative, and all of which were detected by the phage assay. Smear microscopy (three smears per patient) had a sensitivity and specificity of 93 and 64%, respectively. CONCLUSIONS: The phage assay has the potential clinical utility as a simple means of rapid and accurate detection of live Mycobacterium tuberculosis bacilli; however, its performance has been inconsistent across various studies, which highlights that the assay requires a high degree of quality control demanding infrastructure and its performance is vulnerable to common adversities observed in \"out of research\" practice settings like storage, transport and cross-contamination.",
"full_author_list": "S Prakash, S K Katiyar, S Purwar, J P Singh",
"short_author_list": "Prakash S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19384036",
"journal": "Indian journal of medical microbiology",
"journal_volume": "27",
"journal_issue": "2",
"journal_pages": "134-8",
"pub_year": "2009",
"pubmed_id": "19384036"
},
{
"title": "Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements.",
"abstract": "Mycobacteriophages BPs, Angel and Halo are closely related viruses isolated from Mycobacterium smegmatis, and possess the smallest known mycobacteriophage genomes, 41,901 bp, 42,289 bp and 41,441 bp, respectively. Comparative genome analysis reveals a novel class of ultra-small mobile genetic elements; BPs and Halo each contain an insertion of the proposed mobile elements MPME1 and MPME2, respectively, at different locations, while Angel contains neither. The close similarity of the genomes provides a comparison of the pre- and post-integration sequences, revealing an unusual 6 bp insertion at one end of the element and no target duplication. Nine additional copies of these mobile elements are identified in a variety of different contexts in other mycobacteriophage genomes. In addition, BPs, Angel and Halo have an unusual lysogeny module in which the repressor and integrase genes are closely linked. The attP site is located within the repressor-coding region, such that prophage formation results in expression of a C-terminally truncated, but active, form of the repressor.",
"full_author_list": "Timothy Sampson, Gregory W Broussard, Laura J Marinelli, Deborah Jacobs-Sera, Mondira Ray, Ching-Chung Ko, Daniel Russell, Roger W Hendrix, Graham F Hatfull",
"short_author_list": "Sampson T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19556295",
"journal": "Microbiology (Reading, England)",
"journal_volume": "155",
"journal_issue": "Pt 9",
"journal_pages": "2962-77",
"pub_year": "2009",
"pubmed_id": "19556295"
},
{
"title": "Comparison of the performance of two mycobacteriophage D29-based protocols for fluoroquinolone susceptibility testing in Mycobacterium tuberculosis.",
"abstract": "We tested a mycobacteriophage D29-based method for fluoroquinolone susceptibility assessment in clinical isolates of Mycobacteriumtuberculosis. The method was incapable of identifying susceptible strains as such, although a slightly different published protocol successfully identified resistant and susceptible strains. Thus, caution is necessary when choosing an \"in-house\" D29-based protocol for testing of drug resistance.",
"full_author_list": "Emma J Stella, Agustina I de la Iglesia, Héctor R Morbidoni",
"short_author_list": "Stella EJ, de la Iglesia AI, Morbidoni HR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19846046",
"journal": "Journal of microbiological methods",
"journal_volume": "79",
"journal_issue": "3",
"journal_pages": "371-3",
"pub_year": "2009",
"pubmed_id": "19846046"
},
{
"title": "Mycobacteriophages as versatile tools for genetic manipulation of mycobacteria and development of simple methods for diagnosis of mycobacterial diseases.",
"abstract": "Tuberculosis, caused by Mycobacterium tuberculosis, is responsible for over two million deaths per year worldwide. Due to its long doubling time (18 h), the microbiological detection of M. tuberculosis by conventional methods takes up to one month, unless the number of bacilli in the biological sample is high enough. Thus, drug resistance assessment requires at least one month for obtaining the primary culture and another month to determine its susceptibility to antimycobacterial drugs. Moreover, for a long time, the lack of genetic tools for mycobacteria has been a barrier for undertaking studies aimed at understanding the mechanisms of drug resistance and drug target identification, being all these topics of utmost importance considering the increase in the number of drug-resistant clones and the few therapeutic options available. Mycobacteriophages are promising as a novel source of genetic elements for mycobacteria manipulation, as well as for the development of versatile, simple, fast and cheap methods for drug resistance assessment of M. tuberculosis clinical isolates. We herein describe the background related to the use of mycobacteriophages, with emphasis placed on their utilization for drug resistance analysis in our country.",
"full_author_list": "E J Stella, A I de la Iglesia, H R Morbidoni",
"short_author_list": "Stella EJ, de la Iglesia AI, Morbidoni HR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19391526",
"journal": "Revista Argentina de microbiología",
"journal_volume": "41",
"journal_issue": "1",
"journal_pages": "45-55",
"pub_year": "2009",
"pubmed_id": "19391526"
},
{
"title": "Bacteriophage-encoded functions engaged in initiation of homologous recombination events.",
"abstract": "Recombination plays a significant role in bacteriophage biology. Functions promoting recombination are involved in key stages of phage multiplication and drive phage evolution. Their biological role is reflected by the great variety of phages existing in the environment. This work presents the role of recombination in the phage life cycle and highlights the discrete character of phage-encoded recombination functions (anti-RecBCD activities, 5' --> 3' DNA exonucleases, single-stranded DNA binding proteins, single-stranded DNA annealing proteins, and recombinases). The focus of this review is on phage proteins that initiate genetic exchange. Importance of recombination is reviewed based on the accepted coli-phages T4 and lambda models, the recombination system of phage P22, and the recently characterized recombination functions of Bacillus subtilis phage SPP1 and mycobacteriophage Che9c. Key steps of the molecular mechanisms involving phage recombination functions and their application in molecular engineering are discussed.",
"full_author_list": "Agnieszka K Szczepa?ska",
"short_author_list": "Szczepa?ska AK",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19563302",
"journal": "Critical reviews in microbiology",
"journal_volume": "35",
"journal_issue": "3",
"journal_pages": "197-220",
"pub_year": "2009",
"pubmed_id": "19563302"
},
{
"title": "[Establishment and evaluation of nitrate reductase combined with mycobacteriophage assay]",
"abstract": "OBJECTIVE: To establish a rapid, inexpensive, and simple drug susceptibility test (DST) for Mycobacterium tuberculosis (M. tb) and evaluate its feasibility. METHOD: We used nitrate reductase combined with mycobacteriophage assay (PhaB-NRA) to test 49 clinical M. tb isolates of, and the results were compared with those of PhaB-NRA and traditional absolute concentration method. RESULTS: The sensitivity, specificity, and accuracy of PhaB-NRA for rifampicin were 89.1%, 91.67%, and 89.8%; on the contrary, those of isonicotinyl hydrazide were 86.21%, 90.0%, and 87.8%, respectively. The coincidence between PhaB-NRA and traditional assay were 0.746 for rifampicin and 0.750 for isonicotinyl hydrazide. CONCLUSIONS: PhaB-NRA is an inexpensive, rapid, and simple DST method. It is a promising rapid screening technique for DST of M. tb.",
"full_author_list": "Ai-Ying Xing, Zhong-Quan Liu, Hong-Yan Jia, Shu-Xiang Gu, Zong-De Zhang",
"short_author_list": "Xing AY et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/19771725",
"journal": "Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae",
"journal_volume": "31",
"journal_issue": "4",
"journal_pages": "413-6",
"pub_year": "2009",
"pubmed_id": "19771725"
},
{
"title": "Cost-effectiveness analysis of introduction of rapid, alternative methods to identify multidrug-resistant tuberculosis in middle-income countries.",
"abstract": "BACKGROUND: Resistance to commonly used antituberculosis drugs is emerging worldwide. Conventional drug-susceptibility testing (DST) methods are slow and demanding. Alternative, rapid DST methods would permit the early detection of drug resistance and, in turn, arrest tuberculosis transmission. METHODS: A cost-effectiveness analysis of 5 DST methods was performed in the context of a clinical trial that compared rapid with conventional DST methods. The methods under investigation were direct phage-replication assay (FASTPlaque-Response; Biotech), direct amplification and reverse hybridization of the rpoB gene (INNO-LiPA; Innogenetics), indirect colorimetric minimum inhibitory concentration assay (MTT; ICN Biomedicals), and direct proportion method on Löwenstein-Jensen medium. These were compared with the widely used indirect proportion method on Löwenstein-Jensen medium. RESULTS: All alternative DST methods were found to be cost-effective, compared with other health care interventions. DST methods also generate substantial cost savings in settings of high prevalence of multidrug-resistant tuberculosis. Excluding the effects of transmission, the direct proportion method on Löwenstein-Jensen medium was the most cost-effective alternative DST method for patient groups with prevalences of multidrug-resistant tuberculosis of 2%, 5%, 20%, and 50% (cost in US$2004, $94, $36, $8, and $2 per disability-adjusted life year, respectively). CONCLUSION: Alternative, rapid methods for DST are cost-effective and should be considered for use by national tuberculosis programs in middle-income countries.",
"full_author_list": "Carlos Acuna-Villaorduna, Anna Vassall, German Henostroza, Carlos Seas, Humberto Guerra, Lucy Vasquez, Nora Morcillo, Juan Saravia, Richard O'Brien, Mark D Perkins, Jane Cunningham, Luis Llanos-Zavalaga, Eduardo Gotuzzo",
"short_author_list": "Acuna-Villaorduna C et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18636955",
"journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America",
"journal_volume": "47",
"journal_issue": "4",
"journal_pages": "487-95",
"pub_year": "2008",
"pubmed_id": "18636955"
},
{
"title": "Evaluation of a semi-automated reporter phage assay for susceptibility testing of Mycobacterium tuberculosis isolates in South Africa.",
"abstract": "In a prospective study conducted by laboratory technologists in a diagnostic laboratory in Cape Town, South Africa, a semi-automated phage-based antibiotic susceptibility assay was implemented and the performance of the luciferase reporter mycobacteriophage (LRP) system for susceptibility testing of clinical Mycobacterium tuberculosis complex (MTC) isolates against rifampin and isoniazid was evaluated. Two hundred consecutive clinical MGIT cultures of MTC species were included in this study. Antibiotic susceptibility assays were set up manually for the LRP and BACTEC radiometric systems (BACTEC) and read in a plate luminometer and the BACTEC 460 instrument, respectively. Discrepant susceptibility results were resolved by the conventional agar proportion method. Of the 200 secondary cultures prepared for this study, 9 (4.5%) were lost to contamination (LRP 4, BACTEC 1, both 4). All of the remaining 191 cultures underwent susceptibility testing by both methods and the overall agreement between the LRP and BACTEC was 98.4% (rifampin 100%; isoniazid 96.9%). Of the 6 discrepant cultures tested by the agar proportion method, 2 gave results in agreement with the LRP. The sensitivity of the LRP for detection of drug-resistant isolates was 100% for both rifampin (n=9) and isoniazid (n=12). The median turnaround time for susceptibility testing was 2 days with the LRP and 9 days with BACTEC. In conclusion, the semi-automated LRP-based assay offers a rapid and practical approach for accurate susceptibility testing of M. tuberculosis cultures in diagnostic laboratories with limited financial resources, but with competent technologists.",
"full_author_list": "Niaz Banaiee, Vanessa January, Charmaine Barthus, Maureen Lambrick, Denise Roditi, Marcel A Behr, William R Jacobs, Lafras M Steyn",
"short_author_list": "Banaiee N et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17980664",
"journal": "Tuberculosis (Edinburgh, Scotland)",
"journal_volume": "88",
"journal_issue": "1",
"journal_pages": "64-8",
"pub_year": "2008",
"pubmed_id": "17980664"
},
{
"title": "Cloning, characterization and expression analysis of nucleotide metabolism-related genes of mycobacteriophage L5.",
"abstract": "The genomes of mycobacteriophages of the L5 family, which includes the lytic phage D29, contain several genes putatively linked to nucleotide-metabolizing functions. Two such genes, 48 and 50, encoding thymidylate synthase and ribonucleotide reductase (RNR), respectively, were overexpressed in Escherichia coli and the recombinant proteins were biochemically characterized. It was established that Gp50 was a class II RNR having properties similar to that of the corresponding enzyme from Lactobacillus leichmanni, whereas Gp48 was a flavin-dependent thymidylate synthase (ThyX) that resembled the Paramecium bursaria chlorella virus-1 ThyX enzyme in its properties. That both these proteins play a role in phage development was evident from the observation that they were detectable soon after the lytic phase of growth commenced. Gp48 and 50 were also found to coimmunoprecipitate, which indicates the possible existence of an L5 thymidylate synthase complex. Thymidylate synthase assays revealed that during the intracellular stage of phage growth, a significant decrease in the host thymidylate synthase (ThyA) activity occurred. It appears that synthesis of the viral enzyme (ThyX) is necessary to compensate for this loss in activity. In general, the results suggest that phage-encoded nucleotide metabolism-related functions play an important role in the lytic propagation of L5 and related mycobacteriophages.",
"full_author_list": "Bidisha Bhattacharya, Nabanita Giri, Mahasweta Mitra, Sujoy K Das Gupta",
"short_author_list": "Bhattacharya B et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18248423",
"journal": "FEMS microbiology letters",
"journal_volume": "280",
"journal_issue": "1",
"journal_pages": "64-72",
"pub_year": "2008",
"pubmed_id": "18248423"
},
{
"title": "Evaluation of the usefulness of phage amplification technology in the diagnosis of patients with paucibacillary tuberculosis.",
"abstract": "The present study was undertaken to assess the performance of the Fast Plaque TB(TM) (FPTB) test in the diagnostically difficult group of paucibacillary tuberculosis (TB) and to compare its results with the conventional bacteriological methods. The study was conducted on a total of 139 patients, who were negative for TB in sputum-smear examination. Bronchoalveolar lavage (BAL) or pleural biopsy specimens collected from these patients were subjected to smear examination, LJ culture and FPTB test. The smear, culture and the FPTB positivity rates were compared between patients with pulmonary and pleuro-pulmonary involvement. The FPTB test was found to register an overall sensitivity of 58.8% and specificity of 97.9%. The positive and negative predictive values of the test were 98.1 and 56.5, respectively. Among patients with paucibacillary TB, on head-to-head comparison, we found that the sensitivity and specificity values of the FPTB test were marginally better than smear-microscopy and inferior to culture on LJ media.",
"full_author_list": "D Biswas, A Deb, P Gupta, R Prasad, K S Negi",
"short_author_list": "Biswas D et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18227605",
"journal": "Indian journal of medical microbiology",
"journal_volume": "26",
"journal_issue": "1",
"journal_pages": "75-8",
"pub_year": "2008",
"pubmed_id": "18227605"
},
{
"title": "Overexpression of a delayed early gene hlg1 of temperate mycobacteriophage L1 is lethal to both M. smegmatis and E. coli.",
"abstract": "Two genes of temperate mycobacteriophage L5, namely, gp63 and gp64, were hypothesized to be toxic to M. smegmatis. An identical L5 gp64 ortholog (designated hlg1) was cloned from homoimmune mycobacteriophage L1 and characterized at length here. As expected, hlg1 affected the growth of M. smegmatis when overexpressed from a resident plasmid. HLG1 (the protein encoded by hlg1) in fact caused growth retardation of M. smegmatis and the region encompassing its 57-114 C-terminal amino acid residues was found indispensable for its growth-retardation activity. Both nucleic acid and protein biosynthesis were severely impaired in M. smegmatis expressing HLG1. Interestingly, HLG1 also affected E. coli almost similarly. This putative delayed early lipoprotein did not participate in the lytic growth of L1.",
"full_author_list": "Partho Chattoraj, Tridib Ganguly, Ranjan Kumar Nandy, Subrata Sau",
"short_author_list": "Chattoraj P et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18510866",
"journal": "BMB reports",
"journal_volume": "41",
"journal_issue": "5",
"journal_pages": "363-8",
"pub_year": "2008",
"pubmed_id": "18510866"
},
{
"title": "Genome sequence of the lytic bacteriophage P1201 from Corynebacterium glutamicum NCHU 87078: evolutionary relationships to phages from Corynebacterineae.",
"abstract": "P1201 is a lytic corynephage of Corynebacterium glutamicum NCHU 87078. Its genome consists of a linear double-stranded DNA molecule of 70,579 base pairs, with 3'-protruding cohesive ends of ten nucleotides. We have identified 69 putative open reading frames, including three apparent genes (thymidylate synthase, terminase, and RNR alpha subunit genes) that are interrupted by an intein. Protein-splicing activities of these inteins were demonstrated in Escherichia coli. Three structural proteins including major capsid and major tail proteins were separated by SDS-PAGE and identified by both LC-MS-MS and N-terminal sequence analyses. Bioinformatics analysis indicated that only about 8.7% of its putative gene products shared substantial protein sequence similarity with the lytic corynephage BFK20 from Brevibacterium flavum, the only corynephage whose genome had been sequenced to date, revealing that the P1201 genome is distinct from BFK20. The mosaic-like genome of P1201 indicates extensive horizontal gene transfer among P1201, Gordonia terrae phage GTE5, mycobacteriophages, and several regions of Corynebacterium spp. genomes.",
"full_author_list": "Chang-Lin Chen, Tzu-Ying Pan, Shu-Chen Kan, Yi-Chia Kuan, Lian-Yu Hong, Kun-Ruei Chiu, Ching-Sen Sheu, Jui-Sen Yang, Wen-Hwei Hsu, Hui-Yu Hu",
"short_author_list": "Chen CL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18599103",
"journal": "Virology",
"journal_volume": "378",
"journal_issue": "2",
"journal_pages": "226-32",
"pub_year": "2008",
"pubmed_id": "18599103"
},
{
"title": "Construction and evaluation of luciferase reporter phages for the detection of active and non-replicating tubercle bacilli.",
"abstract": "The luciferase reporter phages (LRP) show great promise for diagnostic mycobacteriology. Though conventional constructs developed from lytic phages such as D29 and TM4 are highly specific, they lack sensitivity. We have isolated and characterized Che12, the first true temperate phage infecting M. tuberculosis. Since the tuberculosis (TB) cases among HIV infected population result from the reactivation of latent bacilli, it would be useful to develop LRP that can detect dormant bacteria. During dormancy, pathogenic mycobacteria switch their metabolism involving divergent genes than during normal, active growth phase. Since the promoters of these genes can potentially function during dormancy, they were exploited for the construction of novel mycobacterial luciferase reporter phages. The promoters of hsp60, isocitrate lyase (icl), and alpha crystallin (acr) genes from M. tuberculosis were used for expressing firefly luciferase gene (FFlux) in both Che12 and TM4 phages and their efficiency was evaluated in detecting dormant bacteria from clinical isolates of M. tuberculosis. These LRP constructs exhibited detectable luciferase activity in dormant as well as in actively growing M. tuberculosis. The TM4 ts mutant based constructs showed about one log increase in light output in three of the five tested clinical isolates and in M. tuberculosis H37Rv compared to conventional lytic reporter phage, phAE129. By refining the LRP assay format further, an ideal rapid assay can be designed not only to diagnose active and dormant TB but also to differentiate the species and to find their drug susceptibility pattern.",
"full_author_list": "Azger Dusthackeer, Vanaja Kumar, Selvakumar Subbian, Gomathi Sivaramakrishnan, Guofang Zhu, Balaji Subramanyam, Sameer Hassan, Selvakumar Nagamaiah, John Chan, Narayanan Paranji Rama",
"short_author_list": "Dusthackeer A et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18272245",
"journal": "Journal of microbiological methods",
"journal_volume": "73",
"journal_issue": "1",
"journal_pages": "18-25",
"pub_year": "2008",
"pubmed_id": "18272245"
},
{
"title": "Tape measure protein having MT3 motif facilitates phage entry into stationary phase cells of Mycobacterium tuberculosis.",
"abstract": "Tape measure protein (TMP) having MT3 motif in mycobacteriophage TM4 genome has been reported to enable the phage infection of Mycobacterium smegmatis during stationary phase. In the present work looking at eight additional mycobacteriophage genomes by in silico analysis, six of them have been found to possess MT3 motif in TMP. The absence of MT3 motif in Che12 and D29 probably makes them incapable of infecting stationary phase cells of Mycobacterium tuberculosis which was experimentally evaluated by the performance of respective luciferase reporter phage constructs developed from the parental phages Che12, D29 and TM4.",
"full_author_list": "Azger Dusthackeer, V N Sameer Hassan, Vanaja Kumar",
"short_author_list": "Dusthackeer A, Hassan VN, Kumar V",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18479969",
"journal": "Computational biology and chemistry",
"journal_volume": "32",
"journal_issue": "5",
"journal_pages": "367-9",
"pub_year": "2008",
"pubmed_id": "18479969"
},
{
"title": "Two-step site selection for serine-integrase-mediated excision: DNA-directed integrase conformation and central dinucleotide proofreading.",
"abstract": "Bacteriophage-encoded serine-integrases are members of the large family of serine-recombinases and catalyze site-specific integrative recombination between a phage attP site and a bacterial attB site to form an integrated prophage. Prophage excision involves a second site-specific recombination event, in which the sites generated by integration, attL and attR, are used as substrates to regenerate attP and attB. Excision is catalyzed by integrase but also requires a phage-encoded recombination directionality factor (RDF). The Bxb1 recombination sites, attP and attB, are small (<50 bp), different in sequence, and quasisymmetrical, and they give rise to attL- and attR-recombinant products that are asymmetric but similar to each other, each being composed of B- and P-type half-sites. We show here that the determination of correct excision products is a two-step process, with a presynaptic RDF-dependent step that aligns attL and attR in the correct orientation and a postsynaptic step in which the nonpalindromic central dinucleotide confers identity to attL and attR and prevents each from recombining with itself.",
"full_author_list": "Pallavi Ghosh, Lori A Bibb, Graham F Hatfull",
"short_author_list": "Ghosh P, Bibb LA, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18299577",
"journal": "Proceedings of the National Academy of Sciences of the United States of America",
"journal_volume": "105",
"journal_issue": "9",
"journal_pages": "3238-43",
"pub_year": "2008",
"pubmed_id": "18299577"
},
{
"title": "The lytic cassette of mycobacteriophage Ms6 encodes an enzyme with lipolytic activity.",
"abstract": "dsDNA bacteriophages use the dual system endolysin-holin to achieve lysis of their bacterial host. In addition to these two essential genes, some bacteriophages encode additional proteins within their lysis module. In this report, we describe the activity of a protein encoded by gene lysB from the mycobacteriophage Ms6. lysB is localized within the lysis cassette, between the endolysin gene (lysA) and the holin gene (hol). Analysis of the deduced amino acid sequence of LysB revealed the presence of a conserved motif (Gly-Tyr-Ser-Gln-Gly) characteristic of enzymes with lipolytic activity. A blast search within the sequences of protein databases revealed significant similarities to other putative proteins that are encoded by mycobacteriophages only, indicating that LysB and those proteins may be specific to their mycobacterial hosts. A screening for His(6)-LysB activity on esterase and lipase substrates confirmed the lipolytic activity. Examination of the kinetic parameters of recombinant His(6)-LysB for the hydrolysis of p-nitrophenyl esters indicated that although this protein could use a wide range of chain length substrates (C(4)-C(18)), it presents a higher affinity for p-nitrophenyl esters of longer chain length (C(16) and C(18)). Using p-nitrophenyl butyrate as a substrate, the enzyme showed optimal activity at 23 degrees C and pH 7.5-8.0. Activity was increased in the presence of Ca(2+) and Mn(2+). To the best of our knowledge, this is the first description of a protein with lipolytic activity encoded within a bacteriophage.",
"full_author_list": "Filipa Gil, Maria João Catalão, José Moniz-Pereira, Paula Leandro, Michael McNeil, Madalena Pimentel",
"short_author_list": "Gil F et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18451045",
"journal": "Microbiology (Reading, England)",
"journal_volume": "154",
"journal_issue": "Pt 5",
"journal_pages": "1364-71",
"pub_year": "2008",
"pubmed_id": "18451045"
},
{
"title": "Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution.",
"abstract": "The recognition of the vast numbers of bacteriophages in the biosphere has prompted a renewal of interest in understanding their morphological and genetic diversity, and elucidating the evolutionary mechanisms that give rise to them. We have approached these questions by isolating and characterizing a collection of mycobacteriophages that infect a common bacterial host, Mycobacterium smegmatis. Comparative genomic analysis of 50 mycobacteriophages shows that they are highly diverse, although not uniformly so, that they are pervasively mosaic with a multitude of single gene modules, and that this mosaicism is generated through illegitimate recombination.",
"full_author_list": "Graham F Hatfull, Steven G Cresawn, Roger W Hendrix",
"short_author_list": "Hatfull GF, Cresawn SG, Hendrix RW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18653319",
"journal": "Research in microbiology",
"journal_volume": "159",
"journal_issue": "5",
"journal_pages": "332-9",
"pub_year": "2008",
"pubmed_id": "18653319"
},
{
"title": "Bacteriophage Genomics",
"abstract": "The past three years have seen an escalation in the number of sequenced bacteriophage genomes with more than 500 now in the NCBI phage database, representing a more than threefold increase since 2005. These span at least 70 different bacterial hosts, with two-thirds of the sequenced genomes of phages representing only eight bacterial hosts. Three key features emerge from the comparative analysis of these genomes. First, they span a very high degree of genetic diversity, suggesting early evolutionary origins. Second, the genome architectures are mosaic, reflecting an unusually high degree of horizontal genetic exchange in their evolution. Third, phage genomes contain a very high proportion of novel genetic sequences of unknown function, and probably represent the largest reservoir of unexplored genes. With an estimated 10(31) bacterial and archael viruses in the biosphere, our view of the virosphere will draw into sharper focus as further bacteriophage genomes are characterized.",
"full_author_list": "Hatfull, G. F.",
"short_author_list": "Hatfull, G. F.",
"article_url": "",
"journal": "Current Opinions in Microbiology",
"journal_volume": "11",
"journal_issue": "",
"journal_pages": "447-453",
"pub_year": "2008",
"pubmed_id": "18824125"
},
{
"title": "Characterization of temperate phage Che12 and construction of a new tool for diagnosis of tuberculosis.",
"abstract": "A temperate phage, Che12, able to infect Mycobacterium tuberculosis, was isolated from soil samples taken from tuberculosis sanatorium area in Chennai, India. The plaque morphology of this phage showed varying grades of turbidity on lawns of M. tuberculosis. The temperate nature of Che12 was established by super infection immunity. Phage integration into the host genomic DNA was confirmed by Southern hybridization using Che12 DNA as a probe. PCR amplification and sequencing of a part of the integrated phage genome in a M. tuberculosis lysogen also confirmed the temperate nature of Che12. The morphology of the phage particles was observed by electron microscopy, revealing similarities to other mycobacteriophages like L5, D29 and TM4. A luciferase reporter phage, phAETRC16, was constructed by cloning firefly luciferase gene into Che12. Infection of viable M. tuberculosis cells by phAETRC16 resulted in expression of luciferase leading to sustained light output. Che12, a true temperate phage infecting M. tuberculosis, is thus ideally suited for developing a diagnostic tool facilitating rapid diagnosis of M. tuberculosis.",
"full_author_list": "Vanaja Kumar, Prabakaran Loganathan, Gomathi Sivaramakrishnan, Jordan Kriakov, Azger Dusthakeer, Balaji Subramanyam, John Chan, William R Jacobs, Narayanan Paranji Rama",
"short_author_list": "Kumar V et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18511339",
"journal": "Tuberculosis (Edinburgh, Scotland)",
"journal_volume": "88",
"journal_issue": "6",
"journal_pages": "616-23",
"pub_year": "2008",
"pubmed_id": "18511339"
},
{
"title": "The delayed early gene G23 of temperate mycobacteriophage L1 regulates the expression of deoxyribonuclease, the product of another delayed early gene of the phage.",
"abstract": "To get clues about the genes as well as the gene regulatory circuit controlling the lytic development of temperate mycobacteriophage L1, previously we screened several conditional lethal mutants of L1 and characterized some of them to an extent. One of the mutants, L1 G23ts23, was found defective in both growth and late gene transcription at 42 degrees C but not at 32 degrees C. Here we show that the above phage mutant is also defective in the expression of phage-coded deoxyribonuclease (DNase) at 42 degrees C but not at 32 degrees C. The G23 gene however does not code for the above enzyme. Further analyses using the L1 G23ts23 mutant suggest that synthesis of DNase is also not regulated by G23 at transcriptional level. Expression of functional DNase in fact requires de novo protein synthesis. Among the 25 revertants isolated from the L1 G23ts23 mutant, which are capable of growing at 42 degrees C (by overcoming the ts defect in late transcription), two, R4 and R22, have been shown to retain the ts defect in the expression of the above enzyme and R4, to retain also the G23ts23 mutation. This suggests that R4 (R22 was not tested for the presence of G23ts23 mutation) carries an extragenic suppressor of G23ts23 mutation in a different gene (we call this putative gene as Gx), which now helps bypass the requirement of G23 for late gene transcription. Possible role of G23 on the regulation of L1-coded Gx and deoxyribonuclease has been discussed at length.",
"full_author_list": "Prajna Mandal, Hirock Jyoti Datta, Subrata Sau, Nitai Chandra Mandal",
"short_author_list": "Mandal P et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18646398",
"journal": "Polish journal of microbiology / Polskie Towarzystwo Mikrobiologów = The Polish Society of Microbiol",
"journal_volume": "57",
"journal_issue": "2",
"journal_pages": "113-9",
"pub_year": "2008",
"pubmed_id": "18646398"
},
{
"title": "Evaluation of killing kinetics of anti-tuberculosis drugs on Mycobacterium tuberculosis using a bacteriophage-based assay.",
"abstract": "BACKGROUND: Killing kinetics studies on Mycobacterium tuberculosis are labour intensive and time consuming since it takes nearly 6-7 weeks to get the data from an experiment. A modified protocol is required to increase the throughput and expedite the results. METHODS: The killing kinetics of frontline drugs used for the treatment of tuberculosis was studied using 24-well plates and 2 methods of enumeration of survivors of M. tuberculosis following drug exposure, namely conventional plating (CFU) and a phage-based assay (plaque-forming units) using mycobacteriophage D29. RESULTS: The use of 24-well plates enabled in reducing the volume of the compound required for the studies and the phage-based enumeration speeded up the readout and compared well with the CFU-based enumeration. CONCLUSION: These results were in agreement with the earlier findings reported with respect to rifampicin, isoniazid and moxifloxacin. Also, this study shows for the first time the concentration-dependent killing of streptomycin, the time-dependent killing of ethambutol and the profiling of an experimental anti-mycobacterial compound by these 2 methods.",
"full_author_list": "Nimi Marcel, Ajay Nahta, Meenakshi Balganesh",
"short_author_list": "Marcel N, Nahta A, Balganesh M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18772589",
"journal": "Chemotherapy",
"journal_volume": "54",
"journal_issue": "5",
"journal_pages": "404-11",
"pub_year": "2008",
"pubmed_id": "18772589"
},
{
"title": "BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes.",
"abstract": "Advances in DNA sequencing technology have facilitated the determination of hundreds of complete genome sequences both for bacteria and their bacteriophages. Some of these bacteria have well-developed and facile genetic systems for constructing mutants to determine gene function, and recombineering is a particularly effective tool. However, generally applicable methods for constructing defined mutants of bacteriophages are poorly developed, in part because of the inability to use selectable markers such as drug resistance genes during viral lytic growth. Here we describe a method for simple and effective directed mutagenesis of bacteriophage genomes using Bacteriophage Recombineering of Electroporated DNA (BRED), in which a highly efficient recombineering system is utilized directly on electroporated phage DNA; no selection is required and mutants can be readily detected by PCR. We describe the use of BRED to construct unmarked gene deletions, in-frame internal deletions, base substitutions, precise gene replacements, and the addition of gene tags.",
"full_author_list": "Marinelli LJ, Piuri M, Swigonová Z, Balachandran A, Oldfield LM, van Kessel JC, Hatfull GF",
"short_author_list": "Marinelli LJ, Piuri M, Swigonová Z, Balachandran A, Oldfield",
"article_url": "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003957",
"journal": "PLoS One",
"journal_volume": "3",
"journal_issue": "12",
"journal_pages": "e3957",
"pub_year": "2008",
"pubmed_id": "19088849"
},
{
"title": "Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination.",
"abstract": "A characteristic feature of bacteriophage genomes is that they are architecturally mosaic, with each individual genome representing a unique assemblage of individual exchangeable modules. Plausible mechanisms for generating mosaicism include homologous recombination at shared boundary sequences of module junctions, illegitimate recombination in a non-sequence-directed process, and site-specific recombination. Analysis of the novel mycobacteriophage Giles genome not only extends our current perspective on bacteriophage genetic diversity, with more than 60% of the genes unrelated to other mycobacteriophages, but offers novel insights into how mosaic genomes are created. In one example, the integration/excision cassette is atypically situated within the structural gene operon and could have moved there either by illegitimate recombination or more plausibly via integrase-mediated site-specific recombination. In a second example, a DNA segment has been recently acquired from the host bacterial chromosome by illegitimate recombination, providing further evidence that phage genomic mosaicism is generated by nontargeted recombination processes.",
"full_author_list": "Peter Morris, Laura J Marinelli, Deborah Jacobs-Sera, Roger W Hendrix, Graham F Hatfull",
"short_author_list": "Morris P et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18178732",
"journal": "Journal of bacteriology",
"journal_volume": "190",
"journal_issue": "6",
"journal_pages": "2172-82",
"pub_year": "2008",
"pubmed_id": "18178732"
},
{
"title": "Identification of three cytotoxic early proteins of mycobacteriophage L5 leading to growth inhibition in Mycobacterium smegmatis.",
"abstract": "Mycobacteriophage L5 is a temperate phage with a broad host range among the fast- and slow-growing mycobacteria such as Mycobacterium smegmatis, Mycobacterium tuberculosis, Mycobacterium avium and Mycobacterium ulcerans. L5 switches off host protein synthesis during the early stage of lytic growth, as was previously shown by protein expression profiling. Also, lethal genetic elements have been identified in L5 based on the fact that transformants could not be obtained with these genes. Using an inducible mycobacterial shuttle vector, we have identified three ORFs within an early operon of mycobacteriophage L5 which encode gene products (gp) toxic to the host M. smegmatis when expressed. These ORFs, coding for gp77, gp78 and gp79, presumably function as shut-off genes during early stages of phage replication. There is evidence that cell division is affected by one of the proteins (gp79). The transcription of the cytotoxic polypeptides is directed by a promoter situated in ORF83 and transcription control is achieved through the phage repressor gp71, which is shown by co-expression of this protein. The findings presented here should provide useful tools for the molecular genetics of mycobacteria. Further analysis of these and other mycobacteriophage-derived toxic polypeptides, together with the identification of their cellular targets, might provide a tool for the rapid identification of promising drug targets in emerging and re-emerging mycobacterial pathogens.",
"full_author_list": "Jan Rybniker, Georg Plum, Nirmal Robinson, Pamela L Small, Pia Hartmann",
"short_author_list": "Rybniker J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18667563",
"journal": "Microbiology (Reading, England)",
"journal_volume": "154",
"journal_issue": "Pt 8",
"journal_pages": "2304-14",
"pub_year": "2008",
"pubmed_id": "18667563"
},
{
"title": "Comparative evaluation of FASTPlaque assay with PCR and other conventional in vitro diagnostic methods for the early detection of pulmonary tuberculosis.",
"abstract": "Rapid and accurate diagnosis of symptomatic patients of pulmonary tuberculosis (TB) is highly desirable to minimize the spread of the disease in the society. We, therefore, compared the usefulness of various conventional diagnostic methods, the in-house polymerase chain reaction (PCR), and the FASTPlaque assay in this study. Laboratory data of 150 patients with clinical diagnosis of pulmonary TB and 50 controls were included in this study. The sputa from all these 200 individuals were subjected to acid-fast staining, culture on Lowenstein-Jensen (L-J) slants, automated BACTEC-MGIT-960 culture methods, and a mycobacteriophage assay. A mycobacterium genus and Mycobacterium tuberculosis species-specific PCRs were also done and samples positive on both PCRs were considered as standard for comparison. Of the 5 in vitro diagnostic tests, PCR method was found to be the most rapid, sensitive, and specific, detecting all the 150 cases of pulmonary TB without any false-positive and negative result. In comparison with PCR the sensitivity of MGIT-960 was 90%, followed by FASTPlaque assay (76.7%), L-J culture method (73.3%), and microscopy (60%). The mean detection time for smear-positive and smear-negative samples was 12.5 and 14 days in MGIT-960 and 18 and 25 days for L-J method, respectively. The FASTPlaque failed to detect mycobacteria from the paucibacillary samples. The contamination rates for MGIT-960, L-J, and FASTPlaque assays were 4, 8 and 10%, respectively. The best correlation with mycobacterial load in the specimen was observed in BACTEC-MGIT-960 showing 66.6% detection rate in paucibacillary, 83.3% in 1+ samples, and 100% in 2+ and 3+ samples. Out of the 150 patients, 140 (93.3%) could be diagnosed by one or more nonmolecular methods. Therefore, it could be concluded that combination of three or more in vitro diagnostic methods will have acceptable detection level.",
"full_author_list": "Sarman Singh, Taran Prit Saluja, Manjot Kaur, G C Khilnani",
"short_author_list": "Singh S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18803271",
"journal": "Journal of clinical laboratory analysis",
"journal_volume": "22",
"journal_issue": "5",
"journal_pages": "367-74",
"pub_year": "2008",
"pubmed_id": "18803271"
},
{
"title": "Mycobacterial recombineering.",
"abstract": "Although substantial advances have been made in mycobacterial genetics over the past 15 yr, manipulation of mycobacterial genomes and Mycobacterium tuberculosis in particular, continues to be hindered by problems of relatively poor DNA uptake, slow growth rate, and high levels of illegitimate recombination. In Escherichia coli an effective approach to stimulating recombination frequencies has been developed called \"recombineering,\" in which phage-encoded recombination functions are transiently expressed to promote efficient homologous recombination. Although homologs of these recombination proteins are rare among mycobacteriophages, we have identified one phage, Che9c, encoding relatives of both RecE and RecT of the E. coli rac prophage. Expression of the Che9c proteins from an inducible expression system in either slow- or fast-growing mycobacteria provides elevated recombination frequencies and facilitates simple allelic exchange using linear DNA substrates. Mycobacterial recombineering, therefore, offers a simple approach for constructing gene replacement mutants in M. smegmatis and M. tuberculosis.",
"full_author_list": "Julia C van Kessel, Graham F Hatfull",
"short_author_list": "van Kessel JC, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18370078",
"journal": "Methods in molecular biology (Clifton, N.J.)",
"journal_volume": "435",
"journal_issue": "",
"journal_pages": "203-15",
"pub_year": "2008",
"pubmed_id": "18370078"
},
{
"title": "Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets.",
"abstract": "Construction of genetically isogenic strains of mycobacteria is complicated by poor recombination rates and the lack of generalized transducing phages for Mycobacterium tuberculosis. We report here a powerful method for introducing single point mutations into mycobacterial genomes using oligonucleotide-derived single-stranded DNA recombineering and mycobacteriophage-encoded proteins. Phage Che9c gp61-mediated recombination is sufficiently efficient that single base changes can be introduced without requirement for direct selection, with isogenic mutant strains identified simply by PCR. Efficient recombination requires only short (50 nucleotide) oligonucleotides, but there is an unusually strong strand bias and an oligonucleotide targeting lagging strand DNA synthesis can recombine more than 10,000-fold efficiently than its complementary oligonucleotide. This ssDNA recombineering provides a simple assay for comparing the activities of related phage recombinases, and we find that both Escherichia coli RecET and phage lambda Red recombination proteins function inefficiently in mycobacteria, illustrating the utility of developing recombineering in new bacterial systems using host-specific bacteriophage recombinases. ssDNA mycobacterial recombineering provides a simple approach to characterizing antimycobacterial drug targets, and we have constructed and characterized single point mutations that confer resistance to isoniazid, rifampicin, ofloxacin and streptomycin.",
"full_author_list": "Julia C van Kessel, Graham F Hatfull",
"short_author_list": "van Kessel JC, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18221264",
"journal": "Molecular microbiology",
"journal_volume": "67",
"journal_issue": "5",
"journal_pages": "1094-107",
"pub_year": "2008",
"pubmed_id": "18221264"
},
{
"title": "Recombineering mycobacteria and their phages.",
"abstract": "Bacteriophages are central components in the development of molecular tools for microbial genetics. Mycobacteriophages have proven to be a rich resource for tuberculosis genetics, and the recent development of a mycobacterial recombineering system based on mycobacteriophage Che9c-encoded proteins offers new approaches to mycobacterial mutagenesis. Expression of the phage exonuclease and recombinase substantially enhances recombination frequencies in both fast- and slow-growing mycobacteria, thereby facilitating construction of both gene knockout and point mutants; it also provides a simple and efficient method for constructing mycobacteriophage mutants. Exploitation of host-specific phages thus provides a general strategy for recombineering and mutagenesis in genetically naive systems.",
"full_author_list": "Julia C van Kessel, Laura J Marinelli, Graham F Hatfull",
"short_author_list": "van Kessel JC, Marinelli LJ, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18923412",
"journal": "Nature Reviews Microbiology",
"journal_volume": "6",
"journal_issue": "11",
"journal_pages": "851-7",
"pub_year": "2008",
"pubmed_id": "18923412"
},
{
"title": "The many roads to essential genes",
"abstract": "Antibiotics target functions that are required for bacterial growth and survival. As genetic tools for studying Mycobacterium tuberculosis continue to improve we are increasingly able to identify genes that encode these important effectors. Here we review the strategies that have been used to identify and validate essential genes in mycobacteria and look forward to possible future advances.",
"full_author_list": "Wei J, Rubin, E",
"short_author_list": "Wei J, Rubin, E",
"article_url": "",
"journal": "Tuberculosis",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2008",
"pubmed_id": ""
},
{
"title": "Development of an antimicrobial formulation for control of specimen-related contamination in phage-based diagnostic testing for tuberculosis.",
"abstract": "AIMS: To develop and evaluate an antimicrobial supplement for use with phage-based tests for rapid detection of drug resistance of tuberculosis (TB). METHODS AND RESULTS: An antimicrobial formulation containing nystatin, oxacillin and aztreonam (NOA) (final concentrations of 50,000 IU l(-1), 2 mg l(-1), and 30 mg l(-1) respectively) was developed. This formulation was tested for its influence on detection of a number of Mycobacterium tuberculosis (MTB) strains using the phage amplification (FASTPlaque) assay. Addition of the supplement did not lead to significant reduction in assay sensitivity. Antimicrobial efficacy was assessed with a range of Gram-positive and -negative organisms. The NOA supplement had a broad antimicrobial effect. The supplement was tested for its effect on growth of MTB culture, and on determination of rifampicin resistance using the phage-based methodology (FASTPlaque-Response). NOA did not significantly affect the growth of a range of rifampicin susceptible and resistant MTB strains, nor did it have an adverse effect on the number of interpretable results, nor the ability to discriminate between rifampicin susceptibility and resistance. CONCLUSION, SIGNIFICANCE AND IMPACT OF STUDY: Use of NOA antimicrobial supplement with rapid phage-based tests for TB will increase the proportion of interpretable results obtained, and enable their wider implementation in disease-endemic countries by improved control of specimen-related contamination.",
"full_author_list": "H Albert, A P Trollip, K Linley, C Abrahams, T Seaman, R J Mole",
"short_author_list": "Albert H et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17897191",
"journal": "Journal of applied microbiology",
"journal_volume": "103",
"journal_issue": "4",
"journal_pages": "892-9",
"pub_year": "2007",
"pubmed_id": "17897191"
},
{
"title": "UV light inactivation of Mycobacterium avium subsp. paratuberculosis in milk as assessed by FASTPlaqueTB phage assay and culture.",
"abstract": "UV light inactivation of Mycobacterium avium subsp. paratuberculosis in Middlebrook 7H9 broth and whole and semiskim milk was investigated using a laboratory-scale UV machine that incorporated static mixers within UV-penetrable pipes. UV treatment proved to be less effective in killing M. avium subsp. paratuberculosis suspended in milk (0.5- to 1.0-log(10) reduction per 1,000 mJ/ml) than that suspended in Middlebrook 7H9 broth (2.5- to 3.3-log(10) reduction per 1,000 mJ/ml). The FASTPlaqueTB phage assay provided more rapid enumeration of surviving M. avium subsp. paratuberculosis (within 24 h) than culture on Herrold's egg yolk medium (6 to 8 weeks). Despite the fact that plaque counts were consistently 1 to 2 log(10) lower than colony counts throughout the study, UV inactivation rates for M. avium subsp. paratuberculosis derived using the phage assay and culture results were not significantly different (P = 0.077).",
"full_author_list": "Leslie C Altic, Michael T Rowe, Irene R Grant",
"short_author_list": "Altic LC, Rowe MT, Grant IR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17435001",
"journal": "Applied and environmental microbiology",
"journal_volume": "73",
"journal_issue": "11",
"journal_pages": "3728-33",
"pub_year": "2007",
"pubmed_id": "17435001"
},
{
"title": "Evaluation of rifampicin and isoniazid susceptibility testing of Mycobacterium tuberculosis by a mycobacteriophage D29-based assay.",
"abstract": "Conventional methods for determining drug susceptibility of Mycobacterium tuberculosis require several weeks to obtain results, limiting their usefulness; automated methods and those based on molecular biology techniques have been able to reduce the turnaround time, but their high cost and need for sophisticated equipment restrict their use in developing countries. The goal of the present study was to evaluate the diagnostic accuracy of a rapid (3-4 days) low-cost test based on the use of mycobacteriophage D29 to determine the susceptibility of strains of M. tuberculosis to rifampicin (RIF) and isoniazid (INH). Results obtained show that susceptibility testing for RIF has a high diagnostic accuracy as compared to the standard indirect proportion method on Löwenstein-Jensen medium (sensitivity 100% and specificity 98%). Given the association between the resistance to RIF and INH, which define multidrug resistance (MDR), this test seems suitable for rapid detection of MDR tuberculosis strains (kappa=0.978). Susceptibility testing for INH using mycobacteriophage D29 had a good but lower diagnostic accuracy as compared to the standard method (sensitivity 80.4% and specificity 80.8%); the test would then be of limited usefulness in the management of tuberculosis patients. Further studies to determine the relationship of mycobacteriophage D29 tests to in vivo correlates of sensitivity to specific antituberculosis drugs are warranted.",
"full_author_list": "José A Chauca, Juan-Carlos Palomino, Humberto Guerra",
"short_author_list": "Chauca JA, Palomino JC, Guerra H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17314367",
"journal": "Journal of medical microbiology",
"journal_volume": "56",
"journal_issue": "Pt 3",
"journal_pages": "360-4",
"pub_year": "2007",
"pubmed_id": "17314367"
},
{
"title": "A new look at bacteriophage lambda genetic networks.",
"abstract": "Bacteriophage ? is a temperate bacteriophage, meaning that it can reproduce and develop either in a lytic or lysogenic state. When ? infects its bacterial host Escherichia coli, the phage may develop lytically, causing cell lysis with the release of hundreds of progeny virus, or it may abort lytic development by switching off most viral expression, integrate its genome into the bacterial chromosome, and exist as a quiescent prophage in the lysogenic state. Although very stable, the lysogenic or prophage state can be reverted by inducing agents that damage the host DNA, returning the virus ? to its lytic state. These systems of lytic growth, lysogenic growth, and lysogenic induction from the prophage state are excellent model systems for understanding developmental pathways and the switches between these pathways. Within these pathways are sets of intertwined positive and negative regulators of gene expression acting at the transcription and posttranscription level, which have been studied extensively for more than 40 years. These ? paradigms of developmental pathways and regulatory functions, although well established, continue to evolve with surprising discoveries and accumulated insights.\r\n\r\nThere is a great interest in using systems biology approaches and system theory to understand all interactive processes in a cell and in an organism. This systems approach depends upon generating enormous amounts of data that describe all gene sequences and their transcript and protein levels, as well as their regulatory controls and dynamic interactions. Mathematical models based on this information should then be able to explain the various networks and to make predictions concerning any perturbation of the system. However, models are only as good as the data used to generate them, and good models also depend upon their testability in different genetic and environmental conditions. This will be an intimidating job for most complex organisms as we can infer by the various attempts to describe the genetic and developmental networks of a simple phage like ?. Although ? may be the most completely understood organism, we know that there is a lot more to learn. This review describes several new findings about ? regulation, which add to previously unknown levels of regulation and question certain dogma and which will be essential for meaningful advances in systems biology.",
"full_author_list": "Court DL, Oppenheim AB, Adhya SL.",
"short_author_list": "Court DL, Oppenheim AB, Adhya SL.",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17085553",
"journal": "journal of bacteriology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2007",
"pubmed_id": "17085553"
},
{
"title": "A New Look at Bacteriophage Lambda Genetic Networks",
"abstract": "No Abstract.",
"full_author_list": "Court DL, Oppenheim AB, Adhya SL.",
"short_author_list": "Court DL, Oppenheim AB, Adhya SL.",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/",
"journal": "Journal of Bacteriology",
"journal_volume": "189",
"journal_issue": "2",
"journal_pages": "298-304",
"pub_year": "2007",
"pubmed_id": "17085553"
},
{
"title": "The G23 and G25 genes of temperate mycobacteriophage L1 are essential for the transcription of its late genes.",
"abstract": "Two lysis-defective but DNA synthesis non-defective temperature-sensitive (ts) mutants of mycobacteriophage L1, L1G23ts23 and L1G25ts889 were found to be defective also in phage-specific RNA synthesis in the late period of their growth at 42 degrees C, each to the extent of 50% of that at 32 degrees C. The double mutant, L1G23ts23G25ts889 showed the ts defect in phage RNA synthesis that was nearly additive of those shown individually by the two single-mutant parents. Both G23 and G25 were shown to start functioning sometimes between 30 and 45 min after infection but the former gene might be dispensable after 45 min, while the latter was not. Northern analysis also shows that at 42 degrees C, L1G23ts23 affects RNA synthesis more strongly than L1G25ts889 from L1 DNA segments that serve as the template for late gene transcription. Among the 21 virion and 12 non-virion late proteins synthesized by L1, L1G23ts23 is defective in the synthesis of at least 9 virion and all of non-virion proteins at 42 degrees C. In contrast, L1G25ts889 is completely defective in synthesis of all the 33 late proteins. Possible roles of G23 and G25 in the positive regulation of transcription of different sets of late genes of L1 have been discussed.",
"full_author_list": "Hirock Jyoti Datta, Prajna Mandal, Rajat Bhattacharya, Niranjan Das, Subrata Sau, Nitai Chanda Mandal",
"short_author_list": "Datta HJ et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17394764",
"journal": "Journal of biochemistry and molecular biology",
"journal_volume": "40",
"journal_issue": "2",
"journal_pages": "156-62",
"pub_year": "2007",
"pubmed_id": "17394764"
},
{
"title": "Genome sequence and analysis of a Propionibacterium acnes bacteriophage.",
"abstract": "Cutaneous propionibacteria are important commensals of human skin and are implicated in a wide range of opportunistic infections. Propionibacterium acnes is also associated with inflammatory acne vulgaris. Bacteriophage PA6 is the first phage of P. acnes to be sequenced and demonstrates a high degree of similarity to many mycobacteriophages both morphologically and genetically. PA6 possesses an icosahedreal head and long noncontractile tail characteristic of the Siphoviridae. The overall genome organization of PA6 resembled that of the temperate mycobacteriophages, although the genome was much smaller, 29,739 bp (48 predicted genes), compared to, for example, 50,550 bp (86 predicted genes) for the Bxb1 genome. PA6 infected only P. acnes and produced clear plaques with turbid centers, but it lacked any obvious genes for lysogeny. The host range of PA6 was restricted to P. acnes, but the phage was able to infect and lyse all P. acnes isolates tested. Sequencing of the PA6 genome makes an important contribution to the study of phage evolution and propionibacterial genetics.",
"full_author_list": "Mark D Farrar, Karen M Howson, Richard A Bojar, David West, James C Towler, James Parry, Katharine Pelton, Keith T Holland",
"short_author_list": "Farrar MD et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17400737",
"journal": "Journal of bacteriology",
"journal_volume": "189",
"journal_issue": "11",
"journal_pages": "4161-7",
"pub_year": "2007",
"pubmed_id": "17400737"
},
{
"title": "Repressor of temperate mycobacteriophage L1 harbors a stable C-terminal domain and binds to different asymmetric operator DNAs with variable affinity.",
"abstract": "BACKGROUND: Lysogenic mode of life cycle of a temperate bacteriophage is generally maintained by a protein called 'repressor'. Repressor proteins of temperate lambdoid phages bind to a few symmetric operator DNAs in order to regulate their gene expression. In contrast, repressor molecules of temperate mycobacteriophages and some other phages bind to multiple asymmetric operator DNAs. Very little is known at present about the structure-function relationship of any mycobacteriophage repressor. RESULTS: Using highly purified repressor (CI) of temperate mycobacteriophage L1, we have demonstrated here that L1 CI harbors an N-terminal domain (NTD) and a C-terminal domain (CTD) which are separated by a small hinge region. Interestingly, CTD is more compact than NTD at 25 degrees C. Both CTD and CI contain significant amount of alpha-helix at 30 degrees C but unfold partly at 42 degrees C. At nearly 200 nM concentration, both proteins form appreciable amount of dimers in solution. Additional studies reveal that CI binds to O64 and OL types of asymmetric operators of L1 with variable affinity at 25 degrees C. Interestingly, repressor-operator interaction is affected drastically at 42 degrees C. The conformational change of CI is most possibly responsible for its reduced operator binding affinity at 42 degrees C. CONCLUSION: Repressors encoded by mycobacteriophages differ significantly from the repressor proteins of lambda and related phages at functional level but at structural level they are nearly similar.",
"full_author_list": "Tridib Ganguly, Amitava Bandhu, Partho Chattoraj, Palas K Chanda, Malabika Das, Nitai C Mandal, Subrata Sau",
"short_author_list": "Ganguly T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17598887",
"journal": "Virology journal",
"journal_volume": "4",
"journal_issue": "",
"journal_pages": "64",
"pub_year": "2007",
"pubmed_id": "17598887"
},
{
"title": "In silico analysis of mycobacteriophage Che12 genome: characterization of genes required to lysogenise Mycobacterium tuberculosis.",
"abstract": "Che12 is a temperate Chennai phage infecting Mycobacterium tuberculosis. The nucleotide sequence of the 52,047 bp linear double stranded DNA genome has a GC content of 62.9% with 70 putative ORFs identified. Functions are assigned to 24 genes based on the similarity of the predicted products to known proteins. Che12 genome is highly similar to mycobacteriophage L5 and D29 genomes. The overall genome similarity of Che12 to L5 is 82.5% and D29 is 81.5%. The genes attributing to lysogeny such as integrase, excisionase and repressor protein are identified. The attachment site of Che12 genome attP is homologous to attB sites of Mycobacterium smegmatis and M. tuberculosis. Similarities between certain phage gene products are noted, in particular, the terminases, DNA primase and endonucleases. The complete sequence clarifies the overall transcription map of Che12 and the positions of elements involved in the maintenance of lysogeny.",
"full_author_list": "N S Gomathi, H Sameer, Vanaja Kumar, S Balaji, V N Azger Dustackeer, P R Narayanan",
"short_author_list": "Gomathi NS et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17379577",
"journal": "Computational biology and chemistry",
"journal_volume": "31",
"journal_issue": "2",
"journal_pages": "82-91",
"pub_year": "2007",
"pubmed_id": "17379577"
},
{
"title": "Defining the ‘survivasome’ of Mycobacterium tuberculosis",
"abstract": " ",
"full_author_list": "Lamichhane G, Bishai W",
"short_author_list": "Lamichhane G, Bishai W",
"article_url": "",
"journal": "Nature Medicine",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2007",
"pubmed_id": ""
},
{
"title": "Novel Strategy to Prevent Otitis Media Caused by Colonizing Streptococcus pneumoniae",
"abstract": "None Provided",
"full_author_list": "McCullers JA, Karlström A, Iverson AR, Loeffler JM, Fischetti VA",
"short_author_list": "McCullers JA, Karlström A, Iverson AR, Loeffler JM, Fischett",
"article_url": "",
"journal": "PLoS Pathogens",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2007",
"pubmed_id": ""
},
{
"title": "Colorimetric phage-based assay for detection of rifampin-resistant Mycobacterium tuberculosis.",
"abstract": "Tests based on bacteriophage replication enable rapid screening of Mycobacterium tuberculosis for drug resistance. We describe a novel broth-based colorimetric method for detecting phage replication. When clinical isolates were tested by this novel method, high concordance was observed with both the traditional phage assay and gene mutation analysis for detection of resistance to rifampin.",
"full_author_list": "Ruth McNerney, Kim Mallard, Honorathy M R Urassa, Eshetu Lemma, Helen D Donoghue",
"short_author_list": "McNerney R et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17301279",
"journal": "Journal of clinical microbiology",
"journal_volume": "45",
"journal_issue": "4",
"journal_pages": "1330-2",
"pub_year": "2007",
"pubmed_id": "17301279"
},
{
"title": "Improved contamination control for a rapid phage-based rifampicin resistance test for Mycobacterium tuberculosis.",
"abstract": "A prospective study was conducted of the rapid FASTPlaque-Response test for determination of rifampicin resistance in Mycobacterium tuberculosis with and without the addition of an antimicrobial supplement containing nystatin, oxacillin and aztreonam (NOA) to control specimen-related contamination. A total of 631 smear-positive sputum specimens was tested. The age of specimens ranged from 0 to 21 days. The NOA antimicrobial was effective at controlling contamination, with 4.1 % of specimens contaminated when the NOA antimicrobial supplement was used compared with 13.9 % contamination without NOA. Overall levels of interpretability of the test with NOA were 87.8 % with specimens of < or =3 days and 79.0 % for all specimens. This compared with 70.1 and 73.8 % readable results, respectively, from conventional culture-based drug susceptibility testing (DST). Sensitivity, specificity and overall accuracy of the FASTPlaque-Response test for rifampicin resistance were 98.1, 96.3 and 96.6 %, respectively, for all specimens with NOA, and 93.2, 96.3 and 95.9 % without NOA, when compared with resolved conventional DST results. Inclusion of the NOA supplement reduced contamination, increased the number of interpretable results and did not adversely affect the performance of the FASTPlaque-Response test. Thus, the use of NOA improves the robustness of the test, facilitating its wider implementation.",
"full_author_list": "Richard Mole, Andre Trollip, Celeste Abrahams, Marlein Bosman, Heidi Albert",
"short_author_list": "Mole R et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17893170",
"journal": "Journal of medical microbiology",
"journal_volume": "56",
"journal_issue": "Pt 10",
"journal_pages": "1334-9",
"pub_year": "2007",
"pubmed_id": "17893170"
},
{
"title": "Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria.",
"abstract": "Mycobacteriophage Tweety is a newly isolated phage of Mycobacterium smegmatis. It has a viral morphology with an isometric head and a long flexible tail, and forms turbid plaques from which stable lysogens can be isolated. The Tweety genome is 58 692 bp in length, contains 109 protein-coding genes, and shows significant but interrupted nucleotide sequence similarity with the previously described mycobacteriophages Llij, PMC and Che8. However, overall the genome possesses mosaic architecture, with gene products being related to other mycobacteriophages such as Che9d, Omega and Corndog. A gene encoding an integrase of the tyrosine-recombinase family is located close to the centre of the genome, and a putative attP site has been identified within a short intergenic region immediately upstream of int. This Tweety attP-int cassette was used to construct a new set of integration-proficient plasmid vectors that efficiently transform both fast- and slow-growing mycobacteria through plasmid integration at a chromosomal locus containing a tRNA(Lys) gene. These vectors are maintained well in the absence of selection and are completely compatible with integration vectors derived from mycobacteriophage L5, enabling the simple construction of complex recombinants with genes integrated simultaneously at different chromosomal positions.",
"full_author_list": "Thuy T Pham, Deborah Jacobs-Sera, Marisa L Pedulla, Roger W Hendrix, Graham F Hatfull",
"short_author_list": "Pham TT et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17660435",
"journal": "Microbiology (Reading, England)",
"journal_volume": "153",
"journal_issue": "Pt 8",
"journal_pages": "2711-23",
"pub_year": "2007",
"pubmed_id": "17660435"
},
{
"title": "Nonhomologous end-joining in bacteria: a microbial perspective.",
"abstract": "In eukaryotic cells, repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining (NHEJ) pathway is critical for genomic stability. A functionally homologous repair apparatus, composed of Ku and a multifunctional DNA ligase (LigD), has recently been identified in many prokaryotes. Eukaryotic organisms employ a large number of factors to repair breaks by NHEJ. In contrast, the bacterial NHEJ complex is a two-component system that, despite its relative simplicity, possesses all of the break-recognition, end-processing, and ligation activities required to facilitate the complex task of DSB repair. Here, we review recent discoveries on the structure and function of the bacterial NHEJ repair apparatus. In particular, we discuss the evolutionary origins of this DSB repair pathway, how the diverse activities within the prokaryotic end-joining complex cooperate to facilitate DSB repair, the physiological roles of bacterial NHEJ, and finally, the essential function of NHEJ in the life cycle of mycobacteriophage.",
"full_author_list": "Robert S Pitcher, Nigel C Brissett, Aidan J Doherty",
"short_author_list": "Pitcher RS, Brissett NC, Doherty AJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17506672",
"journal": "Annual review of microbiology",
"journal_volume": "61",
"journal_issue": "",
"journal_pages": "259-82",
"pub_year": "2007",
"pubmed_id": "17506672"
},
{
"title": "Evaluation of codon bias perspectives in phage therapy of Mycobacterium tuberculosis by multivariate analysis.",
"abstract": "To reveal the relative synonymous codon usage and base composition variation in bacteriophages, six mycobacteriophages were used as a model system here and both parameters in these phages and their host bacteria, Mycobacterium tuberculosis, have been determined and compared. As expected for GC-rich genomes, there are predominantly G and C ending codons in all 6 phages. Both N_{c} plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in the 6 phages. Further analysis indicates that among 6 Mycobacterium phages Che9c, Bxz1 and TM4 may be extremely virulent in nature as most of their genes have high translation efficiency. Based on our data we suggest that the genes of above three phages are expressed rapidly by host's translation machinery. The information might be used to select the extremely virulent Mycobacterium tuberculosis phages suitable for phage therapy.",
"full_author_list": "Ashutosh Ranjan, Ambrish Sharan Vidyarthi, Raju Poddar",
"short_author_list": "Ranjan A, Vidyarthi AS, Poddar R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18391235",
"journal": "In silico biology",
"journal_volume": "7",
"journal_issue": "4-5",
"journal_pages": "423-31",
"pub_year": "2007",
"pubmed_id": "18391235"
},
{
"title": "Combining vital staining with fast plaque: TB assay.",
"abstract": "",
"full_author_list": "D Rawat, M R Capoor, A Hasan, D Nair, M Deb, P Aggarwal",
"short_author_list": "Rawat D et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/18087104",
"journal": "Indian journal of medical microbiology",
"journal_volume": "25",
"journal_issue": "4",
"journal_pages": "426-7",
"pub_year": "2007",
"pubmed_id": "18087104"
},
{
"title": "Development of a new, combined rapid method using phage and PCR for detection and identification of viable Mycobacterium paratuberculosis bacteria within 48 hours.",
"abstract": "The FASTPlaqueTB assay is an established diagnostic aid for the rapid detection of Mycobacterium tuberculosis from human sputum samples. Using the FASTPlaqueTB assay reagents, viable Mycobacterium avium subsp. paratuberculosis cells were detected as phage plaques in just 24 h. The bacteriophage used does not infect M. avium subsp. paratuberculosis alone, so to add specificity to this assay, a PCR-based identification method was introduced to amplify M. avium subsp. paratuberculosis-specific sequences from the DNA of the mycobacterial cell detected by the phage. To give further diagnostic information, a multiplex PCR method was developed to allow simultaneous amplification of either M. avium subsp. paratuberculosis or M. tuberculosis complex-specific sequences from plaque samples. Combining the plaque PCR technique with the phage-based detection assay allowed the rapid and specific detection of viable M. avium subsp. paratuberculosis in milk samples in just 48 h.",
"full_author_list": "Emma C Stanley, Richard J Mole, Rebecca J Smith, Sarah M Glenn, Michael R Barer, Michael McGowan, Catherine E D Rees",
"short_author_list": "Stanley EC et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17259362",
"journal": "Applied and environmental microbiology",
"journal_volume": "73",
"journal_issue": "6",
"journal_pages": "1851-7",
"pub_year": "2007",
"pubmed_id": "17259362"
},
{
"title": "Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer.",
"abstract": "Mycobacterium ulcerans is found in aquatic ecosystems and causes Buruli ulcer in humans, a neglected but devastating necrotic disease of subcutaneous tissue that is rampant throughout West and Central Africa. Here, we report the complete 5.8-Mb genome sequence of M. ulcerans and show that it comprises two circular replicons, a chromosome of 5632 kb and a virulence plasmid of 174 kb. The plasmid is required for production of the polyketide toxin mycolactone, which provokes necrosis. Comparisons with the recently completed 6.6-Mb genome of Mycobacterium marinum revealed >98% nucleotide sequence identity and genome-wide synteny. However, as well as the plasmid, M. ulcerans has accumulated 213 copies of the insertion sequence IS2404, 91 copies of IS2606, 771 pseudogenes, two bacteriophages, and multiple DNA deletions and rearrangements. These data indicate that M. ulcerans has recently evolved via lateral gene transfer and reductive evolution from the generalist, more rapid-growing environmental species M. marinum to become a niche-adapted specialist. Predictions based on genome inspection for the production of modified mycobacterial virulence factors, such as the highly abundant phthiodiolone lipids, were confirmed by structural analyses. Similarly, 11 protein-coding sequences identified as M. ulcerans-specific by comparative genomics were verified as such by PCR screening a diverse collection of 33 strains of M. ulcerans and M. marinum. This work offers significant insight into the biology and evolution of mycobacterial pathogens and is an important component of international efforts to counter Buruli ulcer.",
"full_author_list": "Timothy P Stinear, Torsten Seemann, Sacha Pidot, Wafa Frigui, Gilles Reysset, Thierry Garnier, Guillaume Meurice, David Simon, Christiane Bouchier, Laurence Ma, Magali Tichit, Jessica L Porter, Janine Ryan, Paul D R Johnson, John K Davies, Grant A Jenkin, Pamela L C Small, Louis M Jones, Fredj Tekaia, Françoise Laval, Mamadou Daffé, Julian Parkhill, Stewart T Cole",
"short_author_list": "Stinear TP et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17210928",
"journal": "Genome research",
"journal_volume": "17",
"journal_issue": "2",
"journal_pages": "192-200",
"pub_year": "2007",
"pubmed_id": "17210928"
},
{
"title": "Low-cost rapid detection of rifampicin resistant tuberculosis using bacteriophage in Kampala, Uganda.",
"abstract": "BACKGROUND: Resistance to anti-tuberculosis drugs is a serious public health problem. Multi-drug resistant tuberculosis (MDR-TB), defined as resistance to at least rifampicin and isoniazid, has been reported in all regions of the world. Current phenotypic methods of assessing drug susceptibility of M. tuberculosis are slow. Rapid molecular methods to detect resistance to rifampicin have been developed but they are not affordable in some high prevalence countries such as those in sub Saharan Africa. A simple multi-well plate assay using mycobacteriophage D29 has been developed to test M. tuberculosis isolates for resistance to rifampicin. The purpose of this study was to investigate the performance of this technology in Kampala, Uganda. METHODS: In a blinded study 149 M. tuberculosis isolates were tested for resistance to rifampicin by the phage assay and results compared to those from routine phenotypic testing in BACTEC 460. Three concentrations of drug were used 2, 4 and 10 microg/ml. Isolates found resistant by either assay were subjected to sequence analysis of a 81 bp fragment of the rpoB gene to identify mutations predictive of resistance. Four isolates with discrepant phage and BACTEC results were tested in a second phenotypic assay to determine minimal inhibitory concentrations. RESULTS: Initial analysis suggested a sensitivity and specificity of 100% and 96.5% respectively for the phage assay used at 4 and 10 microg/ml when compared to the BACTEC 460. However, further analysis revealed 4 false negative results from the BACTEC 460 and the phage assay proved the more sensitive and specific of the two tests. Of the 39 isolates found resistant by the phage assay 38 (97.4%) were found to have mutations predictive of resistance in the 81 bp region of the rpoB gene. When used at 2 mug/ml false resistant results were observed from the phage assay. The cost of reagents for testing each isolate was estimated to be 1.3 US dollars when testing a batch of 20 isolates on a single 96 well plate. Results were obtained in 48 hours. CONCLUSION: The phage assay can be used for screening of isolates for resistance to rifampicin, with high sensitivity and specificity in Uganda. The test may be useful in poorly resourced laboratories as a rapid screen to differentiate between rifampicin susceptible and potential MDR-TB cases.",
"full_author_list": "Hamidou Traore, Sam Ogwang, Kim Mallard, Moses L Joloba, Francis Mumbowa, Kalpana Narayan, Susan Kayes, Edward C Jones-Lopez, Peter G Smith, Jerrold J Ellner, Roy D Mugerwa, Kathleen D Eisenach, Ruth McNerney",
"short_author_list": "Traore H et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17212825",
"journal": "Annals of clinical microbiology and antimicrobials",
"journal_volume": "6",
"journal_issue": "",
"journal_pages": "1",
"pub_year": "2007",
"pubmed_id": "17212825"
},
{
"title": "Recombineering in Mycobacterium tuberculosis.",
"abstract": "Genetic dissection of M. tuberculosis is complicated by its slow growth and its high rate of illegitimate recombination relative to homologous DNA exchange. We report here the development of a facile allelic exchange system by identification and expression of mycobacteriophage-encoded recombination proteins, adapting a strategy developed previously for recombineering in Escherichia coli. Identifiable recombination proteins are rare in mycobacteriophages, and only 1 of 30 genomically characterized mycobacteriophages (Che9c) encodes homologs of both RecE and RecT. Expression and biochemical characterization show that Che9c gp60 and gp61 encode exonuclease and DNA-binding activities, respectively, and expression of these proteins substantially elevates recombination facilitating allelic exchange in both M. smegmatis and M. tuberculosis. Mycobacterial recombineering thus provides a simple approach for the construction of gene replacement mutants in both slow- and fast-growing mycobacteria.",
"full_author_list": "Julia C van Kessel, Graham F Hatfull",
"short_author_list": "van Kessel JC, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17179933",
"journal": "Nature methods",
"journal_volume": "4",
"journal_issue": "2",
"journal_pages": "147-52",
"pub_year": "2007",
"pubmed_id": "17179933"
},
{
"title": "Bird flu, influenza and 1918: the case for mutant Avian tuberculosis.",
"abstract": "Influenza is Italian for \"influence\", Latin: influentia. It used to be thought that the disease was caused by a bad influence from the heavens. Influenza was called a virus long, long before it was proven to be one. In 2005, an article in the New England Journal of Medicine estimated that a recurrence of the 1918 influenza epidemic could kill between 180 million and 360 million people worldwide. A large part of the current bird-flu hysteria is fostered by a distrust among the lay and scientific community regarding the actual state of our knowledge regarding the bird flu or H5N1 and the killer \"Influenza\" Pandemic of 1918 that it is compared to. And this distrust is not completely unfounded. Traditionally, \"flu\" does not kill. Experts, including Peter Palese of the Mount School of Medicine in Manhattan, remind us that even in 1992, millions in China already had antibodies to H5N1, meaning that they had contracted it and that their immune system had little trouble fending it off. Dr. Andrew Noymer and Michel Garenne, UC Berkely demographers, reported in 2000 convincing statistics showing that undetected tuberculosis may have been the real killer in the 1918 flu epidemic. Aware of recent attempts to isolate the \"Influenza virus\" on human cadavers and their specimens, Noymer and Garenne summed that: \"Frustratingly, these findings have not answered the question why the 1918 virus was so virulent, nor do they offer an explanation for the unusual age profile of deaths\". Bird flu would certainly be diagnosed in the hospital today as Acute Respiratory Distress Syndrome (ARDS). Roger and others favor suspecting tuberculosis in all cases of acute respiratory failure of unknown origin. By 1918, it could be said, in so far as tuberculosis was concerned, that the world was a supersaturated sponge ready to ignite and that among its most vulnerable parts was the very Midwest where the 1918 unknown pandemic began. It is theorized that the lethal pig epidemic that began in Kansas just prior to the first human outbreaks was a disease of avian and human tuberculosis genetically combined through mycobacteriophage interchange, with the pig, susceptible to both, as its involuntary living culture medium. What are the implications of mistaking a virus such as Influenza A for what mycobacterial disease is actually causing? They would be disastrous, with useless treatment and preventative stockpiles. The obvious need for further investigation is presently imminent and pressing.",
"full_author_list": "Lawrence Broxmeyer",
"short_author_list": "Broxmeyer L",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16806732",
"journal": "Medical hypotheses",
"journal_volume": "67",
"journal_issue": "5",
"journal_pages": "1006-15",
"pub_year": "2006",
"pubmed_id": "16806732"
},
{
"title": "Comparison of redox and D29 phage methods for detection of isoniazid and rifampicin resistance in Mycobacterium tuberculosis.",
"abstract": "Rapid, accurate and inexpensive methods are essential to detect drug-resistant Mycobacterium tuberculosis and allow timely application of effective treatment and precautions to prevent transmission. The proportion method, the MTT and Alamar Blue redox methods, and the D29 mycobacteriophage assay, were compared for their ability to detect resistance to isoniazid and rifampicin. When tested against a panel of known M. tuberculosis strains, the redox methods and the D29 assay showed good sensitivity and specificity compared to the proportion method, suggesting that they could be useful alternatives for identifying multidrug resistance in M. tuberculosis.",
"full_author_list": "P A da Silva, M M S Boffo, I G de Mattos, A B S Silva, J C Palomino, A Martin, H E Takiff",
"short_author_list": "da Silva PA et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16451420",
"journal": "Clinical microbiology and infection : the official publication of the European Society of Clinical M",
"journal_volume": "12",
"journal_issue": "3",
"journal_pages": "293-6",
"pub_year": "2006",
"pubmed_id": "16451420"
},
{
"title": "In vivo efficacy of phage therapy for Mycobacterium avium infection as delivered by a nonvirulent mycobacterium.",
"abstract": "The emergence of mycobacteria resistant to currently available antimicrobial agents has become an important problem in modern medicine. Mycobacterium avium and M. tuberculosis are intracellular pathogens that replicate and survive within the mononuclear phagocytes. TM4 is a lytic mycobacteriophage that kills both extracellular M. avium and M. tuberculosis. When delivered by M. smegmatis transiently infected with TM4, it kills both M. avium and M. tuberculosis within RAW 264.7 macrophages. To evaluate the treatment of M. avium infection with phage in vivo, C57 BL/6 mice were infected with M. avium 109 and, 7 days later, treated either once or twice with TM4 phage (7.9 x 10(10) PFU/ml), M. smegmatis (4 x 10(8) cFU/ml), or M. smegmatis with TM4 phage delivered intravenously (i.v.). Treatment with TM4 phage alone or M. smegmatis without TM4 did not show a significant decrease in number of intracellular bacteria in the spleen compared with untreated control. In contrast, administration of M. smegmatis-TM4 resulted in a significant decrease in the number of M. avium in the spleen. However, 23% of bacteria recovered from treated mice were resistant to TM4. These in vivo studies confirmed the in vitro findings that an avirulent mycobacterium can be used as a carrier to deliver antimycobacterial phage intracellularly.",
"full_author_list": "Lia Danelishvili, Lowell S Young, Luiz E Bermudez",
"short_author_list": "Danelishvili L, Young LS, Bermudez LE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16584300",
"journal": "Microbial drug resistance (Larchmont, N.Y.)",
"journal_volume": "12",
"journal_issue": "1",
"journal_pages": "1-6",
"pub_year": "2006",
"pubmed_id": "16584300"
},
{
"title": "Use of a mycobacteriophage-based assay for rapid assessment of susceptibilities of Mycobacterium tuberculosis isolates to isoniazid and influence of resistance level on assay performance.",
"abstract": "We standardized and assessed the performance of an in-house microtiter assay for determining the susceptibilities of Mycobacterium tuberculosis clinical isolates to isoniazid based on mycobacteriophage amplification technology. Seventy isolates (43 resistant and 27 sensitive according to the BACTEC 460 radiometric method and MIC determination) were studied. The isoniazid resistance molecular mechanism was previously determined by sequencing the entire katG gene and the mabA-inhA regulatory region. The sensitivity of the mycobacteriophage-based assay in detecting isoniazid resistance was 86.1%, the specificity achieved was 92.6%, and the overall accuracy was 88.6%. In order to assess the possible influence of resistance levels on the mycobacteriophage-based-assay sensitivity, the results were analyzed according to the isoniazid MICs. All the isolates exhibiting high-level resistance (MIC > or = 2 microg/ml) were scored as resistant by the mycobacteriophage-based assay (100% concordance), and 95% showed mutations or deletions in the catalytic domain of the katG gene. In contrast, 26.1% of the low-level-resistance strains (MICs, 0.25 to 1 microg/ml) were misclassified, and 66.7% had alterations in the mabA-inhA regulatory region. The mycobacteriophage-based assay could be used as a rapid method to detect the isoniazid susceptibility pattern, although data from those areas with high rates of low-level-resistance strains should be interpreted with caution. The features of the assay make it suitable for widespread application due to its low technical demand and cost.",
"full_author_list": "N Galí, J Domínguez, S Blanco, C Prat, F Alcaide, P Coll, V Ausina",
"short_author_list": "Galí N et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16390970",
"journal": "Journal of clinical microbiology",
"journal_volume": "44",
"journal_issue": "1",
"journal_pages": "201-5",
"pub_year": "2006",
"pubmed_id": "16390970"
},
{
"title": "Effects of physical, ionic, and structural factors on the binding of repressor of mycobacteriophage L1 to its cognate operator DNA.",
"abstract": "To determine the factors influencing the binding of L1 repressor to its cognate operator DNA, several gel shift as well as bioinformatic analyses have been carried out. The data show that time, temperature, salt, and pH each greatly affect the binding. In order to achieve optimum operator binding of L1 repressor in Tris buffer, the minimum requirements of time, temperature, salt, and pH were estimated to be 1 min, 32 degrees C, NaCl (50 mM), and 7.9, respectively. Interestingly Na+ but not NH4+, K+, or Li+ was found to augment significantly the binding activity of CI protein above the basal level. Anions like Cl-, citrate-, acetate-, and H2PO4- do not alter the binding of L1 repressor to its operator. We also show that an in frame deletion mutant of L1 repressor which does not carry the putative HTH motif (at its N-terminal end) fails to bind to its cognate operator DNA even at very high concentrations. The putative HTH motif was found highly conserved and evolutionarily very close to that of regulatory proteins of Y. pestis, H. marismortui, A. tumefaciens, etc. Taken together we suggest that N-terminal end of L1 repressor carries a HTH motif. Further analysis of the putative secondary structures of mycobacteriophage repressors reveals that two common regions encompassing more than 90% of primary sequence are present in all the four repressor molecules studied here. The results suggest that these common regions are utilized for carrying out identical functions.",
"full_author_list": "Tridib Ganguly, Palas K Chanda, Amitava Bandhu, Partho Chattoraj, Malabika Das, Subrata Sau",
"short_author_list": "Ganguly T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17073724",
"journal": "Protein and peptide letters",
"journal_volume": "13",
"journal_issue": "8",
"journal_pages": "793-8",
"pub_year": "2006",
"pubmed_id": "17073724"
},
{
"title": "Control of phage Bxb1 excision by a novel recombination directionality factor.",
"abstract": "Mycobacteriophage Bxb1 integrates its DNA at the attB site of the Mycobacterium smegmatis genome using the viral attP site and a phage-encoded integrase generating the recombinant junctions attL and attR. The Bxb1 integrase is a member of the serine recombinase family of site-specific recombination proteins and utilizes small (<50 base pair) substrates for recombination, promoting strand exchange without the necessity for complex higher order macromolecular architectures. To elucidate the regulatory mechanism for the integration and excision reactions, we have identified a Bxb1-encoded recombination directionality factor (RDF), the product of gene 47. Bxb1 gp47 is an unusual RDF in that it is relatively large (approximately 28 kDa), unrelated to all other RDFs, and presumably performs dual functions since it is well conserved in mycobacteriophages that utilize unrelated integration systems. Furthermore, unlike other RDFs, Bxb1 gp47 does not bind DNA and functions solely through direct interaction with integrase-DNA complexes. The nature and consequences of this interaction depend on the specific DNA substrate to which integrase is bound, generating electrophoretically stable tertiary complexes with either attB or attP that are unable to undergo integrative recombination, and weakly bound, electrophoretically unstable complexes with either attL or attR that gain full potential for excisive recombination.",
"full_author_list": "Pallavi Ghosh, Laura R Wasil, Graham F Hatfull",
"short_author_list": "Ghosh P, Wasil LR, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16719562",
"journal": "PLoS biology",
"journal_volume": "4",
"journal_issue": "6",
"journal_pages": "e186",
"pub_year": "2006",
"pubmed_id": "16719562"
},
{
"title": "A novel phage protein mediates the virus's removal from bacterial chromosomes.",
"abstract": "",
"full_author_list": "Liza Gross",
"short_author_list": "Gross L",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/20076596",
"journal": "PLoS biology",
"journal_volume": "4",
"journal_issue": "6",
"journal_pages": "e213",
"pub_year": "2006",
"pubmed_id": "20076596"
},
{
"title": "Inquiry learning. Teaching scientific inquiry.",
"abstract": "Science teachers in kindergarten to 12th grade (K-12) classrooms face a curious paradox. On one hand, according to the generally accepted theory, scientific inquiry in the classroom is “at the heart of the science and science learning” (1). In essence, the teaching of science should mirror the processes used by professional scientific researchers. On the other hand, a school classroom is not a research laboratory. Scientific research typically involves complex methods and problem-solving approaches (2), resulting in conclusions that are subjected to worldwide evaluation (3–6). Capturing these characteristics of professional science within the K-12 school classroom is daunting (7).\r\n\r\nThe goals of scientific research and current pedagogical practice are at odds (8, 9). In our culture, schools are designed to present established understandings, not to promote discovery of new knowledge. The focus on persuading students of the correctness of stated information is intensified by increased reliance on broad-based standardized testing, which—especially in the United States and the United Kingdom—has become a popular mechanism for making schools accountable. The ensuing culture of conformity with established knowledge is the very antithesis of scientific inquiry (8).\r\n\r\nProblems with implementing scientific inquiry in the classroom include the following: (i) Teachers may manipulate classroom science to obtain the expected results (10). (ii) Teachers' demonstrations merely simulate scientific inquiry. (iii) The incomplete development of students' reasoning abilities may limit their ability to construct complex scientific arguments (9–12). (iv) Scientific inquiry often requires detailed knowledge of a topic that students have yet to master.",
"full_author_list": "Hanauer DI, Jacobs-Sera D, Pedulla ML, Cresawn SG, Hendrix RW, Hatfull GF.",
"short_author_list": "Hanauer DI, et al.",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17185586",
"journal": "Science",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2006",
"pubmed_id": "PMID: 17185586"
},
{
"title": "Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform.",
"abstract": "Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 \"phamilies\" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three-encoding tape-measure proteins, lysins, and minor tail proteins-are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education.",
"full_author_list": "Graham F Hatfull, Marisa L Pedulla, Deborah Jacobs-Sera, Pauline M Cichon, Amy Foley, Michael E Ford, Rebecca M Gonda, Jennifer M Houtz, Andrew J Hryckowian, Vanessa A Kelchner, Swathi Namburi, Kostandin V Pajcini, Mark G Popovich, Donald T Schleicher, Brian Z Simanek, Alexis L Smith, Gina M Zdanowicz, Vanaja Kumar, Craig L Peebles, William R Jacobs, Jeffrey G Lawrence, Roger W Hendrix",
"short_author_list": "Hatfull GF et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16789831",
"journal": "PLoS genetics",
"journal_volume": "2",
"journal_issue": "6",
"journal_pages": "e92",
"pub_year": "2006",
"pubmed_id": "16789831"
},
{
"title": "Evaluation of a microcolony detection method and phage assay for rapid detection of Mycobacterium tuberculosis in sputum samples.",
"abstract": "Early and rapid diagnosis of tuberculosis is necessary for both treatment and control of the disease. This study evaluated two microcolony observation techniques based on liquid and solid media and a mycobacteriophage assay, to evaluate their effectiveness in the diagnosis of pulmonary TB compared with a standard culture (BACTEC 460 and LJ medium). Middlebrook7H9 (M7H9) broth based on microcolony determination detected 57/61 positives cultures (n = 200) with a sensitivity of 93.4% and a specificity of 87.1%. M7H11 agar detected 57/62 positive cultures (n = 198) with a sensitivity of 91.9% and a specificity of 89.7%. The mycobacteriophage assay detected 98/143 (68.5%) of positive samples. The time to positivity was 48 hours in the mycobacteriophage assay versus 7 days in both the M7H9 broth and M7H11 agar. The costs in comparison with the culture (BACTEC 460 and LJ) were 33% and 48% for the microcolony and mycobacteriophage methods, respectively. Microcolony methods were rapid and cost effective compared to standard cultures. The mycobacteriophage assay, despite its lower sensitivity, has a short turn around time, and may be recommended as a screening test in countries with a low prevalence of tuberculosis.",
"full_author_list": "Seema Irfan, Rumina Hasan, Akber Kanji, Qaiser Hassan, Iqbal Azam",
"short_author_list": "Irfan S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17333776",
"journal": "The Southeast Asian journal of tropical medicine and public health",
"journal_volume": "37",
"journal_issue": "6",
"journal_pages": "1187-95",
"pub_year": "2006",
"pubmed_id": "17333776"
},
{
"title": "MSTF: a domain involved in bacterial metallopeptidases and surface proteins, mycobacteriophage tape-measure proteins and fungal proteins.",
"abstract": "Here we report a novel domain, MSTF (domain involved in bacterial metallopeptidases, surface proteins and other proteins, also present in mycobacteriophage tape-measure proteins and fungal proteins), which is present in bacteria, phages and fungi. MSTF is about 67-94 amino acids in length with one HxDHxH motif and some highly conserved residues including His, Gly, Ala and Asp. Secondary structure prediction indicated that this domain contains two alpha-helices and one beta-sheet. Identification of MSTF will provide an opportunity to develop new strategies to combat pathogenic microorganisms, especially Mycobacterium tuberculosis.",
"full_author_list": "Xuhui Lai, Jifeng Weng, Xuelian Zhang, Wenjun Shi, Jingjing Zhao, Haipeng Wang, Honghai Wang",
"short_author_list": "Lai X et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16630259",
"journal": "FEMS microbiology letters",
"journal_volume": "258",
"journal_issue": "1",
"journal_pages": "78-82",
"pub_year": "2006",
"pubmed_id": "16630259"
},
{
"title": "Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase.",
"abstract": "Here we report an efficient, site-specific system of genetic integration into Plasmodium falciparum malaria parasite chromosomes. This is mediated by mycobacteriophage Bxb1 integrase, which catalyzes recombination between an incoming attP and a chromosomal attB site. We developed P. falciparum lines with the attB site integrated into the glutaredoxin-like cg6 gene. Transfection of these attB(+) lines with a dual-plasmid system, expressing a transgene on an attP-containing plasmid together with a drug resistance gene and the integrase on a separate plasmid, produced recombinant parasites within 2 to 4 weeks that were genetically uniform for single-copy plasmid integration. Integrase-mediated recombination resulted in proper targeting of parasite proteins to intra-erythrocytic compartments, including the apicoplast, a plastid-like organelle. Recombinant attB x attP parasites were genetically stable in the absence of drug and were phenotypically homogeneous. This system can be exploited for rapid genetic integration and complementation analyses at any stage of the P. falciparum life cycle, and it illustrates the utility of Bxb1-based integrative recombination for genetic studies of intracellular eukaryotic organisms.",
"full_author_list": "Louis J Nkrumah, Rebecca A Muhle, Pedro A Moura, Pallavi Ghosh, Graham F Hatfull, William R Jacobs, David A Fidock",
"short_author_list": "Nkrumah LJ et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16862136",
"journal": "Nature methods",
"journal_volume": "3",
"journal_issue": "8",
"journal_pages": "615-21",
"pub_year": "2006",
"pubmed_id": "16862136"
},
{
"title": "Effect of mycobacteriophage to intracellular mycobacteria in vitro.",
"abstract": "",
"full_author_list": "Li Peng, Bao-wen Chen, Yong-ai Luo, Guo-zhi Wang",
"short_author_list": "Peng L et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16635416",
"journal": "Chinese medical journal",
"journal_volume": "119",
"journal_issue": "8",
"journal_pages": "692-5",
"pub_year": "2006",
"pubmed_id": "16635416"
},
{
"title": "Mycobacteriophage exploit NHEJ to facilitate genome circularization.",
"abstract": "Ku-dependent nonhomologous end joining (NHEJ) is a double-strand break repair process conserved in all branches of cellular life but has not previously been implicated in the DNA metabolic processes of viruses. We identified Ku homologs in Corndog and Omega, two related mycobacteriophages of Mycobacterium smegmatis. These proteins formed homodimers and bound DNA ends in a manner identical to other Ku's and stimulated joining of ends by the host NHEJ DNA ligase (LigD). Omega and Corndog are unusual in having short 4 base cos ends that would not be expected to self-anneal and would therefore require NHEJ during phage genome circularization. Consistently, M. smegmatis LigD null strains are entirely and selectively unable to support infection by Corndog or Omega, with concomitant failure of genome circularization. These results establish a new paradigm for sequestration of the host cell NHEJ process by bacteriophage and provide a framework for understanding similar transactions in eukaryotic viral infections.",
"full_author_list": "Robert S Pitcher, Louise M Tonkin, James M Daley, Phillip L Palmbos, Andrew J Green, Tricia L Velting, Anna Brzostek, Malgorzata Korycka-Machala, Steve Cresawn, Jaroslaw Dziadek, Graham F Hatfull, Thomas E Wilson, Aidan J Doherty",
"short_author_list": "Pitcher RS et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16949369",
"journal": "Molecular cell",
"journal_volume": "23",
"journal_issue": "5",
"journal_pages": "743-8",
"pub_year": "2006",
"pubmed_id": "16949369"
},
{
"title": "A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells.",
"abstract": "The predominant morphotype of mycobacteriophage virions has a DNA-containing capsid attached to a long flexible non-contractile tail, features characteristic of the Siphoviridae. Within these phage genomes the tape measure protein (tmp) gene can be readily identified due to the well-established relationship between the length of the gene and the length of the phage tail--because these phages typically have long tails, the tmp gene is usually the largest gene in the genome. Many of these mycobacteriophage Tmp's contain small motifs with sequence similarity to host proteins. One of these motifs (motif 1) corresponds to the Rpf proteins that have lysozyme activity and function to stimulate growth of dormant bacteria, while the others (motifs 2 and 3) are related to proteins of unknown function, although some of the related proteins of the host are predicted to be involved in cell wall catabolism. We show here that motif 3-containing proteins have peptidoglycan-hydrolysing activity and that while this activity is not required for phage viability, it facilitates efficient infection and DNA injection into stationary phase cells. Tmp's of mycobacteriophages may thus have acquired these motifs in order to avoid a selective disadvantage that results from changes in peptidoglycan in non-growing cells.",
"full_author_list": "Mariana Piuri, Graham F Hatfull",
"short_author_list": "Piuri M, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17083467",
"journal": "Molecular microbiology",
"journal_volume": "62",
"journal_issue": "6",
"journal_pages": "1569-85",
"pub_year": "2006",
"pubmed_id": "17083467"
},
{
"title": "Host range of 14 mycobacteriophages in Mycobacterium ulcerans and seven other mycobacteria including Mycobacterium tuberculosis--application for identification and susceptibility testing.",
"abstract": "The host range of well-characterized mycobacteriophages, such as D29 and TM4, has been determined, together with that of more recently isolated mycobacteriophages, in Mycobacterium ulcerans, Mycobacterium tuberculosis, Mycobacterium bovis BCG, Mycobacterium avium, Mycobacterium marinum, Mycobacterium scrofulaceum, Mycobacterium fortuitum and Mycobacterium chelonae. Here, a set of virulent phages for M. ulcerans, a pathogen with a dramatic increase of incidence over the last decade, is demonstrated. In this work, a mycobacteriophage replication assay was adapted for the identification and rifampicin-susceptibility testing of M. ulcerans. Mycobacteriophages have generated a number of useful tools and enabled insights into mycobacterial genetics. With regard to the neglected pathogen M. ulcerans, the findings presented in this work allow the application of a large range of phage-based vectors and markers. The potential of phage therapy can now be evaluated for this extracellular pathogen.",
"full_author_list": "Jan Rybniker, Stefanie Kramme, Pamela L Small",
"short_author_list": "Rybniker J, Kramme S, Small PL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16388028",
"journal": "Journal of medical microbiology",
"journal_volume": "55",
"journal_issue": "Pt 1",
"journal_pages": "37-42",
"pub_year": "2006",
"pubmed_id": "16388028"
},
{
"title": "Modification of the mycobacteriophage Ms6 attP core allows the integration of multiple vectors into different tRNAala T-loops in slow- and fast-growing mycobacteria.",
"abstract": "BACKGROUND: Mycobacteriophage Ms6 integrates into Mycobacterium smegmatis and M. bovis BCG chromosome at the 3' end of tRNAala genes. Homologous recombination occurs between the phage attP core and the attB site located in the T-loop. Integration-proficient vectors derived from Ms6 are useful genetic tools, but their insertion sites in the BCG chromosome remain poorly defined. The primary objective of this study was to identify Ms6 target genes in M. smegmatis and BCG. We then aimed to modify the attP site in Ms6-derived vectors, to switch integration to other tRNAala loci. This provided the basis for the development of recombinant M. bovis BCG strains expressing several reporter genes inserted into different tRNAala genes. RESULTS: The three tRNAala genes are highly conserved in M. smegmatis and BCG. However, in the T-loop of tRNAalaU and tRNAalaV containing the attB site, a single base difference was observed between the two species. We observed that the tRNAalaU gene was the only site into which Ms6-derived integration-proficient vectors integrated in M. smegmatis, whereas in BCG, the tRNAalaV gene was used as the target. No integration occurred in the BCG tRNAalaU T-loop, despite a difference of only one base from the 26-base Ms6 attP core. We mutated the attP core to give a perfect match with the other tRNAala T-loops from M. smegmatis and BCG. Modification of the seven-base T-loop decreased integration efficiency, identifying this site as a possible site of strand exchange. Finally, two Ms6 vectors were constructed to integrate two reporter genes into the tRNAalaU and tRNAalaV T-loops of the same BCG chromosome. CONCLUSION: Small changes in the 7 bp T-loop attP site of Ms6 made it possible to use another attB site, albeit with a lower integration efficiency. These molecular studies on BCG tRNAala genes made it possible to create valuable tools for the site-directed insertion of several genes in the same BCG strain. These tools will be useful for the development of novel multivalent vaccines and genetic studies.",
"full_author_list": "Tiago Dos Vultos, Isabelle Méderlé, Valérie Abadie, Madalena Pimentel, José Moniz-Pereira, Brigitte Gicquel, Jean-Marc Reyrat, Nathalie Winter",
"short_author_list": "Vultos TD et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17173678",
"journal": "BMC molecular biology",
"journal_volume": "7",
"journal_issue": "",
"journal_pages": "47",
"pub_year": "2006",
"pubmed_id": "17173678"
},
{
"title": "Evaluation of phage assay for rapid phenotypic detection of rifampicin resistance in Mycobacterium tuberculosis.",
"abstract": "BACKGROUND: Conventional methods for susceptibility testing require several months before results can be reported. However, rapid methods to determine drug susceptibility have been developed recently. Phage assay have been reported as a rapid useful tools for antimicrobial susceptibility testing. The aim of this study was to apply the Phage assay for rapid detection of resistance on Mycobacterium tuberculosis strains in Cuba. METHODS: Phage D29 assay was performed on 102 M. tuberculosis strains to detect rifampicin resistance. The results were compared with the proportion method (gold standard) to evaluate the sensitivity and specificity of Phage assay. RESULTS: Phage assay results were available in 2 days whereas Proportion Methods results were obtain in 42 days. A total of 44 strains were detected as rifampicin resistant by both methods. However, one strains deemed resistant by Proportion Methods was susceptible by Phage assay. The sensitivity and specificity of Phage assay were 97.8 % and 100% respectively. CONCLUSION: Phage assay provides rapid and reliable results for susceptibility testing; it's easy to perform, requires no specialized equipment and is applicable to drug susceptibility testing in low income countries where tuberculosis is a major public health problem.",
"full_author_list": "Sergio Luis Yzquierdo, Dihadenys Lemus, Miguel Echemendia, Ernesto Montoro, Ruth McNerney, Anandi Martin, Juan Carlos Palomino",
"short_author_list": "Yzquierdo SL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16630356",
"journal": "Annals of clinical microbiology and antimicrobials",
"journal_volume": "5",
"journal_issue": "",
"journal_pages": "11",
"pub_year": "2006",
"pubmed_id": "16630356"
},
{
"title": "Integration and excision by the large serine recombinase phiRv1 integrase.",
"abstract": "The Mycobacterium tuberculosis prophage-like element phiRv1 encodes a site-specific recombination system utilizing an integrase of the serine recombinase family. Recombination occurs between a putative attP site and the host chromosome, but is unusual in that the attB site lies within a redundant repetitive element (REP13E12) of which there are seven copies in the M. tuberculosis genome; four of these elements contain attB sites suitable for phiRv1 integration in vivo. Although the mechanism of directional control of large serine integrases is poorly understood, a recombination directionality factor (RDF) has been identified that is required for phiRv1 integrase-mediated excisive recombination in vivo. Here we describe defined in vitro recombination reactions for both phiRv1 integrase-mediated integration and excision and show that the phiRv1 RDF is not only required for excision but inhibits integrative recombination; neither reaction requires DNA supercoiling, host factors, or high-energy cofactors. Integration, excision and excise-mediated inhibition of integration require simple substrates sites, indicating that the control of directionality does not involve the manipulation of higher-order protein-DNA architectures as described for the tyrosine integrases.",
"full_author_list": "Lori A Bibb, Maria I Hancox, Graham F Hatfull",
"short_author_list": "Bibb LA, Hancox MI, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15752208",
"journal": "Molecular microbiology",
"journal_volume": "55",
"journal_issue": "6",
"journal_pages": "1896-910",
"pub_year": "2005",
"pubmed_id": "15752208"
},
{
"title": "Report on an ICTV-sponsored symposium on Virus Evolution.",
"abstract": "",
"full_author_list": "U Desselberger",
"short_author_list": "Desselberger U",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15645372",
"journal": "Archives of virology",
"journal_volume": "150",
"journal_issue": "3",
"journal_pages": "629-35",
"pub_year": "2005",
"pubmed_id": "15645372"
},
{
"title": "Synapsis in phage Bxb1 integration: selection mechanism for the correct pair of recombination sites.",
"abstract": "Recombination by site-specific recombinases is a highly concerted process that requires synapsis of the correct pair of DNA substrates. Phage-encoded serine-integrases are unusual among the serine-recombinase family, which includes transposon resolvases and DNA invertases, in that they utilize two simple but different DNA substrates (attB and attP) and do not require accessory sites, additional proteins, or DNA supercoiling. Synapsis must therefore be directed solely by integrase-DNA interactions. We show here that the Bxb1 serine-integrase binds as a dimer to its two DNA substrates (attB, attP) and recombinant products (attL, attR) with similar affinities. However, synapsis occurs only between attP and attB, and not between any of the other nine possible site combinations. The Bxb1 integrase domain structure, the unusual DNA-binding properties of the integrase, and the characterization of a mutant protein with altered site-discrimination, are consistent with synaptic selectivity being derived from DNA sequence-induced changes in the conformations of integrase-DNA complexes.",
"full_author_list": "Pallavi Ghosh, Nicholas R Pannunzio, Graham F Hatfull",
"short_author_list": "Ghosh P, Pannunzio NR, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15890199",
"journal": "Journal of molecular biology",
"journal_volume": "349",
"journal_issue": "2",
"journal_pages": "331-48",
"pub_year": "2005",
"pubmed_id": "15890199"
},
{
"title": "The viriosphere, diversity, and genetic exchange within phage communities",
"abstract": "Natural phage communities are reservoirs of the greatest uncharacterized genetic diversity on Earth. Yet, identical phage sequences can be found in extremely different environments, which implies that there is wide circulation of viral genes among distantly related host populations. Further evidence of genetic exchange among phage and host communities is the presence in phage of genes coding for proteins that are essential for photosynthesis. These observations support the idea that a primary role of host populations in phage ecology and evolution is to serve as vectors for genetic exchange.",
"full_author_list": "Hambly E, Suttle CA\r\n",
"short_author_list": "Hambly E and Suttle CA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/?term=15979387",
"journal": "Current Opinion in Microbiology",
"journal_volume": "8",
"journal_issue": "4",
"journal_pages": "444-50",
"pub_year": "2005",
"pubmed_id": "15979387"
},
{
"title": "[Comparison between bacteriophage-based assay and BACTEC-960 system in detection of ethambutol resistance in Mycobacterium tuberculosis]",
"abstract": "OBJECTIVE: To set up phage amplified biologically assay (PhaB) for rapid detection ethambutol (EMB) resistance and to evaluate the use of PhaB in the detection of EMB resistance. METHODS: To detect the EMB resistance of 138 clinical isolates of Mycobacterium tuberculosis (MTB) by PhaB and compare it with the results of BACTEC-960 system. The minimal inhibitory concentration (MIC) was detected for all the discrepant isolates. RESULTS: Of all the 138 strains of MTB clinical isolates, 114 strains were EMB-susceptible and 24 strains were EMB-resistant with BACTEC-960 system while 118 strains were EMB-susceptible and 20 strains were EMB-resistant with PhaB. 112 of the 138 strains were EMB-susceptible and 18 strains were EMB-resistant with the two methods. The concordant isolates in determination of EMB resistance were 130 strains in the two methods and the concordance rate was 94.2%. The disconcordant isolates were 8 strains and the discrepancy rate was 5.8%. The sensitivity, specificity, positive and negative predictive value as well as overall accuracy for the PhaB assay was 75.0% (18/24), 98.2% (112/114), 90.0% (18/20), 94.9% (112/118) and 94.2% (130/138) respectively if the judgment standard was adopted by BACTEC-960 method. CONCLUSIONS: The PhaB assay can be used for detection of EMB resistance in isolates of MTB easily and quickly in three days. This method do not need special instrument and may be used in rapid screening method for EMB resistance of MTB.",
"full_author_list": "Xiao-wei Ma, Zhong-yi Hu, Jie Wang, Ying-rong Zhang, Zhen-ling Cui, Xiang-yuan Cao, Xin-hua Weng",
"short_author_list": "Ma XW et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15840261",
"journal": "Zhonghua nei ke za zhi [Chinese journal of internal medicine]",
"journal_volume": "44",
"journal_issue": "3",
"journal_pages": "202-5",
"pub_year": "2005",
"pubmed_id": "15840261"
},
{
"title": "Mycobacteriophage and their application to disease control.",
"abstract": "",
"full_author_list": "R McNerney, H Traoré",
"short_author_list": "McNerney R, Traoré H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16033452",
"journal": "Journal of applied microbiology",
"journal_volume": "99",
"journal_issue": "2",
"journal_pages": "223-33",
"pub_year": "2005",
"pubmed_id": "16033452"
},
{
"title": "GroEL1: a dedicated chaperone involved in mycolic acid biosynthesis during biofilm formation in mycobacteria.",
"abstract": "Mycobacteria are unusual in encoding two GroEL paralogs, GroEL1 and GroEL2. GroEL2 is essential--presumably providing the housekeeping chaperone functions--while groEL1 is nonessential, contains the attB site for phage Bxb1 integration, and encodes a putative chaperone with unusual structural features. Inactivation of the Mycobacterium smegmatis groEL1 gene by phage Bxb1 integration allows normal planktonic growth but prevents the formation of mature biofilms. GroEL1 modulates synthesis of mycolates--long-chain fatty acid components of the mycobacterial cell wall--specifically during biofilm formation and physically associates with KasA, a key component of the type II Fatty Acid Synthase involved in mycolic acid synthesis. Biofilm formation is associated with elevated synthesis of short-chain (C56-C68) fatty acids, and strains with altered mycolate profiles--including an InhA mutant resistant to the antituberculosis drug isoniazid and a strain overexpressing KasA--are defective in biofilm formation.",
"full_author_list": "Anil Ojha, Mridula Anand, Apoorva Bhatt, Laurent Kremer, William R Jacobs, Graham F Hatfull",
"short_author_list": "Ojha A et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16325580",
"journal": "Cell",
"journal_volume": "123",
"journal_issue": "5",
"journal_pages": "861-73",
"pub_year": "2005",
"pubmed_id": "16325580"
},
{
"title": "Bacteriophage-based assays for the rapid detection of rifampicin resistance in Mycobacterium tuberculosis: a meta-analysis.",
"abstract": "OBJECTIVE: To summarize, using meta-analysis, the accuracy of bacteriophage-based assays for the detection of rifampicin resistance in Mycobacterium tuberculosis. METHODS: By searching multiple databases and sources we identified a total of 21 studies eligible for meta-analysis. Of these, 14 studies used phage amplification assays (including eight studies on the commercial FASTPlaque-TB kits), and seven used luciferase reporter phage (LRP) assays. Sensitivity, specificity, and agreement between phage assay and reference standard (e.g. agar proportion method or BACTEC 460) results were the main outcomes of interest. RESULTS: When performed on culture isolates (N=19 studies), phage assays appear to have relatively high sensitivity and specificity. Eleven of 19 (58%) studies reported sensitivity and specificity estimates > or =95%, and 13 of 19 (68%) studies reported > or =95% agreement with reference standard results. Specificity estimates were slightly lower and more variable than sensitivity; 5 of 19 (26%) studies reported specificity <90%. Only two studies performed phage assays directly on sputum specimens; although one study reported sensitivity and specificity of 100 and 99%, respectively, another reported sensitivity of 86% and specificity of 73%. CONCLUSIONS: Current evidence is largely restricted to the use of phage assays for the detection of rifampicin resistance in culture isolates. When used on culture isolates, these assays appear to have high sensitivity, but variable and slightly lower specificity. In contrast, evidence is lacking on the accuracy of these assays when they are directly applied to sputum specimens. If phage-based assays can be directly used on clinical specimens and if they are shown to have high accuracy, they have the potential to improve the diagnosis of MDR-TB. However, before phage assays can be successfully used in routine practice, several concerns have to be addressed, including unexplained false positives in some studies, potential for contamination and indeterminate results.",
"full_author_list": "Madhukar Pai, Shriprakash Kalantri, Lisa Pascopella, Lee W Riley, Arthur L Reingold",
"short_author_list": "Pai M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16002146",
"journal": "The Journal of infection",
"journal_volume": "51",
"journal_issue": "3",
"journal_pages": "175-87",
"pub_year": "2005",
"pubmed_id": "16002146"
},
{
"title": "[The in vitro killing of intracellular Mycobacterium smegmatis by Mycobacteriophage]",
"abstract": "OBJECTIVE: To study the effect of Mycobacteriophage on the lysis of intracellular Mycobacterium smegmatis. METHODS: Peritoneal macrophages from BALB/C mice were incubated with Mycobacterium smegmatis for 4 h, and the extracellular bacteria were removed. Then the infected macrophages were treated for 2 h with normal saline, or different doses of Mycobacteriophages (2.1 x 10(7) PFU, 2.1 x 10(6) PFU, and 2.1 x 10(5) PFU, respectively), all in a volume of 0.1 ml, and then the extracellular phages and Mycobacterium smegmatis were removed by washing. After incubation for 24 h, the number of viable intracellular bacteria was determined. The intracellular changes after infection of host bacteria by bacteriophages in the macrophages were observed by electron microscopy. RESULTS: The logarithm 10 of viable intracellular bacteria unit was 5.74 +/- 0.18 in the saline group, 4.77 +/- 0.08 in the high dose phage group (P < 0.01), 4.97 +/- 0.17 in the moderate dose phage group (P < 0.01), and 5.33 +/- 0.13 in the low dose phage group (P > 0.05). Electron microscopy confirmed the infection of intracellular bacteria by the bacteriophages and the production of filial bacteriophages. CONCLUSIONS: Mycobacteriophages phagocytosed by macrophages are capable of killing the infected mycobacteria. The result suggests that the use of Mycobacteriophages is a potentially novel strategy in the treatment of intracellular bacterial infection.",
"full_author_list": "Li Peng, Bao-wen Chen, Yong-ai Luo, Xiao-bing Shen, You-lun Li, Guo-zhi Wang",
"short_author_list": "Peng L et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16207431",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "28",
"journal_issue": "9",
"journal_pages": "619-22",
"pub_year": "2005",
"pubmed_id": "16207431"
},
{
"title": "Diagnostic yield of fast plaque TB test for rapid detection of Mycobacterium in tuberculosis suspects.",
"abstract": "OBJECTIVE: To compare the diagnostic yield of FAST Plaque TB test with the conventional methods for detection of mycobacterium tuberculosis in sputum of Tuberculosis suspects at Jinnah Postgraduate Medical Center Karachi Pakistan. METHODS: A comparative study of diagnostic yield of FAST Plaque TB test with the culture and ZN staining, conducted from January to June 2004. RESULTS: The study was completed on 48 samples, 31 (64.58%) male and 17 females (35.42%). Half of the cases were sputum positive. Culture positive was in 17 (35.41%) and negative in 28 (58.3%) wereas 3 (6.25%) were contaminated. FAST Plaque TB test was positive in 16 (33.33%) and negative in 32 (66.6%) specimens. Out of 17 culture positive, 2 (11.7%) were negative and in 28 culture negative, 1 (3.57%) specimen was positive for FAST Plaque TB test. Out of 24 smear positive, 11 (45.83%) were negative and in 24 smear negative, 3 (12.5%) were positive, for FAST Plaque TB test. Compared to culture it has sensitivity of 86.23% and specificity of 96.42%, positive predictive value of 93.75% and negative predictive value of 93.1%. CONCLUSION: FAST Plaque TB test is a simple test that can detect viable mycobacterium in 2 days. It has a good sensitivity and specificity. The cost is three times less than the other available tests like PCR. Thus it can be useful in the diagnosis of tuberculosis as an adjunct to sputum microscopy in endemic countries.",
"full_author_list": "Manzoor Ali Phulpoto, Shahina Qayyum, Nadeem Rizvi, Shafi Muhammad Khuhawar",
"short_author_list": "Phulpoto MA et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15813629",
"journal": "JPMA. The Journal of the Pakistan Medical Association",
"journal_volume": "55",
"journal_issue": "2",
"journal_pages": "57-60",
"pub_year": "2005",
"pubmed_id": "15813629"
},
{
"title": "Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes.",
"abstract": "To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, M. smegmatis had been determined and compared. As all the organisms are GC-rich, the GC contents at third codon positions were found in fact higher than the second codon positions as well as the first + second codon positions in all the organisms indicating that directional mutational pressure is strongly operative at the synonymous third codon positions. Nc plot indicates that codon usage variation in all these organisms are governed by the forces other than compositional constraints. Correspondence analysis suggests that: (i) there are codon usage variation among the genes and genomes of the fourteen mycobacteriophages and M. smegmatis, i.e., codon usage patterns in the mycobacteriophages is phage-specific but not the M. smegmatis-specific; (ii) synonymous codon usage patterns of Barnyard, Che8, Che9d, and Omega are more similar than the rest mycobacteriophages and M. smegmatis; (iii) codon usage bias in the mycobacteriophages are mainly determined by mutational pressure; and (iv) the genes of comparatively GC rich genomes are more biased than the GC poor genomes. Translational selection in determining the codon usage variation in highly expressed genes can be invoked from the predominant occurrences of C ending codons in the highly expressed genes. Cluster analysis based on codon usage data also shows that there are two distinct branches for the fourteen mycobacteriophages and there is codon usage variation even among the phages of each branch.",
"full_author_list": "K Sahu, S K Gupta, S Sau, T C Ghosh",
"short_author_list": "Sahu K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15918677",
"journal": "Journal of biomolecular structure & dynamics",
"journal_volume": "23",
"journal_issue": "1",
"journal_pages": "63-71",
"pub_year": "2005",
"pubmed_id": "15918677"
},
{
"title": "[Molecular mechanism of the integration and lysis of mycobacteriophage]",
"abstract": "Tuberculosis remains one of the major threats to public health. China is one of the heavy TB burden countries. Novel drugs and vaccines are urgently needed to combat the increasingly multidrug resistant TB. Mycobacteriophage is one of the hot topic in TB novel drugs discovery and drug susceptibility test. Phages can multiply via two alternative mechanisms: the lytic cycle or the lysogenic cycle. The lytic cycle ends with the lysis and death of the host cell, whereas the host cell remains alive in the lysogenic cycle. Lysogenic mycobacteriophages were intensively studied to elucidate the integration and lysis mechanisms of mycobacteriophage. The integration of mycobacteriophage requires for attP of bacteriopahge genome, attB of Mycobacterium genome, integrase and integration host factor. Some lysogenic phage, eg. mycobacteriophage Ms6, employ lytic cycle, form new phage, lysis host by the cooperation of lysin and holin, and release phages. There is no reports as to the mycobacteriophage unique to China clinical or environmental isolates. Studies on the integration and lysis molecular mechanism of mycobacteriophage might facilitate future new anti-TB drugs development.",
"full_author_list": "Yan-jie Shen, Chang-hua Hu, Hong-hai Wang, Jian-ping Xie",
"short_author_list": "Shen YJ et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/16342784",
"journal": "Wei sheng wu xue bao = Acta microbiologica Sinica",
"journal_volume": "45",
"journal_issue": "5",
"journal_pages": "808-11",
"pub_year": "2005",
"pubmed_id": "16342784"
},
{
"title": "In-house phage amplification assay is a sound alternative for detecting rifampin-resistant Mycobacterium tuberculosis in low-resource settings.",
"abstract": "An in-house mycobacteriophage amplification assay for detecting rifampin-resistant Mycobacterium tuberculosis showed 100% sensitivity, 97.7% specificity, and 95.2% predictive value for resistance in a test of 129 isolates from a hot spot area of multidrug-resistant M. tuberculosis. The applicability of the test was demonstrated in the routine work flow of a low-resource reference laboratory.",
"full_author_list": "Norberto Símboli, Howard Takiff, Ruth McNerney, Beatriz López, Anandi Martin, Juan Carlos Palomino, Lucía Barrera, Viviana Ritacco",
"short_author_list": "Símboli N et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15616326",
"journal": "Antimicrobial agents and chemotherapy",
"journal_volume": "49",
"journal_issue": "1",
"journal_pages": "425-7",
"pub_year": "2005",
"pubmed_id": "15616326"
},
{
"title": "Rapid detection of rifampicin susceptibility of Mycobacterium tuberculosis in sputum specimens by mycobacteriophage assay.",
"abstract": "OBJECTIVE: To evaluate the performance of FASTPlaqueTB-RIF, a newly introduced bacteriophage assay for rapid detection of rifampicin susceptibility of Mycobacterium tuberculosis in sputum specimens. METHODS: A comparative study of 40 sputum specimens from patients of pulmonary tuberculosis, using FASTPlaqueTB-RIF and Bactec 460 TB system carried out at the Armed Forces Institute of Pathology, Rawalpindi between September and November 2001. RESULTS: Of the 40 clinical isolates of Mycobacterium tuberculosis tested for rifampicin (RIF) susceptibility using the Bactec 460 TB system, 28 isolates were resistant to RIF and 12 isolates were susceptible. FASTPlaqueTB-RIF identified 24 specimens as resistant to RIF. Three specimens that revealed susceptible isolates on Bactec 460, were resistant by FASTPlaqueTB-RIF while four specimens which revealed resistant isolates on Bactec 460, demonstrated susceptibility to RIF by FASTPlaqueTB-RIF. The sensitivity and specificity of FASTPlaqueTB-RIF were 86% and 73% respectively. The predictive values of positive and negative tests were 0.89 and 0.67 respectively. The overall accuracy of the technique was 82%. The phage assay took 48 hours to perform. CONCLUSION: Early detection of rifampicin resistance by the mycobacteriophage technique direct from sputum specimens is a potentially useful new test which would allow decision regarding appropriate therapy to be made early thus having a positive impact on patient care and on prevention of spread of MDR TB.",
"full_author_list": "T Butt, R N Ahmad, R K Afzal, A Mahmood, M Anwar",
"short_author_list": "Butt T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15449922",
"journal": "JPMA. The Journal of the Pakistan Medical Association",
"journal_volume": "54",
"journal_issue": "7",
"journal_pages": "379-82",
"pub_year": "2004",
"pubmed_id": "15449922"
},
{
"title": "Rapid diagnosis of pulmonary tuberculosis by mycobacteriophage assay.",
"abstract": "We evaluated FASTPlaqueTB, a recently introduced bacteriophage assay for rapid detection of Mycobacterium tuberculosis complex in sputum specimens, using 169 non-duplicate sputum specimens from patients suspected of pulmonary tuberculosis. The results of 160 specimens were analysed. FASTPlaqueTB assay detected tuberculosis in 77% (46/60) of culture-positive cases. Among the AFB smear-positive cases (n = 47) it had a sensitivity of 76% and specificity of 60% while among AFB smear-negative cases (n = 113) its sensitivity and specificity were 78% and 98%, respectively. The overall sensitivity and specificity of the technique were 77% and 96%, respectively, and the positive and negative predictive values were respectively 92% and 87%. The overall efficiency of the test was 89%. Test results were available in 48 h.",
"full_author_list": "T Butt, R N Ahmad, S Y Kazmi, A Mahmood",
"short_author_list": "Butt T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15260284",
"journal": "The international journal of tuberculosis and lung disease : the official journal of the Internation",
"journal_volume": "8",
"journal_issue": "7",
"journal_pages": "899-902",
"pub_year": "2004",
"pubmed_id": "15260284"
},
{
"title": "What is a Markov Model?",
"abstract": "Statistical models called hidden Markov models are a recurring theme in computational biology. What are hidden Markov models, and why are they so useful for so many different problems?",
"full_author_list": "Eddy, SR",
"short_author_list": "Eddy, SR",
"article_url": "http://www.nature.com/nbt/journal/v22/n10/full/nbt1004-1315.html",
"journal": "Nature Biotechnology",
"journal_volume": "10",
"journal_issue": "",
"journal_pages": "1315-6",
"pub_year": "2004",
"pubmed_id": "15470472"
},
{
"title": "An evaluation of mycophage therapy, chemotherapy and vaccination for control of Mycobacterium avium subsp. paratuberculosis infection.",
"abstract": "The control of ovine Johne's disease (OJD) is important for domestic trade, the viability of farming units and possibly also for public health. Current strategies in Australia have included quarantine and pasture spelling to decrease prevalence and shedding rates and reduce numbers of Mycobacterium paratuberculosis (Mptb) ingested by susceptible sheep. However, alternative procedures are needed and vaccination with Gudair has recently commenced. This review examines prospects for the control of OJD by chemotherapy, vaccination and mycophages. Current chemotherapeutic regimes for treatment of M. paratuberculosis in ruminants are prohibitively expensive and of dubious efficacy, and apart from environmental concerns, mycophage therapy lacks a track record of success against intracellular bacteria. There is substantial evidence that live and killed mycobacterial vaccines reduce the incidence of clinical disease and shedding rates in OJD. An appraisal of recent experimental results suggests that neonatal vaccination with a defined dose of M. paratuberculosis offers the best prospects for the induction of protective Th1-type immunity.",
"full_author_list": "David L Emery, Richard J Whittington",
"short_author_list": "Emery DL, Whittington RJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15564023",
"journal": "Veterinary microbiology",
"journal_volume": "104",
"journal_issue": "3-4",
"journal_pages": "143-55",
"pub_year": "2004",
"pubmed_id": "15564023"
},
{
"title": "A point mutation at the C-terminal half of the repressor of temperate mycobacteriophage L1 affects its binding to the operator DNA.",
"abstract": "The wild-type repressor CI of temperate mycobacteriophage L1 and the temperature-sensitive (ts) repressor CIts391 of a mutant L1 phage, L1cIts391, have been separately overexpressed in E. coli. Both these repressors were observed to specifically bind with the same cognate operator DNA. The operator-binding activity of CIts391 was shown to differ significantly than that of the CI at 32 to 42 degrees C. While 40-95% operator-binding activity was shown to be retained at 35 to 42 degrees C in CI, more than 75% operator-binding activity was lost in CIts391 at 35 to 38 degrees C, although the latter showed only 10% less binding compared to that of the former at 32 degrees C. The CIts391 showed almost no binding at 42 degrees C. An in vivo study showed that the CI repressor inhibited the growth of a clear plaque former mutant of the L1 phage more strongly than that of the CIts391 repressor at both 32 and 42 degrees C. The half-life of the CIts391-operator complex was found to be about 8 times less than that of the CI-operator complex at 32 degrees C. Interestingly, the repressor-operator complexes preformed at 0 degrees C have shown varying degrees of resistance to dissociation at the temperatures which inhibit the formation of these complexes are inhibited. The CI repressor, but not that of CIts391, regains most of the DNA-binding activity on cooling to 32 degrees C after preincubation at 42 to 52 degrees C. All these data suggest that the 131(st) proline residue at the C-terminal half of CI, which changed to leucine in the CIts391, plays a crucial role in binding the L1 repressor to the cognate operator DNA, although the helix-turn-helix DNA-binding motif of the L1 repressor is located at its N-terminal end.",
"full_author_list": "Tridib Ganguly, Partho Chattoraj, Malabika Das, Palas K Chanda, Nitai C Mandal, Chia Y Lee, Subrata Sau",
"short_author_list": "Ganguly T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15607030",
"journal": "Journal of biochemistry and molecular biology",
"journal_volume": "37",
"journal_issue": "6",
"journal_pages": "709-14",
"pub_year": "2004",
"pubmed_id": "15607030"
},
{
"title": "Childhood tuberculosis and its early diagnosis.",
"abstract": "Traditional methods for laboratory diagnosis of tuberculosis are unsatisfactory, especially for children, in whose specimens mycobacteria are usually sparse. Recent changes in tuberculosis epidemiology in developed countries, including a large increase in incidence in children from certain ethnic minorities, have prompted interest in newer diagnostic methods. Liquid-based culture detection systems offer improved sensitivity and speed of diagnosis, although the time taken for detection of growth is still upwards of 1 week. Nucleic acid amplification techniques offer more rapid results, but perform best on smear-positive samples; sensitivities may be as low as 50% in smear-negative specimens. Although these newer techniques are widely used in some developed countries, in others, they are not perceived as offering sufficient benefit to justify their routine use. The diagnostic accuracy of mycobacteriophage and serologic methods is insufficient to justify their wide use even in developing countries. Despite recent developments, there is still no panacea for diagnosis of childhood tuberculosis.",
"full_author_list": "James W Gray",
"short_author_list": "Gray JW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15183293",
"journal": "Clinical biochemistry",
"journal_volume": "37",
"journal_issue": "6",
"journal_pages": "450-5",
"pub_year": "2004",
"pubmed_id": "15183293"
},
{
"title": "[Analysis and evaluation of phage amplified biologically assay, DNA sequencing analysis and single-strand conformational polymorphism for the drug susceptibility testing of Mycobacterium tuberculosis]",
"abstract": "OBJECTIVE: To rapidly identify drug-resistant Mycobacterium tuberculosis using phenotypic and genotypic methods and to evaluate the clinical significance of rapid phenotypic susceptibility test by phage amplified biologically assay (PhaB). METHODS: PhaB, DNA sequencing and polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) were performed on the 91 rifampicin (RFP)-resistant strains (including 82 multi-drug resistant Mycobacterium tuberculosis strains), 42 RFP-susceptible strains, 75 ofloxacin (OFLX)-resistant strains and 40 OFLX-susceptible strains at the same time. RESULTS: The results obtained using PhaB assay, DNA sequencing and PCR-SSCP were compared with the absolute concentration method. For RFP susceptibility, the accordance, sensitivity and specificity of PhaB were 93%, 92% and 95% respectively; the accordance, sensitivity and specificity of DNA sequencing were 93%, 90% and 100% respectively; those of PCR-SSCP were 90%, 86% and 100% respectively. For OFLX susceptibility, the accordance, sensitivity and specificity of PhaB assay were 95%, 95% and 95%; those of DNA sequencing were 80%, 71% and 98% respectively; those of PCR-SSCP were 75%, 63% and 98% respectively. CONCLUSIONS: PhaB assay is a low-cost, rapid, and sensitive method and shows high accordance with absolute concentration technology. It can give drug susceptibility test results within 48 - 96 h, and is a promising technology in clinical laboratory.",
"full_author_list": "Xi-Qin Han, Yu Ma, Wei-Wei Gao, Chuan-You Li, Xiao-You Chen, Zong-de Zhang, Shu-Xiang Gu, Guang-Lu Jiang",
"short_author_list": "Han XQ et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15730780",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "27",
"journal_issue": "12",
"journal_pages": "815-9",
"pub_year": "2004",
"pubmed_id": "15730780"
},
{
"title": "Recent advances in molecular methods for early diagnosis of tuberculosis and drug-resistant tuberculosis.",
"abstract": "Tuberculosis (TB) remains the main infectious cause of deaths in the world. Due to the slow metabolism of the causative agent, Mycobacterium tuberculosis, the isolation, identification and drug susceptibility testing requires several weeks. New techniques have improved specificity, turnaround time and cost effectiveness. Although these methods yield results within hours from sample collection, the clinical significance of each positive result requires rigorous evaluation in most cases. Herein the advantages and disadvantages of the most promising molecular techniques for detection of TB and drug resistance are discussed.",
"full_author_list": "Manzour Hernando Hazbón",
"short_author_list": "Hazbón MH",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15495583",
"journal": "Biomédica : revista del Instituto Nacional de Salud",
"journal_volume": "24 Supp 1",
"journal_issue": "",
"journal_pages": "149-62",
"pub_year": "2004",
"pubmed_id": "15495583"
},
{
"title": "[Phage amplified biologically assay and its application in rapid detection of Mycobacterium tuberculosis]",
"abstract": "",
"full_author_list": "Zhong-Yi Hu",
"short_author_list": "Hu ZY",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15730788",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "27",
"journal_issue": "12",
"journal_pages": "850-2",
"pub_year": "2004",
"pubmed_id": "15730788"
},
{
"title": "[Application of rapid detection for rifampin resistance in clinical isolates of Mycobacterium tuberculosis by phage amplified biologically assay]",
"abstract": "OBJECTIVE: To set up a rapid detection method for rifampin susceptibility with phage amplified biologically (PhaB) assay and to evaluates its value in the detection of rifampin resistance in clinical isolates of Mycobacterium tuberculosis. METHODS: The assay was established to detect rifampin resistance in 524 clinical isolates of Mycobacterium tuberculosis, and the result was compared to that of the absolute concentration method. The minimum inhibitory concentration (MIC) was detected by BACTEC MGIT 960 method for the discrepant isolates. RESULTS: Rifampin susceptibility results were available for 524 strains of Mycobacterium tuberculosis. A total of 223 strains were found to be rifampin resistant and 301 strains were rifampin susceptible detected by PhaB assay, but 211 and 313 strains were respectively found to be rifampin resistant and susceptible by conventional methods. There were 198 and 288 rifampin resistant and susceptible strains both detected by the two methods. The drug susceptibility of 35 strains was the same in 38 discrepant isolates by the PhaB assay and absolute concentration method. The sensitivity, specificity, positive and negative predictive values as well as the overall accuracy for the PhaB assay was 93.8%, 92.0%, 88.8%, 95.7% and 92.7% respectively if the judgment standard was adopted by conventional methods. CONCLUSION: The result of PhaB assay was available within 2 days. This method, which is simple and does not need special equipment, can be used for rapid screening for rifampin resistance from Mycobacterium tuberculosis.",
"full_author_list": "Zhong-Yi Hu, An-Jia Jin, Hui-Ping Chen, Zhen-Ling Cui, Ling-Jie Jing, Jie Wang, Xin-Hua Weng",
"short_author_list": "Hu ZY et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15730778",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "27",
"journal_issue": "12",
"journal_pages": "811-4",
"pub_year": "2004",
"pubmed_id": "15730778"
},
{
"title": "[Study on the method for rapid detection of Mycobacterium tuberculosis by phage amplified biologically assay]",
"abstract": "OBJECTIVE: To set up a method for rapid detection of Mycobacterium tuberculosis (MTB) by phage amplified biologically (PhaB) assay and to investigate the optimal test condition. METHODS: Various test conditions were compared in order to observe the influence on detective results after MTB was infected by Mycobacteriophage. The test condition established was used for detection of sputum samples, and the results were compared with BIOTEC Lab test. RESULTS: The bacterial concentration of MTB in 200 - 500/ml was detected by PhaB assay at 1 x 10(9) plaque forming unite (PFU)/ml of Mycobacteriophage, 37 degrees C for 60 min. The optimal concentration of virucidal for inactivation of Mycobacteriophage was 100 mmol/ml for 5 min at room temperature. The bacteriolytic plaque was clear at the concentration of 1 x 10(8)/ml indicator cells. Bacterium inactivated by heat can not be infected by Mycobacteriophage. Positive result was observed for control strains of H(37)Rv, H(37)Ra and M. bovis while negative result was obtained for 7 strains of non-Mycobacterium and 16 control strains of non-Tuberculosis Mycobacteria (NTM). The 4 strains of NTM (M. fortuitum, M. intrcellulare, M. aurum, M. phlei) showed positive reaction at higher concentrations (> 1 x 10(5)/ml). The repetition test showed that the differentiation coefficient in batch and inner was all under 15%. There was a significantly difference (P < 0.01) in positive rate between two digestion-decontamination procedure with N-acetyl-cysteine-NaOH liquefacient (94%) and NaOH liquefacient (62%). The positive rate of the samples cultured one day (65%) was significantly higher than that of the samples without preculture (40%). The results for detection of clinical samples by two reagents, ours and BIOTEC Lab, were nearly the same. CONCLUSION: Because its rapidity, simplicity, and sensitivity, PhaB assay can be used for rapid detection of MTB, but the condition of test is very important.",
"full_author_list": "Zhong-Yi Hu, Lian-di Ni, An-Jia Jin, Hui-Xian Dong, Min Zhong, Jian-Nong Li, Xin-Hua Weng",
"short_author_list": "Hu ZY et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15730776",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "27",
"journal_issue": "12",
"journal_pages": "801-5",
"pub_year": "2004",
"pubmed_id": "15730776"
},
{
"title": "The genome of phiAsp2, an actinoplanes infecting phage.",
"abstract": "The first genome of a virus infecting a representative of the eubacterial genus Actinoplanes is presented. Phage phiAsp2 has a circularly permutated chromosome that consists of 58,638 bp; its G/C-bias of 70.39% resembles the hosts G + C-content (71-73% within the genus). A total of 76 open reading frames (orfs) were identified, the majority of which (63) displaying equal transcriptional orientations. Functional gene clustering is obvious as orfs coding for head and tail proteins are located close to the center in the first half of the genome and putative DNA-modifying enzymes are encoded by centrally located genes; DNA repair and recombination functions are situated in the remaining part of the genome, adjacent to a small gene cluster, the predicted proteins of which are involved in DNA packaging. Close to the left terminus there are two small regions (approximately 4.5 kb each, separated by 2.8 kb) which are homologous to the recently sequenced mycobacteriophage rosebush, however, the unique overall structure of the phiAsp2-genome does not bear resemblance to any other known viral genome. The nucleotide sequence was deposited in GenBank with the accession no. AY576796.",
"full_author_list": "Martin Jarling, Kai Bartkowiak, Hermann Pape, Friedhelm Meinhardt",
"short_author_list": "Jarling M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15215690",
"journal": "Virus genes",
"journal_volume": "29",
"journal_issue": "1",
"journal_pages": "117-29",
"pub_year": "2004",
"pubmed_id": "15215690"
},
{
"title": "Bxz1, a new generalized transducing phage for mycobacteria.",
"abstract": "We have isolated and characterized a new generalized transducing phage, Bxz1, from soil sampling at a neighboring Wildlife Preservation Park. The hosts of the phage, measured by the formation of plaques, include fast growing Mycobacterium smegmatis and Mycobacterium vaccae. Bxz1 is capable of transducing chromosomal markers, point mutations, and plasmids at frequencies ranging from 10(-8) to 10(-6) per plaque forming unit between strains of M. smegmatis. We also demonstrated cotransduction of a transposon insertion linked to a point mutation of the ndh gene.",
"full_author_list": "Sunhee Lee, Jordan Kriakov, Catherine Vilcheze, Zhiyan Dai, Graham F Hatfull, William R Jacobs",
"short_author_list": "Lee S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15598543",
"journal": "FEMS microbiology letters",
"journal_volume": "241",
"journal_issue": "2",
"journal_pages": "271-6",
"pub_year": "2004",
"pubmed_id": "15598543"
},
{
"title": "Development of a bacteriophage phage replication assay for diagnosis of pulmonary tuberculosis.",
"abstract": "Successful infection and replication of bacteriophages is indicative of the presence of viable bacteria. We describe here the development of a bacteriophage replication assay for the detection of Mycobacterium tuberculosis by using mycobacteriophage D29. Optimization of phage inoculate and incubation times allowed highly sensitive detection of M. bovis BCG. Fewer than 10 CFU (100 CFU/ml) were detected. No false-positive results were observed in negative samples. Application of the assay to 496 sputum specimens in the National Reference Laboratory of Zambia produced sensitivity, specificity, and positive and negative predictive values of 44.1, 92.6, 82.2, and 67.5%, respectively, compared to culture on Lowenstein-Jensen medium. The equivalent corresponding results for direct fluorescent smear microscopy were 42.3, 96.8, 91.2, and 67.6%. The small increase in sensitivity over that of direct microscopy does not justify the introduction of this technique for routine diagnosis of pulmonary tuberculosis at this time.",
"full_author_list": "Ruth McNerney, Bupe S Kambashi, Juliana Kinkese, Ruth Tembwe, Peter Godfrey-Faussett",
"short_author_list": "McNerney R et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15131178",
"journal": "Journal of clinical microbiology",
"journal_volume": "42",
"journal_issue": "5",
"journal_pages": "2115-20",
"pub_year": "2004",
"pubmed_id": "15131178"
},
{
"title": "[A study of standardization to the rapid detection of Mycobacterium tuberculosis based on phage amplified biologically assay]",
"abstract": "OBJECTIVE: To evaluate the phage amplified biologically (PhaB) assay in the rapid detection of Mycobacteria tuberculosis in samples. METHODS: The conditions of the PhaB assay, including various infection times prior to addition of virucide and the effect of the inactivation agents which could inactive the extracellular phages, were investigated and compared. The sensitivity, specificity and accuracy of PhaB assay were tested when it was used in rapid detection of Mycobacterium tuberculosis. Some agents of the method, including Mycobacteriophage, virucide and help cells (Mycobacterium smegmatis) were investigated at different times when they were preserved at 4 degrees C. RESULTS: (1) The optimal infection time prior to addition of virucide was between 3 and 4 hours. Four percent FAS (ferrous ammonium sulphate) could inactive 1 x 10(9) PFU (plaque-forming unit) in five minutes. (2) The samples were positive when 80 - 200 CFU of Mycobacterium tuberculosis were present. However, the positive rate of non-Tuberculosis Mycobateria (NTM) was varied. All bacteria lived in the respiratory tract were negative. (3) The important agents used in this test showed optical effect when they were preserved at 4 degrees C. CONCLUSIONS: The method based on mycobacteriophage-amplified biologically assay could rapidly detect Mycobacterium tuberculosis, and it was effective, accurate, and simple to perform. It was appropriate for using in developing countries, compared with a variety of molecular techniques.",
"full_author_list": "Li Peng, Yong-Ai Luo, Guo-Zhi Wang",
"short_author_list": "Peng L, Luo YA, Wang GZ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15730777",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "27",
"journal_issue": "12",
"journal_pages": "806-10",
"pub_year": "2004",
"pubmed_id": "15730777"
},
{
"title": "Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M. smegmatis: identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species.",
"abstract": "The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were predominant in both the organisms. Multivariate statistical analysis showed that in both organisms, the genes were separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. The second major explanatory axis differentiates the genes according to their genome type. A comparison of the relative synonymous codon usage between 20 highly- and 20 lowly expressed genes from Bxz1 identified 21 codons, which are statistically over represented in the former group of genes. Further analysis found that the Bxz1- specific tRNA species could recognize 13 out of the 21 over represented synonymous codons, which incorporated 13 amino acid residues preferentially into the highly expressed proteins of Bxz1. In contrast, seven amino acid residues were preferentially incorporated into the lowly expressed proteins by 10 other tRNA species of Bxz1. This analysis predicts for the first time that the Bxz1-specific tRNA species modulates the optimal expression of its proteins during development.",
"full_author_list": "Keya Sahu, Sanjib Kumar Gupta, Tapash Chandra Ghosh, Subrata Sau",
"short_author_list": "Sahu K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15469738",
"journal": "Journal of biochemistry and molecular biology",
"journal_volume": "37",
"journal_issue": "4",
"journal_pages": "487-92",
"pub_year": "2004",
"pubmed_id": "15469738"
},
{
"title": "Detection of viable Mycobacterium avium subsp. paratuberculosis using luciferase reporter systems.",
"abstract": "Plasmid- and phage-based firefly luciferase reporter constructs were evaluated as rapid detection systems for viable Mycobacterium avium subsp. paratuberculosis (MAP). A MAP strain bearing a luciferase-encoding plasmid was detectable at 100 cells/mL in skim milk and 1000 cells/mL in whole milk. Three luciferase-encoding mycobacteriophage were evaluated for detection of wild-type MAP. The best of these, phAE85, allowed detection of >1000 cells/mL within 24-48 h. Membrane filtration did not improve the sensitivity of detection for either plasmid or phage reporters. Luciferase reporters show promise for rapid detection of viable MAP.",
"full_author_list": "Kyle C Sasahara, Michael J Gray, Sang J Shin, Kathryn J Boor",
"short_author_list": "Sasahara KC et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15992288",
"journal": "Foodborne pathogens and disease",
"journal_volume": "1",
"journal_issue": "4",
"journal_pages": "258-66",
"pub_year": "2004",
"pubmed_id": "15992288"
},
{
"title": "Cloning and sequencing analysis of the repressor gene of temperate mycobacteriophage L1.",
"abstract": "The wild-type and temperature-sensitive (ts) repressor genes were cloned from the temperate mycobacteriophage L1 and its mutant L1cIts391, respectively. A sequencing analysis revealed that the 131st proline residue of the wild-type repressor was changed to leucine in the ts mutant repressor. The 100% identity that was discovered between the two DNA regions of phages L1 and L5, carrying the same sets of genes including their repressor genes, strengthened the speculation that L1 is a minor variant of phage L5 or vice versa. A comparative analysis of the repressor proteins of different mycobacteriophages suggests that the mycobacteriophage-specific repressor proteins constitute a new family of repressors, which were possibly evolved from a common ancestor. Alignment of the mycobacteriophage-specific repressor proteins showed at least 7 blocks (designated I-VII) that carried 3-8 identical amino acid residues. The amino acid residues of blocks V, VI, and some residues downstream to block VI are crucial for the function of the L1 (or L5) repressor. Blocks I and II possibly form the turn and helix 2 regions of the HTH motif of the repressor. Block IV in the L1 repressor is part of the most charged region encompassing amino acid residues 72-92, which flanks the putative N-terminal basic (residues 1-71) and C-terminal acidic (residues 93-183) domains of L1 repressor.",
"full_author_list": "Subrata Sau, Partho Chattoraj, Tridib Ganguly, Chia Yen Lee, Nitai Chandra Mandal",
"short_author_list": "Sau S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15469704",
"journal": "Journal of biochemistry and molecular biology",
"journal_volume": "37",
"journal_issue": "2",
"journal_pages": "254-9",
"pub_year": "2004",
"pubmed_id": "15469704"
},
{
"title": "Method to integrate multiple plasmids into the mycobacterial chromosome.",
"abstract": "In order to create a system in which two independent plasmids can be integrated into a mycobacterial chromosome, a mycobacterial plasmid was constructed containing the phage attachment site attP from the mycobacteriophage L5 genome and additionally containing the bacterial attachment site, attB. This plasmid will integrate into the mycobacterial chromosome via recombination of the plasmid-borne attP site with the chromosomal attB site in the presence of a mycobacterial vector carrying the L5 integrase (int) gene. The integrated plasmid has a plasmid-borne attB site that is preserved and will accept the integration of additional mycobacterial plasmids containing the L5 attP site. This system should be useful in the construction of novel mycobacterial strains. In particular, this system provides a method by which several recombinant antigens or reporter constructs can be sequentially inserted into a mycobacterial strain and subsequently tested.",
"full_author_list": "Beatrice Saviola, William R Bishai",
"short_author_list": "Saviola B, Bishai WR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14718555",
"journal": "Nucleic acids research",
"journal_volume": "32",
"journal_issue": "1",
"journal_pages": "e11",
"pub_year": "2004",
"pubmed_id": "14718555"
},
{
"title": "Conserved translational frameshift in dsDNA bacteriophage tail assembly genes",
"abstract": "A programmed translational frameshift similar to frameshifts in retroviral gag-pol genes and bacterial insertion elements was found to be strongly conserved in tail assembly genes of dsDNA phages and to be independent of sequence similarities. In bacteriophage lambda, this frameshift controls production of two proteins with overlapping sequences, gpG and gpGT, that are required for tail assembly. We developed bioinformatic approaches to identify analogous -1 frameshifting sites and experimentally confirmed our predictions for five additional phages. Clear evidence was also found for an unusual but analogous -2 frameshift in phage Mu. Frameshifting sites could be identified for most phages with contractile or noncontractile tails whose length is controlled by a tape measure protein. Phages from a broad spectrum of hosts spanning Eubacteria and Archaea appear to conserve this frameshift as a fundamental component of their tail assembly mechanisms, supporting the idea that their tail genes share a common, distant ancestry.",
"full_author_list": "Xu J,\r\nHendrix RW,\r\nDuda RL",
"short_author_list": "Xu J, Hendrix RW, and Duda RL",
"article_url": "http://www.sciencedirect.com/science/article/pii/S1097276504005398",
"journal": "Mol Cell",
"journal_volume": "16",
"journal_issue": "1",
"journal_pages": "11-21",
"pub_year": "2004",
"pubmed_id": "15469818"
},
{
"title": "Characterization of polynucleotide kinase/phosphatase enzymes from Mycobacteriophages omega and Cjw1 and vibriophage KVP40.",
"abstract": "Coliphage T4 Pnkp is a bifunctional polynucleotide 5'-kinase/3'-phosphatase that catalyzes the end-healing steps of a RNA repair pathway. Here we show that mycobacteriophages Omega and Cjw1 and vibriophage KVP40 also encode bifunctional Pnkp enzymes consisting of a proximal 5'-kinase module with an essential P-loop motif, GXGK(S/T), and a distal 3'-phosphatase module with an essential acyl-phosphatase motif, DX- DGT. Biochemical characterization of the viral Pnkp proteins reveals several shared features, including an alkaline pH optimum for the kinase component, an intrinsic RNA kinase activity, and a homotetrameric or homodimeric quaternary structure, that distinguish them from the monomeric DNA-specific phosphatase/kinase enzymes found in mammals and fission yeast. Whereas the phage 5'-kinases differ from each other in their preferences for phosphorylation of 5' overhangs, blunt ends, or recessed ends, none of them displays the preference for recessed ends reported for mammalian DNA kinase. We hypothesize that Pnkp provides phages that have it with a means to evade an RNA-damaging antiviral host response. Genetic complementation of the essential end-healing steps of yeast tRNA splicing by the Omega and Cjw1 Pnkp enzymes establishes their capacity to perform RNA repair reactions in vivo. A supportive correlation is that Omega and Cjw1, which are distinguished from other mycobacteriophages by their possession of a Pnkp enzyme, are also unique among the mycobacteriophages in their specification of putative RNA ligases.",
"full_author_list": "Hui Zhu, Shenmin Yin, Stewart Shuman",
"short_author_list": "Zhu H, Yin S, Shuman S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15056675",
"journal": "The Journal of biological chemistry",
"journal_volume": "279",
"journal_issue": "25",
"journal_pages": "26358-69",
"pub_year": "2004",
"pubmed_id": "15056675"
},
{
"title": "[The prospect of application research on Mycobacteriophages]",
"abstract": "",
"full_author_list": "Yu-Hui Zhuang",
"short_author_list": "Zhuang YH",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15730775",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "27",
"journal_issue": "12",
"journal_pages": "799-800",
"pub_year": "2004",
"pubmed_id": "15730775"
},
{
"title": "Usefulness of a new mycobacteriophage-based technique for rapid diagnosis of pulmonary tuberculosis.",
"abstract": "A new mycobacteriophage-based technique (PhageTek MB) was compared with standard culture and staining techniques for diagnosis of pulmonary tuberculosis. A total of 2,048 respiratory specimens from 1,466 patients collected from February 2000 to March 2001 were studied by both (i) conventional methods (direct microscopic examination [auramine-rhodamine fluorochrome], and culture in BacT/ALERT 3D and solid media) and (ii) the PhageTek MB assay. This phenotypic test utilizes specific mycobacteriophages to detect the presence of live Mycobacterium tuberculosis complex organisms within a decontaminated clinical sample. Overall, 205 (10%) specimens were positive for mycobacteria (134 patients): 144 (70.2%) M. tuberculosis isolates and 61 (29.8%) nontuberculous mycobacterium isolates (30 Mycobacterium kansasii, 12 Mycobacterium xenopi, 9 Mycobacterium gordonae, 7 Mycobacterium avium complex, 2 Mycobacterium chelonae, and 1 Mycobacterium fortuitum isolate). PhageTek MB was more likely to give a positive result with specimens in which high numbers of acid-fast bacilli were observed on the smear. The sensitivity, specificity, and positive and negative predictive values of this mycobacteriophage-based technique versus culture for M. tuberculosis were 58.3, 99.1, 83.2, and 96.9%, respectively. PhageTek MB is a rapid (48-h), specific, safe, and easy-to-perform test. According to the prevalence of the disease in the population studied, the test would require improved sensitivity in order to be used as a screening test for routine diagnosis of respiratory tuberculosis in our setting.",
"full_author_list": "Fernando Alcaide, Nuria Galí, José Domínguez, Pilar Berlanga, Silvia Blanco, Pilar Orús, Rogelio Martín",
"short_author_list": "Alcaide F et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12843014",
"journal": "Journal of clinical microbiology",
"journal_volume": "41",
"journal_issue": "7",
"journal_pages": "2867-71",
"pub_year": "2003",
"pubmed_id": "12843014"
},
{
"title": "Rapid identification and susceptibility testing of Mycobacterium tuberculosis from MGIT cultures with luciferase reporter mycobacteriophages.",
"abstract": "In a prospective study conducted in a diagnostic laboratory in Mexico City, luciferase reporter mycobacteriophages (LRPs) were evaluated for their utility and performance in identification and antibiotic-susceptibility testing of Mycobacterium tuberculosis complex (MTC) isolates from MGIT-960 cultures. Eighty-four consecutive MGIT cultures recovered from 54 patients were included in this study. The LRPs confirmed mycobacterial growth in 79 (94 %) of 84 MGIT cultures. Failure to confirm growth was due to low inoculum (n = 1) or growth with non-tuberculous mycobacteria (n = 4). The median time to confirmation of MGIT cultures was 1 day (range 1-55). Confirmed cultures were identified with p-nitro-alpha-acetylamino-beta-hydroxypropiophenone (NAP), a selective inhibitor of MTC species, and results obtained with LRPs were compared with those obtained by BACTEC-460. The sensitivity and specificity of the LRP NAP test were respectively 97 and 100 %, and the median turnaround time for identification was 3 days with both methods. The accuracy and speed of the LRPs for susceptibility testing with rifampicin, streptomycin, isoniazid and ethambutol were compared with BACTEC-460 and discrepant results were tested by the conventional agar proportion method. In total, 72 MTC cultures were tested. The overall agreement between the LRPs and BACTEC-460 was 98.6 %. Four isolates (5.6 %) were falsely identified as ethambutol-resistant. The median turnaround time for susceptibility testing was 3 days (range 3-57) with the LRPs and 9 days (range 7-29) with BACTEC-460. LRPs offer an accurate and rapid approach for identification and susceptibility testing of M. tuberculosis from MGIT-960 cultures.",
"full_author_list": "Niaz Banaiee, Miriam Bobadilla-del-Valle, Paul F Riska, Svetoslav Bardarov, Peter M Small, Alfredo Ponce-de-Leon, William R Jacobs, Graham F Hatfull, Jose Sifuentes-Osornio",
"short_author_list": "Banaiee N et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12808076",
"journal": "Journal of medical microbiology",
"journal_volume": "52",
"journal_issue": "Pt 7",
"journal_pages": "557-61",
"pub_year": "2003",
"pubmed_id": "12808076"
},
{
"title": "An update on the diagnosis of tuberculosis.",
"abstract": "Tuberculosis (TB) continues to be the bane of mankind. Early diagnosis is the cornerstone of tuberculosis control strategies. Recent years have seen major advances in the fields of biotechnology and molecular biology with introduction of several new diagnostic techniques for tuberculosis and improvement in the existing ones. The new automated culture techniques have appreciably reduced the time required for detection and antimicrobial susceptibility testing. The molecular amplification techniques like the Polymerase Chain Reaction (PCR) have made the same-day diagnosis a reality. Improvements in serology and introduction of novel new techniques like the bacteriophage assays have also shown a lot of promise. However, most of these new techniques are too expensive and sophisticated to be of any practical benefit to the vast majority of TB patients living in underdeveloped countries like Pakistan for whom an early and inexpensive diagnosis remains as elusive as ever. In this article various existing modalities as well as the new advances in TB diagnostics are reviewed.",
"full_author_list": "Tariq Butt, Rifat Nadeem Ahmad, Syed Yousaf Kazmi, Raja Kamran Afzal, Abid Mahmood",
"short_author_list": "Butt T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/15569566",
"journal": "Journal of the College of Physicians and Surgeons--Pakistan : JCPSP",
"journal_volume": "13",
"journal_issue": "12",
"journal_pages": "728-34",
"pub_year": "2003",
"pubmed_id": "15569566"
},
{
"title": "Cloning and characterization of the promoters of temperate mycobacteriophage L1.",
"abstract": "Four putative promoters of the temperate mycobacteriophage L1 were cloned by detecting the beta-galactosidase reporter expression in E. coli transformants that carried L1 specific operon-fusion library. All of the four L1 promoters were also found to express differentially in the homologous environment of mycobacteria. Of the four promoters, two were suggested to be the putative early promoters of L1 since they express within 0 to 10 min of the initiation of the lytic growth of L1. One of the putative early promoters showed a relatively better and almost identical activity in both E. coli and M. smegmatis. By a sequence analysis, we suggest that the L1 insert that contained the stronger early promoter possibly carries two convergent E. coli sigma70-like L1 promoters, which are separated from each other by about 300 nucleotides. One of them is the early promoter of L1 as it showed a 100% similarity with the early Pleft promoter of the homoimmune phage L5. The second promoter, designated P4, was suggested for its appreciable level of reporter activity in the absence of the -10 element of the Pleft equivalent of L1. By analyzing most of the best characterized mycobacteriophages-specific promoters, including the L1 promoter P4, we suggest that both the -10 and -35 hexamers of the mycobacteriophage promoters are highly conserved and almost similar to the consensus -10 and -35 hexamers of the E. coli sigma70 promoters.",
"full_author_list": "Chandrani Chattopadhyay, Subrata Sau, Nitai C Mandal",
"short_author_list": "Chattopadhyay C, Sau S, Mandal NC",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14659078",
"journal": "Journal of biochemistry and molecular biology",
"journal_volume": "36",
"journal_issue": "6",
"journal_pages": "586-92",
"pub_year": "2003",
"pubmed_id": "14659078"
},
{
"title": "Transformation of Rhodococcus rhodnii, a symbiont of the Chagas disease vector Rhodnius prolixus, with integrative elements of the L1 mycobacteriophage.",
"abstract": "Elimination of vector populations through the use of insecticides is the principal means of controlling Chagas disease. Because of the limitations of insecticide use, we have been developing a new potential method of control, to be used in conjunction with insecticide programs, a method which utilizes genetically modified symbiotic bacteria. These transformed bacteria can express anti-parasitic agents in the gut of the bug where the trypanosomes also are found. Previous studies have shown that it is possible to transform Rhodococcus rhodnii with a shuttle plasmid that contains the gene for cecropin A, an insect anti-microbial peptide. The bacteria expressed this peptide and reduced or eliminated the number of trypanosomes in the bug Rhodnius prolixus [Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 3274]. In an effort to improve efficacy and transformation stability, we have begun using plasmids that contain integrative elements from the L1 mycobacteriophage to insert DNA into the genome of the bacterium. The integrative plasmid pBP5 contains the attachment site (attP) and integrase gene (int) of the L1 mycobacteriophage, an antibiotic resistance gene and the lacZ gene. After transforming R. rhodnii with pBP5, nine positive clones were obtained and six different insertions sites were identified. In each clone, the integrative plasmid is inserted only once, the lacZ gene is expressed intensely and, all clones but one, remained stable for 100 generations of culture in the absence of antibiotic selection. In addition, the construct remains stable throughout the life cycle of the bug. These data demonstrate that L1 mycobacteriophage integrative plasmids are significantly more stable than episomally located plasmids used in previous studies and will be greatly beneficial for use in the transformation of symbiotic bacteria of Chagas disease vectors.",
"full_author_list": "Ellen M Dotson, Bonnie Plikaytis, Thomas M Shinnick, Ravi V Durvasula, Charles B Beard",
"short_author_list": "Dotson EM et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12809804",
"journal": "Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in i",
"journal_volume": "3",
"journal_issue": "2",
"journal_pages": "103-9",
"pub_year": "2003",
"pubmed_id": "12809804"
},
{
"title": "Utility of an in-house mycobacteriophage-based assay for rapid detection of rifampin resistance in Mycobacterium tuberculosis clinical isolates.",
"abstract": "A rapid in-house mycobacteriophage-based assay to identify multidrug resistance by detecting the rifampin susceptibility of Mycobacterium tuberculosis in a microtiter plate format was evaluated. The sensitivity, specificity, and overall accuracy of the assay were 100%. This test is rapid to perform and suitable for widespread implementation.",
"full_author_list": "N Galí, J Domínguez, S Blanco, C Prat, M D Quesada, L Matas, V Ausina",
"short_author_list": "Galí N et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12791894",
"journal": "Journal of clinical microbiology",
"journal_volume": "41",
"journal_issue": "6",
"journal_pages": "2647-9",
"pub_year": "2003",
"pubmed_id": "12791894"
},
{
"title": "The orientation of mycobacteriophage Bxb1 integration is solely dependent on the central dinucleotide of attP and attB.",
"abstract": "Integration of the mycobacteriophage Bxb1 genome into its host chromosome is catalyzed by a serine-integrase, a member of the transposon-resolvase family of site-specific recombinases. These enzymes use a concerted mechanism of strand exchange involving double-stranded cleavages with two-base extensions, and covalent protein-DNA linkages via phosphoserine bonds. In contrast to the resolvase/invertase recombination systems--where there are strict requirements for a specific synaptic complex within which the catalytic potential of the enzyme is activated--synapsis of attP and attB by Bxb1 integrase is completely promiscuous, aligning the sites with equal proclivity in parallel and antiparallel alignments. Moreover, the catalytic potential of Bxb1 integrase is fully active in either alignment. As a consequence, the nonpalindromic central dinucleotide (5'-GT) at the center of attP and attB is the sole determinant of Bxb1 prophage orientation, and a single base pair substitution in the two sites is sufficient to eliminate orientation control.",
"full_author_list": "Pallavi Ghosh, Amy I Kim, Graham F Hatfull",
"short_author_list": "Ghosh P, Kim AI, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14636570",
"journal": "Molecular cell",
"journal_volume": "12",
"journal_issue": "5",
"journal_pages": "1101-11",
"pub_year": "2003",
"pubmed_id": "14636570"
},
{
"title": "Photographic and luminometric detection of luciferase reporter phages for drug susceptibility testing of clinical Mycobacterium tuberculosis isolates.",
"abstract": "Luciferase reporter phages (LRPs) have proven to be efficient tools for drug susceptibility testing of Mycobacterium tuberculosis. Luminometric detection of LRP activity offers higher sensitivity and quantitative results, while a Polaroid film detection method offers a \"low-tech\" inexpensive alternative that is called the Bronx box. In this work we evaluated, improved, and compared the performance of the luminometer and the Bronx box formats for drug susceptibility testing with LRPs by using 51 clinical isolates of M. tuberculosis, with the agar proportion method (PM) serving as reference. The sensitivity in detecting resistance to isoniazid and rifampin, antibiotics that define multidrug resistance (MDR), was 100% for both methods. The turnaround time for results was reduced from 3 weeks for PM to 54 or 94 h for luminometry or the Bronx box, respectively. These results support the utility of LRPs as a screening test for the surveillance of MDR tuberculosis.",
"full_author_list": "Manzour Hernando Hazbón, Nora Guarín, Beatriz Eugenia Ferro, Ana Lucía Rodríguez, Luz Angela Labrada, Rafael Tovar, Paul F Riska, William R Jacobs",
"short_author_list": "Hazbón MH et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14532245",
"journal": "Journal of clinical microbiology",
"journal_volume": "41",
"journal_issue": "10",
"journal_pages": "4865-9",
"pub_year": "2003",
"pubmed_id": "14532245"
},
{
"title": "Mycobacteriophage Bxb1 integrates into the Mycobacterium smegmatis groEL1 gene.",
"abstract": "Mycobacteriophage Bxb1 is a temperate phage of Mycobacterium smegmatis and forms stable lysogens in which the Bxb1 genome is integrated into the host chromosome. Bxb1 encodes an integrase of the large serine recombinase family that catalyses integration and excision of the Bxb1 genome. We show here that Bxb1 integrates into a chromosomal attB site located within the 3' end of the groEL1 gene such that integration results in alteration of the C-terminal 21 amino acid residues. An integration-proficient plasmid vector containing the Bxb1 integrase gene and flanking DNA sequences efficiently transforms M. smegmatis via integration at attB. Bxb1-integrated recombinants are stable and fully compatible with L5 integration vectors. Strand exchange occurs within an 8 bp common core sequence present in attB and within an attP site situated immediately upstream of the phage integrase gene. Establishment of a defined in vitro system for Bxb1 integration shows that recombination occurs efficiently without requirement for high-energy cofactors, divalent metals, DNA supercoiling or additional proteins.",
"full_author_list": "Amy I Kim, Pallavi Ghosh, Michelle A Aaron, Lori A Bibb, Shruti Jain, Graham F Hatfull",
"short_author_list": "Kim AI et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14617171",
"journal": "Molecular microbiology",
"journal_volume": "50",
"journal_issue": "2",
"journal_pages": "463-73",
"pub_year": "2003",
"pubmed_id": "14617171"
},
{
"title": "Control of directionality in L5 integrase-mediated site-specific recombination.",
"abstract": "Mycobacteriophage L5 is a temperate phage that forms lysogens in Mycobacterium smegmatis. These lysogens carry an integrated L5 prophage inserted at a specific chromosomal location and undergo subsequent excision during induction of lytic growth. Both the integrative and excisive site-specific recombination events are catalyzed by the phage-encoded tyrosine integrase (Int-L5) and require the host-encoded protein, mIHF. The directionality of these recombination events is determined by a second phage-encoded protein, Excise, the product of gene 36 (Xis-L5); integration occurs efficiently in the absence of Xis-L5 while excision is dependent upon it. We show here that Xis-L5 binds to attR DNA, introduces a DNA bend, and facilitates the formation of an intasome-R complex. This complex, which requires mIHF, Xis-L5 and Int-L5, readily recombines with a second intasome formed by Int-L5, mIHF and attL DNA (intasome-L) to generate the attP and attB products of excision. Xis-L5 also strongly inhibits Int-L5-mediated integrative recombination but does not prevent either the protein-DNA interactions that form the attP intasome (intasome-P) or the capture of attB, but acts later in the reaction presumably by preventing the formation of a recombinagenic synaptic intermediate. The mechanism of action of Xis-L5 appears to be purely architectural, influencing the assembly of protein-DNA structures solely through its DNA-binding and DNA-bending properties.",
"full_author_list": "John A Lewis, Graham F Hatfull",
"short_author_list": "Lewis JA, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12581642",
"journal": "Journal of molecular biology",
"journal_volume": "326",
"journal_issue": "3",
"journal_pages": "805-21",
"pub_year": "2003",
"pubmed_id": "12581642"
},
{
"title": "Evaluation of a rapid bacteriophage-based method for the detection of Mycobacterium tuberculosis in clinical samples.",
"abstract": "Rapid, sensitive and low-cost methods are needed urgently for the detection of Mycobacterium tuberculosis in clinical samples, especially in developing countries. To this end, the clinical performance of FASTPlaqueTB(TM) (a bacteriophage-based method) has been studied in parallel with microscopy, standard microbiological culture and in-house IS6110-based PCR methods. A total of 64 samples, including 42 sputum samples and 22 urine samples, were tested in this study. The sensitivity, specificity and overall accuracy values for the FASTPlaqueTB assay relative to that of culture were respectively 76.5, 95 and 90 %. The corresponding values for the in-house IS6110-based PCR assay were 88, 91 and 90 % and, for Ziehl-Neelsen staining, were 59, 95 and 85 %. FASTPlaqueTB gave better clinical performance with urine samples than with sputum samples (sensitivity, specificity and overall accuracy were 100 % with urine samples and 64, 93 and 84 % with sputum samples). The 100 % sensitivity of FASTPlaqueTB was higher than that of the corresponding values for PCR (67 %) with urine samples. In conclusion, FASTPlaqueTB proved to be sensitive, cheap relative to the PCR and rapid. It is able to detect M. tuberculosis in clinical samples within 1 day, reducing the time to diagnosis in comparison with culture.",
"full_author_list": "Ayman Mohamed Marei, Eman Mohamed El-Behedy, Heba Ali Mohtady, Afify Fahmy Afify",
"short_author_list": "Marei AM et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12676872",
"journal": "Journal of medical microbiology",
"journal_volume": "52",
"journal_issue": "Pt 4",
"journal_pages": "331-5",
"pub_year": "2003",
"pubmed_id": "12676872"
},
{
"title": "Strategies for mycobacterial genetics.",
"abstract": "Molecular genetics is one of the most rational approaches to determine particular gene functions. Inactivation of putative virulence genes is a powerful tool not only for characterization of pathogenic bacteria. This review summarizes recently described strategies for DNA transfer and gene inactivation in mycobacteria.",
"full_author_list": "Christian Morsczeck",
"short_author_list": "Morsczeck C",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14503790",
"journal": "International journal of medical microbiology : IJMM",
"journal_volume": "293",
"journal_issue": "4",
"journal_pages": "251-9",
"pub_year": "2003",
"pubmed_id": "14503790"
},
{
"title": "Phage evolution: new worlds of genomic diversity.",
"abstract": "A recent comparative survey of genomes of phages infecting mycobacteria reveals a vast combinatorial network of gene rearrangements and may provide general models for pattern and process in genome evolution.",
"full_author_list": "R Thane Papke, W Ford Doolittle",
"short_author_list": "Papke RT, Doolittle WF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12906814",
"journal": "Current biology : CB",
"journal_volume": "13",
"journal_issue": "15",
"journal_pages": "R606-7",
"pub_year": "2003",
"pubmed_id": "12906814"
},
{
"title": "Efficient switching of mycobacteriophage L5-based integrating plasmids in Mycobacterium tuberculosis.",
"abstract": "We previously used a mycobacteriophage L5-derived integrating vector to demonstrate that glnE and aroK are essential genes in Mycobacterium tuberculosis by showing that we were unable to excise the integrated vector when it carried the only functional copy of these genes. We tested three systems to replace the integrated copy with alternative alleles. The most efficient method was to transform the strain with a second copy of the integrating vector. Excision of the resident vector and integration of the incoming vector occurred at an extremely high efficiency. This technique will allow us to study the role and functionality of essential genes in this important human pathogen.",
"full_author_list": "Carey A Pashley, Tanya Parish",
"short_author_list": "Pashley CA, Parish T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14680701",
"journal": "FEMS microbiology letters",
"journal_volume": "229",
"journal_issue": "2",
"journal_pages": "211-5",
"pub_year": "2003",
"pubmed_id": "14680701"
},
{
"title": "Origins of highly mosaic mycobacteriophage genomes.",
"abstract": "Bacteriophages are the most abundant organisms in the biosphere and play major roles in the ecological balance of microbial life. The genomic sequences of ten newly isolated mycobacteriophages suggest that the bacteriophage population as a whole is amazingly diverse and may represent the largest unexplored reservoir of sequence information in the biosphere. Genomic comparison of these mycobacteriophages contributes to our understanding of the mechanisms of viral evolution and provides compelling evidence for the role of illegitimate recombination in horizontal genetic exchange. The promiscuity of these recombination events results in the inclusion of many unexpected genes including those implicated in mycobacterial latency, the cellular and immune responses to mycobacterial infections, and autoimmune diseases such as human lupus. While the role of phages as vehicles of toxin genes is well established, these observations suggest a much broader involvement of phages in bacterial virulence and the host response to bacterial infections.",
"full_author_list": "Marisa L Pedulla, Michael E Ford, Jennifer M Houtz, Tharun Karthikeyan, Curtis Wadsworth, John A Lewis, Debbie Jacobs-Sera, Jacob Falbo, Joseph Gross, Nicholas R Pannunzio, William Brucker, Vanaja Kumar, Jayasankar Kandasamy, Lauren Keenan, Svetsoslav Bardarov, Jordan Kriakov, Jeffrey G Lawrence, William R Jacobs, Roger W Hendrix, Graham F Hatfull",
"short_author_list": "Pedulla ML et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12705866",
"journal": "Cell",
"journal_volume": "113",
"journal_issue": "2",
"journal_pages": "171-82",
"pub_year": "2003",
"pubmed_id": "12705866"
},
{
"title": "Global phage diversity.",
"abstract": "Ten new mycobacteriophage genomes presented by show that most phage diversity remains uncharacterized. Extrapolation suggests that less than 0.0002% of the global phage metagenome has been sampled. The new genomes also contain a number of potential virulence factors that may be important in pathogenesis.",
"full_author_list": "Forest Rohwer",
"short_author_list": "Rohwer F",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12705861",
"journal": "Cell",
"journal_volume": "113",
"journal_issue": "2",
"journal_pages": "141",
"pub_year": "2003",
"pubmed_id": "12705861"
},
{
"title": "Transposition of Tn5367 in Mycobacterium marinum, using a conditionally recombinant mycobacteriophage.",
"abstract": "Mycobacterium marinum is a close relative of the obligate human pathogen Mycobacterium tuberculosis. As with M. tuberculosis, M. marinum causes intracellular infection of poikilothermic vertebrates and skin infection in humans. It is considered a valid model organism for the study of intracellular pathogenesis of mycobacteria. Low transformation efficiencies for this species have precluded approaches using mutant libraries in pathogenesis studies. We have adapted the conditionally replicating mycobacteriophage phAE94, originally developed as a transposon mutagenesis tool for M. tuberculosis, to meet the specific requirements of M. marinum. Conditions permissive for phage replication in M. tuberculosis facilitated highly efficient transposon delivery in M. marinum. Using this technique we succeeded in generating a representative mutant library of this species, and we conclude that TM4-derived mycobacteriophages are temperature-independent suicide vectors for M. marinum.",
"full_author_list": "Jan Rybniker, Martina Wolke, Christiane Haefs, Georg Plum",
"short_author_list": "Rybniker J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12591896",
"journal": "Journal of bacteriology",
"journal_volume": "185",
"journal_issue": "5",
"journal_pages": "1745-8",
"pub_year": "2003",
"pubmed_id": "12591896"
},
{
"title": "Mycothiol is essential for growth of Mycobacterium tuberculosis Erdman.",
"abstract": "Mycothiol (MSH) is the major low-molecular-mass thiol in mycobacteria and is associated with the protection of Mycobacterium tuberculosis from toxic oxidants and antibiotics. The biosynthesis of MSH is a multistep process, with the enzymatic reaction designated MshC being the ligase step in MSH production. A targeted disruption of the native mshC gene in M. tuberculosis Erdman produced no viable clones possessing either a disrupted mshC gene or reduced levels of MSH. However, when a second copy of the mshC gene was incorporated into the chromosome prior to the targeted disruption, multiple clones having the native gene disrupted and the second copy of mshC intact were obtained. These clones produced normal levels of MSH. These results demonstrate that the mshC gene and, more generally, the production of MSH are essential for the growth of M. tuberculosis Erdman under laboratory conditions.",
"full_author_list": "Dipti Sareen, Gerald L Newton, Robert C Fahey, Nancy A Buchmeier",
"short_author_list": "Sareen D et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14594852",
"journal": "Journal of bacteriology",
"journal_volume": "185",
"journal_issue": "22",
"journal_pages": "6736-40",
"pub_year": "2003",
"pubmed_id": "14594852"
},
{
"title": "Genome scale comparison of Mycobacterium avium subsp. paratuberculosis with Mycobacterium avium subsp. avium reveals potential diagnostic sequences.",
"abstract": "The genetic similarity between Mycobacterium avium subsp. paratuberculosis and other mycobacterial species has confounded the development of M. avium subsp. paratuberculosis-specific diagnostic reagents. Random shotgun sequencing of the M. avium subsp. paratuberculosis genome in our laboratories has shown >98% sequence identity with Mycobacterium avium subsp. avium in some regions. However, an in silico comparison of the largest annotated M. avium subsp. paratuberculosis contigs, totaling 2,658,271 bp, with the unfinished M. avium subsp. avium genome has revealed 27 predicted M. avium subsp. paratuberculosis coding sequences that do not align with M. avium subsp. avium sequences. BLASTP analysis of the 27 predicted coding sequences (genes) shows that 24 do not match sequences in public sequence databases, such as GenBank. These novel sequences were examined by PCR amplification with genomic DNA from eight mycobacterial species and ten independent isolates of M. avium subsp. paratuberculosis. From these analyses, 21 genes were found to be present in all M. avium subsp. paratuberculosis isolates and absent from all other mycobacterial species tested. One region of the M. avium subsp. paratuberculosis genome contains a cluster of eight genes, arranged in tandem, that is absent in other mycobacterial species. This region spans 4.4 kb and is separated from other predicted coding regions by 1,408 bp upstream and 1,092 bp downstream. The gene upstream of this eight-gene cluster has strong similarity to mycobacteriophage integrase sequences. The GC content of this 4.4-kb region is 66%, which is similar to the rest of the genome, indicating that this region was not horizontally acquired recently. Southern hybridization analysis confirmed that this gene cluster is present only in M. avium subsp. paratuberculosis. Collectively, these studies suggest that a genomics approach will help in identifying novel M. avium subsp. paratuberculosis genes as candidate diagnostic sequences.",
"full_author_list": "John P Bannantine, Emily Baechler, Qing Zhang, LingLing Li, Vivek Kapur",
"short_author_list": "Bannantine JP et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11923349",
"journal": "Journal of clinical microbiology",
"journal_volume": "40",
"journal_issue": "4",
"journal_pages": "1303-10",
"pub_year": "2002",
"pubmed_id": "11923349"
},
{
"title": "Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis.",
"abstract": "The authors have developed a simple and highly efficient system for generating allelic exchanges in both fast- and slow-growing mycobacteria. In this procedure a gene of interest, disrupted by a selectable marker, is cloned into a conditionally replicating (temperature-sensitive) shuttle phasmid to generate a specialized transducing mycobacteriophage. The temperature-sensitive mutations in the mycobacteriophage genome permit replication at the permissive temperature of 30 degrees C but prevent replication at the non-permissive temperature of 37 degrees C. Transduction at a non-permissive temperature results in highly efficient delivery of the recombination substrate to virtually all cells in the recipient population. The deletion mutations in the targeted genes are marked with antibiotic-resistance genes that are flanked by gammadelta-res (resolvase recognition target) sites. The transductants which have undergone a homologous recombination event can be conveniently selected on antibiotic-containing media. To demonstrate the utility of this genetic system seven different targeted gene disruptions were generated in three substrains of Mycobacterium bovis BCG, three strains of Mycobacterium tuberculosis, and Mycobacterium smegmatis. Mutants in the lysA, nadBC, panC, panCD, leuCD, Rv3291c and Rv0867c genes or operons were isolated as antibiotic-resistant (and in some cases auxotrophic) transductants. Using a plasmid encoding the gammadelta-resolvase (tnpR), the resistance genes could be removed, generating unmarked deletion mutations. It is concluded from the high frequency of allelic exchange events observed in this study that specialized transduction is a very efficient technique for genetic manipulation of mycobacteria and is a method of choice for constructing isogenic strains of M. tuberculosis, BCG or M. smegmatis which differ by defined mutations.",
"full_author_list": "Stoyan Bardarov, Svetoslav Bardarov Jr, Martin S Pavelka Jr, Vasan Sambandamurthy, Michelle Larsen, JoAnn Tufariello, John Chan, Graham Hatfull, William R Jacobs Jr",
"short_author_list": "Bardarov S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12368434",
"journal": "Microbiology (Reading, England)",
"journal_volume": "148",
"journal_issue": "Pt 10",
"journal_pages": "3007-17",
"pub_year": "2002",
"pubmed_id": "12368434"
},
{
"title": "Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns",
"abstract": "All genetic markers from phage T2 are partially excluded from the progeny of mixed infections with the related phage T4 (general, or phage exclusion). Several loci, including gene 56 of T2, are more dramatically excluded, being present in only ?1% of the progeny. This phenomenon is referred to as localized marker exclusion. Gene 69 is adjacent to gene 56 of T4 but is absent in T2, being replaced by completely nonhomologous DNA. We describe SegF, a novel site-specific DNA endonuclease encoded by gene 69, which is similar to GIY–YIG homing endonucleases of group I introns. Interestingly, SegF preferentially cleaves gene 56 of T2, both in vitro and in vivo, compared with that of phage T4. Repair of the double-strand break (DSB) results in the predominance of T4 genes 56 and segF in the progeny, with exclusion of the corresponding T2 sequences. Localized exclusion of T2 gene 56 is dependent on full-length SegF and is likely analogous to group I intron homing, in which repair of a DSB results in coconversion of markers in the flanking DNA. Phage T4 has many optional homing endonuclease genes similar to segF, whereas similar endonuclease genes are relatively rare in other members of the T-even family of bacteriophages. We propose that the general advantage enjoyed by T4 phage, over almost all of its relatives, is a cumulative effect of many of these localized events.",
"full_author_list": "Belle, A., M. Landthaler and D. A. Shub. ",
"short_author_list": "Belle, A., M. Landthaler and D. A. Shub. ",
"article_url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155333/",
"journal": "Genes Dev. ",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2002",
"pubmed_id": "155333"
},
{
"title": "Integration and excision of the Mycobacterium tuberculosis prophage-like element, phiRv1.",
"abstract": "The genomes of Mycobacterium tuberculosis H37Rv and CDC1551 each contain two prophage-like elements, phiRv1 and phiRv2. The phiRv1 element is not only absent from Mycobacterium bovis BCG but is in different locations within the two sequenced M. tuberculosis genomes; in both cases phiRv1 is inserted into a REP13E12 repeated sequence, which presumably contains the bacterial attachment site, attB, for phiRv1. Although phiRv1 is probably too small to encode infectious phage particles, it may nevertheless have an active integration/excision system and be capable of moving from one chromosomal position to another. We show here that the M. tuberculosis H37Rv phiRv1 element does indeed encode an active site-specific recombination system in which an integrase of the serine recombinase family (Rv1586c) catalyses integration and excision and a small, basic phiRv1-encoded protein (Rv1584c) controls the directionality of re-combination. Integration-proficient plasmid vectors derived from phiRv1 efficiently transform BCG, can utilize four of the seven REP13E12 sites present in BCG as attachment sites, and can occupy more than one site simultaneously.",
"full_author_list": "Lori A Bibb, Graham F Hatfull",
"short_author_list": "Bibb LA, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12354222",
"journal": "Molecular microbiology",
"journal_volume": "45",
"journal_issue": "6",
"journal_pages": "1515-26",
"pub_year": "2002",
"pubmed_id": "12354222"
},
{
"title": "Killing of Mycobacterium avium and Mycobacterium tuberculosis by a mycobacteriophage delivered by a nonvirulent mycobacterium: a model for phage therapy of intracellular bacterial pathogens.",
"abstract": "Mycobacterium avium causes disseminated infection in patients with acquired immune deficiency syndrome. Mycobacterium tuberculosis is a pathogen associated with the deaths of millions of people worldwide annually. Effective therapeutic regimens exist that are limited by the emergence of drug resistance and the inability of antibiotics to kill dormant organisms. The present study describes a system using Mycobacterium smegmatis, an avirulent mycobacterium, to deliver the lytic phage TM4 where both M. avium and M. tuberculosis reside within macrophages. These results showed that treatment of M. avium-infected, as well as M. tuberculosis-infected, RAW 264.7 macrophages, with M. smegmatis transiently infected with TM4, resulted in a significant time- and titer-dependent reduction in the number of viable intracellular bacilli. In addition, the M. smegmatis vacuole harboring TM4 fuses with the M. avium vacuole in macrophages. These results suggest a potentially novel concept to kill intracellular pathogenic bacteria and warrant future development.",
"full_author_list": "Lawrence Broxmeyer, Danuta Sosnowska, Elizabeth Miltner, Ofelia Chacón, Dirk Wagner, Jeffery McGarvey, Raúl G Barletta, Luiz E Bermudez",
"short_author_list": "Broxmeyer L et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12355367",
"journal": "The Journal of infectious diseases",
"journal_volume": "186",
"journal_issue": "8",
"journal_pages": "1155-60",
"pub_year": "2002",
"pubmed_id": "12355367"
},
{
"title": "Selective identification of new therapeutic targets of Mycobacterium tuberculosis by IVIAT approach.",
"abstract": "The in vivo induced antigen technology (IVIAT)(1) has been used for the identification of open reading frames (ORFs) which could be possible therapeutic targets. A recombinant lambdagt11:: Mycobacterium tuberculosis H37Rv expression library was screened with pooled TB patient sera preabsorbed with in vitro grown M. tuberculosis H37Rv. Preabsorption of pooled TB patient sera allowed identification of antigens specifically expressed or upregulated during infection and growth in vivo. Six ORFs were identified, of which four (rv0287, rv2402, rv3878 and rv1045) were of hypothetical functions. Rv0287 is a probable regulatory protein. Rv3878 is present uniquely in M. tuberculosis H37Rv and is a part of RDI deletion region of M. bovis BCG, which includes esat 6 region. This could be exploited as a tool for diagnosis. Two ORFs were assigned function solely on the basis of homology, dnaQ (rv3711c) and lpdA (rv3303c). dnaQ codes for the epsilon subunit of DNA polymerase III, which is responsible for the proofreading activity of the complex. lpdA codes for dihydrolipoamide dehydrogenase, which is a part of many multienzyme complexes such as pyruvate dehydrogenase, keto-acid dehydrogenase and alpha-ketoglutarate dehydrogenase. These two enzymes appear to be potential targets for drug development.",
"full_author_list": "D K Deb, P Dahiya, K K Srivastava, R Srivastava, B S Srivastava",
"short_author_list": "Deb DK et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12464489",
"journal": "Tuberculosis (Edinburgh, Scotland)",
"journal_volume": "82",
"journal_issue": "4-5",
"journal_pages": "175-82",
"pub_year": "2002",
"pubmed_id": "12464489"
},
{
"title": "Expression of Mycobacteriophage Ms6 lysis genes is driven by two sigma(70)-like promoters and is dependent on a transcription termination signal present in the leader RNA.",
"abstract": "A mycobacteriophage Ms6 strong promoter region (P(lys)) was isolated by using transcriptional fusions with the lacZ reporter gene. Two tandem sigma(70)-like promoter sequences (P1 and P2) were found in this region. DNA sequencing of the promoter downstream region revealed a 214-bp leader sequence followed by five adjacent coding regions of 231 bp (ORF1), 1,152 bp (ORF2), 996 bp (ORF3), 231 bp (ORF4), and 372 (ORF5). ORF1 has the potential to encode a 77-amino-acid protein which revealed similarity to mycobacteriophage TM4 gp90, a predicted protein with unknown function. ORF2 encodes a 384-amino-acid protein which is related to several bacteriophage amidases. This protein induced cell lysis upon addition of chloroform, confirming its mureinolytic activity. ORF3 encodes a 332-amino-acid protein which is related to TM4 gp30, a protein with sequence similarity to amidases. ORF4 encodes a 77-amino-acid holin-like protein with significant similarity to the holin of Lactococcus lactis r1t bacteriophage. ORF5 encodes a 124-amino-acid protein which is related to mycobacteriophage L5 gp30, a protein with unknown function. These data indicate that the promoter region P(lys) drives the transcription of the Ms6 lysis genes. An intrinsic transcription termination signal was identified in the leader sequence. Experiments using lacZ fusions showed that beta-galactosidase synthesis is inhibited when this transcription termination signal is present in the leader sequence. In conclusion, mycobacteriophage Ms6 cell lysis genes are expressed by their own promoter region, independently of virion structure and assembly protein genes. Moreover, an antitermination mechanism might be involved in their transcription regulation.",
"full_author_list": "Miguel Garcia, Madalena Pimentel, José Moniz-Pereira",
"short_author_list": "Garcia M, Pimentel M, Moniz-Pereira J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12003945",
"journal": "Journal of bacteriology",
"journal_volume": "184",
"journal_issue": "11",
"journal_pages": "3034-43",
"pub_year": "2002",
"pubmed_id": "12003945"
},
{
"title": "Rapid detection of rifampicin resistance in M. tuberculosis by phage assay.",
"abstract": "Increase in multidrug-resistant M. tuberculosis (MDR-TB) has become a great cause of concern and rifampicin resistance is considered to be a good predictor of MDR-TB in many parts of the world. Its rapid detection will allow alteration in treatment regimens in time to reduce the spread of the disease. Detection of rifampicin resistance by phage assay is a useful tool as mycobacteriophages are specific for M. tuberculosis complex and detect viable cells only. In our study, we analyzed 85 samples for rifampicin resistance using a novel mycobacteriophage based test (Phage assay) and radiometric BACTEC 460 TB. Of the 85 samples, 70 (82.35%) were resistant and 12 (14.10%) were sensitive by both methods. Our study yielded a sensitivity and specificity of 100% and 80% respectively. A good correlation was observed with conventional LJ proportion method. We conclude that phage assay allows determination of rifampicin resistance within 48 hours from culture, reducing the time taken to define susceptibility results by BACTEC 460 TB and LJ proportion method (5-7 days and 6-8 weeks respectively).",
"full_author_list": "A Krishnamurthy, C Rodrigues, A P Mehta",
"short_author_list": "Krishnamurthy A, Rodrigues C, Mehta AP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/17657073",
"journal": "Indian journal of medical microbiology",
"journal_volume": "20",
"journal_issue": "4",
"journal_pages": "211-4",
"pub_year": "2002",
"pubmed_id": "17657073"
},
{
"title": "Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches.",
"abstract": "The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral \"species\" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.",
"full_author_list": "Lawrence JG, Hatfull GF, Hendrix RW.",
"short_author_list": "Lawrence JG, Hatfull GF, Hendrix RW.",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12169615",
"journal": "Journal of Bacteriology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "2002",
"pubmed_id": "12169615"
},
{
"title": "Plasmidic versus insertional cloning of heterologous genes in Mycobacterium bovis BCG: impact on in vivo antigen persistence and immune responses.",
"abstract": "Bivalent recombinant strains of Mycobacterium bovis BCG (rBCG) expressing the early regulatory nef and the structural gag(p26) genes from the simian immunodeficiency virus (SIV) SIVmac251 were engineered so that both genes were cotranscribed from a synthetic operon. The expression cassette was cloned into a multicopy-replicating vector, and the expression levels of both nef and gag in the bivalent rBCG(nef-gag) strain were found to be comparable to those of monovalent rBCG(nef) or rBCG(gag) strains. However, extrachromosomal cloning of the nef-gag operon into a replicative plasmid resulted in strains of low genetic stability that rapidly lost the plasmid in vivo. Thus, the nef-gag operon was inserted site specifically into the BCG chromosome by means of mycobacteriophage Ms6-derived vectors. The resulting integrative rBCG(nef-gag) strains showed very high genetic stability both in vitro and in vivo. The in vivo expression of the heterologous genes was much longer lived when the expression cassette was inserted into the BCG chromosome. In one of the strains obtained, integrative cloning did not reduce the expression levels of the genes even though a single copy was present. Accordingly, this strain induced cellular immune responses of the same magnitude as that of the replicative rBCG strain containing several copies of the genes.",
"full_author_list": "I Méderlé, I Bourguin, D Ensergueix, E Badell, J Moniz-Peireira, B Gicquel, N Winter",
"short_author_list": "Méderlé I et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11748196",
"journal": "Infection and immunity",
"journal_volume": "70",
"journal_issue": "1",
"journal_pages": "303-14",
"pub_year": "2002",
"pubmed_id": "11748196"
},
{
"title": "Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus.",
"abstract": "We report the complete 36,717 bp genome sequence of bacteriophage Mu and provide an analysis of the sequence, both with regard to the new genes and other genetic features revealed by the sequence itself and by a comparison to eight complete or nearly complete Mu-like prophage genomes found in the genomes of a diverse group of bacteria. The comparative studies confirm that members of the Mu-related family of phage genomes are genetically mosaic with respect to each other, as seen in other groups of phages such as the phage lambda-related group of phages of enteric hosts and the phage L5-related group of mycobacteriophages. Mu also possesses segments of similarity, typically gene-sized, to genomes of otherwise non-Mu-like phages. The comparisons show that some well-known features of the Mu genome, including the invertible segment encoding tail fiber sequences, are not present in most members of the Mu genome sequence family examined here, suggesting that their presence may be relatively volatile over evolutionary time. The head and tail-encoding structural genes of Mu have only very weak similarity to the corresponding genes of other well-studied phage types. However, these weak similarities, and in some cases biochemical data, can be used to establish tentative functional assignments for 12 of the head and tail genes. These assignments are strongly supported by the fact that the order of gene functions assigned in this way conforms to the strongly conserved order of head and tail genes established in a wide variety of other phages. We show that the Mu head assembly scaffolding protein is encoded by a gene nested in-frame within the C-terminal half of another gene that encodes the putative head maturation protease. This is reminiscent of the arrangement established for phage lambda.",
"full_author_list": "Gregory J Morgan, Graham F Hatfull, Sherwood Casjens, Roger W Hendrix",
"short_author_list": "Morgan GJ et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11922669",
"journal": "Journal of molecular biology",
"journal_volume": "317",
"journal_issue": "3",
"journal_pages": "337-59",
"pub_year": "2002",
"pubmed_id": "11922669"
},
{
"title": "The common aromatic amino acid biosynthesis pathway is essential in Mycobacterium tuberculosis.",
"abstract": "Attempts to construct Mycobacterium tuberculosis strains with a defect in the common aromatic amino acid biosynthesis pathway were made. In other bacteria the genes of this pathway (aro) can be disrupted in the presence of suitable media supplements. The genomic organization of the aro genes in M. tuberculosis reveals that there is one operon (aroCKBQ) and three isolated aro genes (aroE, aroG and aroA). The aroK gene was chosen as a target for disruption; this encodes shikimate kinase, which catalyses the fifth step in chorismate biosynthesis. Attempts to replace the wild-type aroK gene with a disrupted allele (aroKDelta::hyg) by a two-step homologous recombination procedure were unsuccessful in a wild-type strain. When a second functional copy of aroK was integrated into the chromosome, it was possible to isolate a strain carrying the disrupted gene. Excision of the L5-integrated copy of aroK by the L5 excisionase could be not be achieved in the strain carrying the disrupted copy, but was possible in a strain carrying a wild-type copy. These results demonstrate that the chorismate pathway is essential for the viability of M. tuberculosis.",
"full_author_list": "Tanya Parish, Neil G Stoker",
"short_author_list": "Parish T, Stoker NG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/12368440",
"journal": "Microbiology (Reading, England)",
"journal_volume": "148",
"journal_issue": "Pt 10",
"journal_pages": "3069-77",
"pub_year": "2002",
"pubmed_id": "12368440"
},
{
"title": "Luciferase reporter mycobacteriophages for detection, identification, and antibiotic susceptibility testing of Mycobacterium tuberculosis in Mexico.",
"abstract": "The utility of luciferase reporter mycobacteriophages (LRPs) for detection, identification, and antibiotic susceptibility testing of Mycobacterium tuberculosis was prospectively evaluated in a clinical microbiology laboratory in Mexico City, Mexico. Five hundred twenty-three consecutive sputum samples submitted to the laboratory during a 5-month period were included in this study. These specimens were cultivated in Middlebrook 7H9 (MADC), MGIT, and Löwenstein-Jensen (LJ) media. Of the 71 mycobacterial isolates recovered with any of the three media, 76% were detected with the LRPs, 97% were detected with the MGIT 960 method, and 90% were detected with LJ medium. When contaminated specimens were excluded from the analysis, the LRPs detected 92% (54 of 59) of the cultures. The median time to detection of bacteria was 7 days with both the LRPs and the MGIT 960 method. LRP detection of growth in the presence of p-nitro-alpha-acetylamino-beta-hydroxypropiophenone (NAP) was used for selective identification of M. tuberculosis complex (MTC) and compared to identification with BACTEC 460. Using the LRP NAP test, 47 (94%) out of 50 isolates were correctly identified as tuberculosis complex. The accuracy and speed of LRP antibiotic susceptibility testing with rifampin, streptomycin, isoniazid, and ethambutol were compared to those of the BACTEC 460 method, and discrepant results were checked by the conventional proportion method. In total, 50 MTC isolates were tested. The overall agreement between the LRP and BACTEC 460 results was 98.5%. The median LRP-based susceptibility turnaround time was 2 days (range, 2 to 4 days) compared to 10.5 days (range, 7 to 16 days) by the BACTEC 460 method. Phage resistance was not detected in any of the 243 MTC isolates tested. Mycobacteriophage-based approaches to tuberculosis diagnostics can be implemented in clinical laboratories with sensitivity, specificity, and rapidity that compare favorably with those of the MGIT 960 and BACTEC 460 methods. The phages currently provide the fastest phenotypic assay for susceptibility testing.",
"full_author_list": "N Banaiee, M Bobadilla-Del-Valle, S Bardarov, P F Riska, P M Small, A Ponce-De-Leon, W R Jacobs, G F Hatfull, J Sifuentes-Osornio",
"short_author_list": "Banaiee N et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11682502",
"journal": "Journal of clinical microbiology",
"journal_volume": "39",
"journal_issue": "11",
"journal_pages": "3883-8",
"pub_year": "2001",
"pubmed_id": "11682502"
},
{
"title": "Use of the mycobacteriophage L5 excisionase in Mycobacterium tuberculosis to demonstrate gene essentiality.",
"abstract": "SWTTING: Demonstrating that a gene is essential is always difficult, but this is particularly true for a slow-growing organism such as Mycobacterium tuberculosis. One method currently used is to show that homologous recombination leading to gene inactivation only occurs in the presence of a second copy of the gene, but obtaining statistically significant data can be prohibitively difficult. L5-based integrating plasmids have been widely used in the genetic analysis of mycobacteria. The L5 excisionase has been used in Mycobacterium smegmatis to excise and recover these plasmids from chromosome. OBJECTIVE: Our aims were to establish whether the L5 excisionase could function in M. tuberculosis to remove an L5-based integrated plasmid and, if so, to use this technology as the basis for an improved method for determining whether a gene is essential. DESIGN: We took two strains of M. tuberculosis carrying the essential gene glnE integrated into the chromosome on an L5-based plasmid, one of which lacked the functional chromosomal copy of the gene. We transformed these with vectors expressing the L5 excisionase and looked for loss of the integrated plasmid. RESULTS: We obtained efficient excision of an integrated vector from the wild-type strain. However, when the integrated vector carried the only functional copy of the essential gene glnE, the numbers of colonies recovered were reduced to background levels. CONCLUSION: The L5 excisionase does function in M. tuberculosis and can be used to confirm the essentiality of a gene. This technology also allows further analysis of essential genes that is difficult or impossible using current methods.",
"full_author_list": "T Parish, J Lewis, N G Stoker",
"short_author_list": "Parish T, Lewis J, Stoker NG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11800587",
"journal": "Tuberculosis (Edinburgh, Scotland)",
"journal_volume": "81",
"journal_issue": "5-6",
"journal_pages": "359-64",
"pub_year": "2001",
"pubmed_id": "11800587"
},
{
"title": "Instability and site-specific excision of integration-proficient mycobacteriophage L5 plasmids: development of stably maintained integrative vectors.",
"abstract": "Integrative vectors expressing foreign genes are used as tools for the development of recombinant vaccines in mycobacteria since it is assumed that these vectors are stably maintained even without antibiotic selection. We here demonstrate that integration-proficient vectors are lost from the mycobacterial genome in high frequency. Loss of integrated vectors occurred in recA+ and in recA-strains, indicating a RecA-independent mechanism. Loss of the integrated vector was prevented when integrase gene function was carried on a separate plasmid that is unable to replicate in mycobacteria, indicating that excision is a function of integrase. By providing attP in cis and integrase function in trans, vectors integrating at the attB site are stably maintained, even when carrying genes that deleteriously affect the host.",
"full_author_list": "B Springer, P Sander, L Sedlacek, K Ellrott, E C Böttger",
"short_author_list": "Springer B et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11310445",
"journal": "International journal of medical microbiology : IJMM",
"journal_volume": "290",
"journal_issue": "8",
"journal_pages": "669-75",
"pub_year": "2001",
"pubmed_id": "11310445"
},
{
"title": "A high yielding mutant of mycobacteriophage L1 and its application as a diagnostic tool.",
"abstract": "L1 is a lysogenic phage of mycobacteria, which along with L5 and D29 constitute a closely linked family of homoimmune mycobacteriophages. These phages can be potentially used for genetic engineering of mycobacteria and diagnosis of mycobacterial infection. The effectiveness of such phage based systems depends on the efficiency with which they infect and grow within target cells. While working with phage L1c1ts which is a temperature sensitive mutant of phage L1, we observed that high yielding phage stocks were generated by repeated passage through the host, Mycobacterium smegmatis. A plaque purified mutant L1-P2, obtained from one such high yielding stock, when analyzed further was found to infect host cells with increased efficiency. The DNA obtained from L1-P2 was examined by restriction digestion, and it was observed that spontaneous loss of DNA fragment from the right arm, which encodes early regulatory factors, had occurred. It has been further demonstrated that the high yielding property of the mutant phage could be utilized to increase the sensitivity of mycobacteriophage-based detection systems.",
"full_author_list": "S Chatterjee, M Mitra, S K Das Gupta",
"short_author_list": "Chatterjee S, Mitra M, Das Gupta SK",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10867233",
"journal": "FEMS microbiology letters",
"journal_volume": "188",
"journal_issue": "1",
"journal_pages": "47-53",
"pub_year": "2000",
"pubmed_id": "10867233"
},
{
"title": "Transcriptional regulation and immunity in mycobacteriophage Bxb1.",
"abstract": "Mycobacteriophage Bxb1 is a temperate phage of Mycobacterium smegmatis that shares a similar genome organization to mycobacteriophage L5, although the two phages are heteroimmune. We have investigated the regulatory circuitry of Bxb1 and found that it encodes a repressor, gp69, which regulates at least two promoters, an early lytic promoter, Pleft, and the divergent promoter, Pright. Bxb1 gp69 is 41% identical to the L5 repressor (gp71) and binds to repressor binding sites that conform to a similar, but distinct, 13 bp asymmetric consensus sequence to that for the L5 gp71 binding sites. The two phage repressors have a strong preference for their cognate binding sites, thus accounting for their immunity phenotypes. The Bxb1 genome contains 34 putative repressor binding sites located throughout the genome, but situated within short intergenic spaces and orientated in only one direction relative to the direction of transcription. Comparison with the locations of repressor binding sites within the L5 genome provides insights into how these unusual regulatory systems evolve.",
"full_author_list": "S Jain, G F Hatfull",
"short_author_list": "Jain S, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11123672",
"journal": "Molecular microbiology",
"journal_volume": "38",
"journal_issue": "5",
"journal_pages": "971-85",
"pub_year": "2000",
"pubmed_id": "11123672"
},
{
"title": "Functional role of mycobacteriophage transfer RNAs.",
"abstract": "",
"full_author_list": "T Kunisawa",
"short_author_list": "Kunisawa T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10860710",
"journal": "Journal of theoretical biology",
"journal_volume": "205",
"journal_issue": "1",
"journal_pages": "167-70",
"pub_year": "2000",
"pubmed_id": "10860710"
},
{
"title": "Identification and characterization of mycobacteriophage L5 excisionase.",
"abstract": "The well-characterized mycobacteriophage L5 forms stable lysogens in Mycobacterium smegmatis. Establishment of lysogeny involves integration of the phage genome into the chromosome of its mycobacterial hosts through an integrase-mediated site-specific recombination event. As L5 lysogens spontaneously generate free phage particles, prophage excision must also occur, although an L5 excisionase gene had not been identified. We show here that L5 gene 36 encodes the phage excisionase and is a small, heat-stable 56-amino-acid protein that strongly stimulates excisive recombination both in vivo and in vitro. The ability to manipulate the highly directional phage integration and excision reactions will provide powerful tools for the introduction, curing and recovery of foreign genes in recombinant mycobacterial strains.",
"full_author_list": "J A Lewis, G F Hatfull",
"short_author_list": "Lewis JA, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10652095",
"journal": "Molecular microbiology",
"journal_volume": "35",
"journal_issue": "2",
"journal_pages": "350-60",
"pub_year": "2000",
"pubmed_id": "10652095"
},
{
"title": "[Rapid rifampicin susceptibility test by using recombinant mycobacteriophages]",
"abstract": "OBJECTIVE: To set up a fast, sensitive and specific way to detect mycobacteria and rifampicin susceptibility to mycobacteria by using recombinant mycobacteriophages and bioluminescent method. METHODS: Firstly detected the luciferase activity in different bacteria by using mycobacteriophages, then assessed the best drug concentration of rifampicin for drug susceptibility test in luciferase reporter assay, and lastly used the above conditions to decide rifampicin susceptibilities to different mycobacteria and compare the result with L-J medium culture. RESULTS: Bacteriophages had high light production specifically in mycobacteria and only very low light production in E. coli, the difference being obvious. The light production of rifampicin-resisitant mycobacterium strains was much higher than that of sensitive strains in culture with rifampicin(P < 0.05). Different drug concentrations of rifampicin were used to optimize drug concentration for rifampicin drug susceptibility test and the optimum concentration was found to be 2 micrograms/ml. The correlation of drug susceptibility test between luciferase reporter phages to L-J medium in standard strains and clinical isolates was the sarce. Temperature sensitive Phage 88 was more sensitive than Phage 40(P < 0.05). The time for drug resistance test was 72 hours. CONCLUSIONS: Luciferase reporter phage can detect mycobacteria specifically and can be used in rifampicin susceptibility test. This assay is a fast, sensitive and specific method to detect mycobacterium strains and their resistance to rifampicin.",
"full_author_list": "B Lü, Z Fu, S Xu",
"short_author_list": "Lü B, Fu Z, Xu S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11778263",
"journal": "Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and",
"journal_volume": "23",
"journal_issue": "8",
"journal_pages": "480-4",
"pub_year": "2000",
"pubmed_id": "11778263"
},
{
"title": "Rapid screening of Mycobacterium tuberculosis for susceptibility to rifampicin and streptomycin.",
"abstract": "OBJECTIVE: To investigate rapid detection of drug-resistant tuberculosis using the genotypic Inno-LiPA Rif TB assay and a novel, low-cost, bacteriophage-based susceptibility assay. DESIGN: The performance of the microwell phage replication assay (MPRA) on 18 isolates from suspected multidrug-resistant tuberculosis patients was compared to the LiPA assay performed directly on sputum specimens. Mutations in the rpoB gene identified by LiPA that confer resistance to rifampicin (RMP) were confirmed by DNA sequencing, while susceptibilities were confirmed by the proportion method and BACTEC. A further 19 isolates undergoing routine screening for both RMP and streptomycin susceptibility were included for comparison. RESULTS: Susceptibility to RMP was determined for 17/18 (94.4%) sputum specimens tested by LiPA. Correlation between MPRA, molecular and conventional methods was 100% for the detection of RMP susceptibility. However, for susceptibility to streptomycin one discrepant result was found: an isolate susceptible to streptomycin by the proportion method was found resistant by MPRA to 2 microg/ml of streptomycin. Similarly, an isolate initially resistant by MPRA upon re-testing was found susceptible in agreement with the conventional method. CONCLUSION: LiPA enables rapid detection of drug-resistant infection, while MPRA offers simple, low-tech testing of drug susceptibilities that may be appropriate for application in low-income countries.",
"full_author_list": "R McNerney, P Kiepiela, K S Bishop, P M Nye, N G Stoker",
"short_author_list": "McNerney R et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10654647",
"journal": "The international journal of tuberculosis and lung disease : the official journal of the Internation",
"journal_volume": "4",
"journal_issue": "1",
"journal_pages": "69-75",
"pub_year": "2000",
"pubmed_id": "10654647"
},
{
"title": "Genome organization and characterization of mycobacteriophage Bxb1.",
"abstract": "Mycobacteriophage Bxb1 is a temperate phage of Mycobacterium smegmatis. The morphology of Bxb1 particles is similar to that of mycobacteriophages L5 and D29, although Bxb1 differs from these phages in other respects. First, it is heteroimmune with L5 and efficiently forms plaques on an L5 lysogen. Secondly, it has a different host range and fails to infect slow-growing mycobacteria, using a receptor system that is apparently different from that of L5 and D29. Thirdly, it is the first mycobacteriophage to be described that forms a large prominent halo around plaques on a lawn of M. smegmatis. The sequence of the Bxb1 genome shows that it possesses a similar overall organization to the genomes of L5 and D29 and shares weak but detectable DNA sequence similarity to these phages within the structural genes. However, Bxb1 uses a different system of integration and excision, a repressor with different specificity to that of L5 and encodes a large number of novel gene products including several with enzymatic functions that could degrade or modify the mycobacterial cell wall.",
"full_author_list": "J Mediavilla, S Jain, J Kriakov, M E Ford, R L Duda, W R Jacobs, R W Hendrix, G F Hatfull",
"short_author_list": "Mediavilla J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11123671",
"journal": "Molecular microbiology",
"journal_volume": "38",
"journal_issue": "5",
"journal_pages": "955-70",
"pub_year": "2000",
"pubmed_id": "11123671"
},
{
"title": "Assembly and activation of site-specific recombination complexes.",
"abstract": "Site-specific recombination is responsible for a broad range of biological phenomena, including DNA inversion, resolution of transposition intermediates, and the integration and excision of bacteriophage genomes. Integration of mycobacteriophage L5 is catalyzed by a phage-encoded integrase with recombination occurring between specific attachment sites on the phage and mycobacterial chromosomes (attP and attB, respectively). Although some site-specific recombination systems simply involve binding of the recombinase to the sites of strand exchange, synapsis, and recombination, phage systems typically require the assembly of higher-order structures within which the recombinational potential of integrase is activated. The requirement for these structures derives from the necessity to regulate the directionality of recombination-either integration or excision-which must be closely coordinated with other aspects of the phage growth cycles. We show herein that there are multiple pathways available for the assembly of L5 recombination complexes, including the early synapsis of the attP and attB DNAs. This process is in contrast to the model for lambda integration and illustrates the different usage of molecular machineries to accomplish the same biological outcome.",
"full_author_list": "C E Peña, J M Kahlenberg, G F Hatfull",
"short_author_list": "Peña CE, Kahlenberg JM, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10869430",
"journal": "Proceedings of the National Academy of Sciences of the United States of America",
"journal_volume": "97",
"journal_issue": "14",
"journal_pages": "7760-5",
"pub_year": "2000",
"pubmed_id": "10869430"
},
{
"title": "Simple low-cost test for drug-resistant tuberculosis.",
"abstract": "",
"full_author_list": "T Toma",
"short_author_list": "Toma T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/11143200",
"journal": "Bulletin of the World Health Organization",
"journal_volume": "78",
"journal_issue": "11",
"journal_pages": "1370",
"pub_year": "2000",
"pubmed_id": "11143200"
},
{
"title": "Evaluation of reverse transcription-PCR and a bacteriophage-based assay for rapid phenotypic detection of rifampin resistance in clinical isolates of Mycobacterium tuberculosis.",
"abstract": "New rapid phenotypic assays for the detection of rifampin resistance in Mycobacterium tuberculosis have recently been described, but most of these require liquid cultures, which reduces the utility of many tests in terms of turnaround times. In the United Kingdom, over 90% of rifampin-resistant isolates are also resistant to isoniazid, so rifampin resistance can be used as a sensitive marker for multidrug-resistant tuberculosis. In this study, two new rapid phenotypic assays were compared to the standard resistance ratio method on 91 clinical isolates of M. tuberculosis. One, the phage amplified biologically (PhaB) assay, has been described previously and is based on the inability of susceptible isolates of M. tuberculosis to support the replication of bacteriophage D29 in the presence of inhibitory doses of rifampin. The other employed reverse transcription (RT)-PCR to demonstrate a reduction in inducible dnaK mRNA levels in susceptible isolates treated with rifampin. After incubation for 18 h with 4 microg of rifampin per ml, the PhaB assay showed concordance with the resistance ratio method for 46 of 46 (100%) susceptible and 31 of 31 (100%) resistant isolates, while RT-PCR showed concordance for 46 of 48 (96%) susceptible and 35 of 36 (97%) resistant isolates. We believe these assays provide a reliable rapid means of susceptibility testing with a total turnaround time of only 48 h, although the PhaB assay is better in terms of its lower technical demand and cost and its applicability to tuberculosis susceptibility testing in developing countries.",
"full_author_list": "I J Eltringham, F A Drobniewski, J A Mangan, P D Butcher, S M Wilson",
"short_author_list": "Eltringham IJ et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10523546",
"journal": "Journal of clinical microbiology",
"journal_volume": "37",
"journal_issue": "11",
"journal_pages": "3524-7",
"pub_year": "1999",
"pubmed_id": "10523546"
},
{
"title": "Evaluation of a bacteriophage-based assay (phage amplified biologically assay) as a rapid screen for resistance to isoniazid, ethambutol, streptomycin, pyrazinamide, and ciprofloxacin among clinical isolates of Mycobacterium tuberculosis.",
"abstract": "Rapid molecular assays for the detection of mutations associated with rifampin resistance in Mycobacterium tuberculosis are commercially available. However, they are complex and expensive and have predictive values of 90 to 95%. Molecular assays for other drugs are less predictive of resistance. Ideally, assays based on phenotypic markers should be used for susceptibility testing, but these can take weeks to complete. We previously described a rapid phenotypic assay, the phage amplified biologically (PhaB) assay, for the rapid determination of rifampin and isoniazid susceptibility in clinical isolates of M. tuberculosis. In this study, we extended the assay to the study of ethambutol, pyrazinamide, streptomycin, and ciprofloxacin. After the optimization of antibiotic concentrations and incubation conditions, the assay was applied to each drug for a total of 157 isolates. The correlations between the results of the PhaB assay and the resistance ratio method were 94% for isoniazid, 96% for streptomycin, 100% for ciprofloxacin, 88% for ethambutol, and 87% for pyrazinamide. For ciprofloxacin, ethambutol, and pyrazinamide, significantly better correlations were found when a 90% reduction in plaque count was used as the cutoff. Turnaround times for the PhaB assay were 2 to 3 days, compared with 10 days for the resistance ratio method. We believe that this low-cost assay may have widespread applicability for the rapid screening of drug resistance in M. tuberculosis isolates, especially in developing countries.",
"full_author_list": "I J Eltringham, S M Wilson, F A Drobniewski",
"short_author_list": "Eltringham IJ, Wilson SM, Drobniewski FA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10523547",
"journal": "Journal of clinical microbiology",
"journal_volume": "37",
"journal_issue": "11",
"journal_pages": "3528-32",
"pub_year": "1999",
"pubmed_id": "10523547"
},
{
"title": "New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv.",
"abstract": "The genome sequence of Mycobacterium tuberculosis H37Rv was found to contain 56 loci with homology to insertion sequences (ISs). As well as the previously described IS6110, IS1081, IS1547 and IS-like elements, new ISs belonging to the IS3, IS5, IS21, IS30, IS110, IS256 and ISL3 families were identified. In addition, six ISs created a grouping of their own to form a new family (the IS1535 family). Elements with similarity to ISs in other actinomycetes were identified, suggesting the movement of ISs between related genera. The location of ISs on the chromosome revealed that an approximately 600 kb region close to the origin of replication lacks ISs, pointing to the possible detrimental effect of insertions in this area. Analysis of the distribution of ISs through the tubercle strains Mycobacterium africanum, M. microti, M. bovis, M. bovis BCG Pasteur, M. tuberculosis H37Ra, M. tuberculosis CSU#93 and 29 clinical isolates revealed that only IS1532, IS1533, 1S1534, and IS1561' were absent from some of the strains tested. A novel repeated sequence, the REP13E12 family, is described that is present in seven copies on the M. tuberculosis H37Rv chromosome and which contains a probable phage attachment site. This study therefore offers an insight into the possible role of ISs and repetitive elements in the evolution of the M. tuberculosis genome, as well as identifying genetic markers that may be useful for phylogenetic and epidemiological analysis of the tubercle complex.",
"full_author_list": "S V Gordon, B Heym, J Parkhill, B Barrell, S T Cole",
"short_author_list": "Gordon SV et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10220167",
"journal": "Microbiology (Reading, England)",
"journal_volume": "145 ( Pt 4)",
"journal_issue": "",
"journal_pages": "881-92",
"pub_year": "1999",
"pubmed_id": "10220167"
},
{
"title": "Development of a transposon mutagenesis system for Mycobacterium avium subsp. paratuberculosis.",
"abstract": "Mycobacterium avium subspecies paratuberculosis, a slow-growing Mycobacterium, is the causative agent of Johne's disease. Although M. paratuberculosis is difficult to manipulate genetically, our laboratory has recently demonstrated the ability to introduce DNA into these bacteria by transformation and phage infection. In the current study we develop the first transposon mutagenesis system for M. paratuberculosis using the conditionally replicating mycobacteriophage phAE94 to introduce the mycobacterial transposon Tn5367. Southern blotting and sequence analysis demonstrated that the transposon insertion sites are distributed relatively randomly throughout the M. paratuberculosis genome. We constructed a comprehensive bank of 5620 insertion mutants using this transposon. The transposition frequency obtained using this delivery system was 1.0 x 10(-6) transposition events per recipient cell. Auxotrophic mutants were observed in this library at a frequency of 0.3%.",
"full_author_list": "N B Harris, Z Feng, X Liu, S L Cirillo, J D Cirillo, R G Barletta",
"short_author_list": "Harris NB et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10361705",
"journal": "FEMS microbiology letters",
"journal_volume": "175",
"journal_issue": "1",
"journal_pages": "21-6",
"pub_year": "1999",
"pubmed_id": "10361705"
},
{
"title": "Molecular cloning, sequencing, and expression of two late proteins of bacteriophage MB78.",
"abstract": "Bacteriophage MB78, a virulent phage of Salmonella typhimurium, does not allow other phages, such as P22 and 9NA, to grow in its presence. A detailed physical map of this phage has been constructed in our laboratory. In an ongoing effort to understand the genetics of this interesting phage, various genes were characterized. Here, we report cloning, sequencing, and expression of two late proteins, coded in a SalI-HindIII fragment (SH9), by using the minicell expression system. Further, we performed a kinetic study of phage proteins by infection the host LT2 cells and compared the proteins produced, with proteins obtained by the minicell expression system. Both sets of proteins run exactly parallel and migrated as 14- and 15-kDa proteins on a polyacrylamide gel. The synthesis of these two proteins started 15 min after infection with MB78 and was prominent after 45 min. One of the proteins exhibited 57% homology to the structural protein of mycobacteriophage L5.",
"full_author_list": "V Kolla, P Datta, M Chakravorty",
"short_author_list": "Kolla V, Datta P, Chakravorty M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10637764",
"journal": "IUBMB life",
"journal_volume": "48",
"journal_issue": "5",
"journal_pages": "493-7",
"pub_year": "1999",
"pubmed_id": "10637764"
},
{
"title": "TB: the return of the phage. A review of fifty years of mycobacteriophage research.",
"abstract": "The first mycobacteriophage was isolated in 1947, and since that time over 250 of these viruses have been identified. Phages have made a significant contribution to our knowledge of mycobacteria over the past fifty years, and following the development of typing techniques in the 1960s and 1970s they were widely used in epidemiological studies of tuberculosis. Unfortunately, attempts to use lytic phages therapeutically during tuberculosis infection have so far failed to elicit cure in experimentally infected animals. During the past decade phages have become important in molecular studies of mycobacteria, both in terms of studying phage biology and as tools in recombinant DNA technology, thus facilitating the investigation of mycobacterial pathogenesis. Today their potential as diagnostics reagents is also being realised with the development of exciting new techniques for rapid bacterial detection and drug susceptibility testing. This review outlines the history of these remarkable organisms, from their discovery fifty years ago to the current developments in rapid diagnostic techniques.",
"full_author_list": "R McNerney",
"short_author_list": "McNerney R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10094316",
"journal": "The international journal of tuberculosis and lung disease : the official journal of the Internation",
"journal_volume": "3",
"journal_issue": "3",
"journal_pages": "179-84",
"pub_year": "1999",
"pubmed_id": "10094316"
},
{
"title": "Exposure to antibiotics induces expression of the Mycobacterium tuberculosis sigF gene: implications for chemotherapy against mycobacterial persistors.",
"abstract": "The sigF gene encodes an alternate sigma factor found in Mycobacterium tuberculosis and related pathogenic mycobacteria. Determination of conditions of sigF expression is an important step in understanding the conditional gene regulation which may govern such processes as virulence and dormancy in mycobacteria. We constructed an in-frame translational lacZ-kan fusion within the sigF gene to determine the conditions of sigF expression. This reporter construct was expressed from a multicopy plasmid in a strain of BCG harboring an integrated luciferase reporter gene under the control of the mycobacteriophage L5 gp71 promoter. Antibiotic exposure, in particular, ethambutol, rifampin, streptomycin, and cycloserine treatment, increased the level of SigF reporter specific expression in a dose-dependent fashion. The level of SigF reporter specific expression increased over 100-fold in late-stationary-phase growth compared to that in exponential growth. During the exponential phase, SigF specific expression could be induced by a number of other stresses. Anaerobic metabolism induced SigF by greater than 150-fold, particularly in the presence of metronidazole. Cold shock increased the level of SigF specific expression, while heat shock decreased it. Oxidative stress was also an important inducer of SigF specific expression; a greater induction was seen with cumene hydroperoxide than with hydrogen peroxide. Comparisons of bacterial viability as determined by the luciferase assay or by plating serial dilutions revealed that luciferase gp71-dependent activity was an unreliable predictor of the numbers of CFU during stationary-phase growth and anaerobic metabolism. The induction of sigF following antibiotic exposure suggests that this bacterial transcription factor may control genes which are important for mycobacterial persistence in the host during chemotherapy.",
"full_author_list": "T M Michele, C Ko, W R Bishai",
"short_author_list": "Michele TM, Ko C, Bishai WR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9925509",
"journal": "Antimicrobial agents and chemotherapy",
"journal_volume": "43",
"journal_issue": "2",
"journal_pages": "218-25",
"pub_year": "1999",
"pubmed_id": "9925509"
},
{
"title": "Protein-DNA complexes in mycobacteriophage L5 integrative recombination.",
"abstract": "The temperate mycobacteriophage L5 integrates site specifically into the genomes of Mycobacterium smegmatis, Mycobacterium tuberculosis, and Mycobacterium bovis bacillus Calmette-Guérin. This integrative recombination event occurs between the phage L5 attP site and the mycobacterial attB site and requires the phage-encoded integrase and mycobacterial-encoded integration host factor mIHF. Here we show that attP, Int-L5, and mIHF assemble into a recombinationally active complex, the intasome, which is capable of attB capture and formation of products. The arm-type integrase binding sites within attP play specialized roles in the formation of specific protein-DNA architectures; the intasome is constructed by the formation of intramolecular integrase bridges between one pair of sites, P4-P5, and the attP core, while an additional pair of sites, P1-P2, is required for interaction with attB.",
"full_author_list": "C E Peña, J M Kahlenberg, G F Hatfull",
"short_author_list": "Peña CE, Kahlenberg JM, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9882658",
"journal": "Journal of bacteriology",
"journal_volume": "181",
"journal_issue": "2",
"journal_pages": "454-61",
"pub_year": "1999",
"pubmed_id": "9882658"
},
{
"title": "Generation of a recombinant bacteriophage antibody library to mycobacterium tuberculosis.",
"abstract": "Monoclonal antibodies to Mycobacterium tuberculosis (Mtb) may be useful for laboratory diagnosis, antigenic characterization, and studying the immune response to infection and vaccination. To investigate the potential of the recombinant phage antibody technique for the isolation of single-chain fragments (ScFv) reactive with Mtb culture proteins, we generated a bacteriophage antibody library from splenic tissue of mice immunized with heat-killed Mtb. Heavy- and light-chain immunoglobulin genes were isolated and amplified by the polymerase chain reaction (PCR), and the products were assembled into ScFv gene fragments and cloned into the pCANTAB5-E phagemid. Phagemids were introduced into E. coli TG1 by electrotransformation, followed by rescue of antibody-expressing phage using M13K07 helper-phage superinfection. Immunoselection of the Mtb phage library against Mtb cell wall extract or culture filtrate proteins selected antigen-specific and cross-reactive phage antibodies, none of which demonstrated reactivity to the immunodominant 65-kDa Mtb antigen. These results suggest that the phage antibody system has the potential to generate a diverse population of the reactive phage that may prove useful for investigating the immune response to Mtb infection and vaccination.",
"full_author_list": "P J Cummings, N E Hooper, S S Rowland",
"short_author_list": "Cummings PJ, Hooper NE, Rowland SS",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9627055",
"journal": "Hybridoma",
"journal_volume": "17",
"journal_issue": "2",
"journal_pages": "151-6",
"pub_year": "1998",
"pubmed_id": "9627055"
},
{
"title": "Expression systems for study of mycobacterial gene regulation and development of recombinant BCG vaccines.",
"abstract": "Successful genetic engineering of mycobacteria is crucial for developing new approaches to combat tuberculosis as well as for dissecting out the molecular basis of pathogenesis of Mycobacterium tuberculosis. We have constructed a Mycobacterium-Escherichia coli shuttle expression vector pSD5. It carries a modular expression cassette which provides sites for cloning of promoters, a ribosome binding site (RBS) with an appropriately placed initiation codon and multiple cloning sites for cloning the genes of interest. We also constructed pDK20, an integration proficient derivative of pSD5, by incorporating mycobacteriophage L5 integration signals in lieu of the origin of DNA replication for mycobacteria. This vector permits stable expression of genes in M.bovis BCG, M.smegmatis, and M.tuberculosis under the transcriptional control of a mycobacterial promoter. These vectors enable the expression of a gene to be regulated by several hundred fold depending upon the strength of mycobacterial promoter. We propose that expression of protective antigens using an appropriate promoter derivative of pDK20 should help in development of recombinant BCG vaccines that can induce an optimal immune response from the host. We have further employed the integration proficient expression system for comparing the efficiency and specificity of transcriptional recognition in M.bovis BCG, M.tuberculosis, and M.smegmatis. We show that fast growing M.smegmatis and slow growing M.tuberculosis and M.bovis BCG recognize mycobacterial promoters with comparable efficiency inspite of differences in their growth rates.",
"full_author_list": "S K DasGupta, S Jain, D Kaushal, A K Tyagi",
"short_author_list": "DasGupta SK et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9618292",
"journal": "Biochemical and biophysical research communications",
"journal_volume": "246",
"journal_issue": "3",
"journal_pages": "797-804",
"pub_year": "1998",
"pubmed_id": "9618292"
},
{
"title": "Identification of an early positive regulatory gene of mycobacteriophage L1.",
"abstract": "Among 14 temperature-sensitive, growth-defective mutants of mycobacteriophage L1 showing a lysis-defective phenotype at 42 degrees C, six are, in addition, defective in phage DNA synthesis at 42 degrees C. In the present study, we show that one of the latter six mutants, L1G27ts901, is also defective in the synthesis of both an L1-specific exonuclease (a representative delayed early protein), and of RNA in both the delayed early and late periods but not in the immediate early period. The results of a temperature-shift experiment suggest that the synthesis of L1 exonuclease is regulated by G27 at the level of transcription. Furthermore, the temperature-sensitive defect in delayed early and late RNA synthesis could be largely overcome when the L1G27ts901-infected culture was shifted from 32 to 42 degrees C at 10 min but not at zero time post-infection. These results suggest that the primary effect of the G27ts901 mutation is to make the phage defective in transcription of delayed early genes at 42 degrees C, and the defect in late RNA synthesis by this mutant is a secondary effect which is caused by its inability to express regulatory gene products. We conclude that G27 is involved in the positive regulation of expression of the delayed early genes of L1 at the transcriptional level.",
"full_author_list": "H J Datta, N C Mandal",
"short_author_list": "Datta HJ, Mandal NC",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9460943",
"journal": "The Journal of general virology",
"journal_volume": "79 ( Pt 1)",
"journal_issue": "",
"journal_pages": "205-10",
"pub_year": "1998",
"pubmed_id": "9460943"
},
{
"title": "The rapid diagnosis of isoniazid and rifampicin resistance in Mycobacterium tuberculosis--a molecular story.",
"abstract": "Isoniazid and rifampicin resistance are assayed phenotypically by the resistance ratio, absolute concentration or proportion methods. Assay methods are often difficult to standardise and the World Health Organization (WHO) Global Programme on Drug Resistance is attempting to produce standardised drug resistance data worldwide. Broth-based methods are faster than solid media systems, and a commercial radiometric system, the Bactec 460, is arguably the fastest method and permits testing to be completed within 7-14 days; however, this method is expensive and requires disposal of radioactive material. Novel phenotypic methods that utilise mycobacteriophages have shown promise. Other molecular detection systems require knowledge of the genes encoding the drug target (the inhA/mabA, katG, oxyR and ahpC genes for isoniazid; rpoB for rifampicin) and the mutations producing resistance. These genotypic methods are limited in that not all resistance mechanisms are known, but advanced assays for rifampicin resistance that use gene sequencing, heteroduplex analysis, solid-phase hybridisation or single-strand conformation polymorphism analysis are becoming available.",
"full_author_list": "F A Drobniewski, S M Wilson",
"short_author_list": "Drobniewski FA, Wilson SM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9511823",
"journal": "Journal of medical microbiology",
"journal_volume": "47",
"journal_issue": "3",
"journal_pages": "189-96",
"pub_year": "1998",
"pubmed_id": "9511823"
},
{
"title": "Mycobacteriophage TM4: genome structure and gene expression.",
"abstract": "Mycobacteriophage TM4 is a dsDNA-tailed phage that infects both fast-growing and slow-growing strains of mycobacteria. While TM4 has been used extensively for the construction of mycobacterial shuttle phasmids and for the delivery of reporter genes and transposons into mycobacterial cells, little is known about its genetics or molecular biology. We describe here the complete 52,797 bp genome sequence of TM4 and a map of its genome organization. While not a close relative of other mycobacteriophages, TM4 encodes several proteins with sequence similarity to those of other bacteriophages--including L5 and D29--indicating that they have common ancestry. In addition, TM4 encodes proteins with similarity to haloperoxidases, glutaredoxins and the WhiB family of transcriptional regulators. Following infection, TM4 genes are expressed in a defined temporal pattern, with the virion structural proteins expressed late in the phage growth cycle. Understanding the genetics of TM4 will greatly facilitate its use as a tool for the genetic manipulation of the mycobacteria.",
"full_author_list": "M E Ford, C Stenstrom, R W Hendrix, G F Hatfull",
"short_author_list": "Ford ME et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/10645443",
"journal": "Tubercle and lung disease : the official journal of the International Union against Tuberculosis and",
"journal_volume": "79",
"journal_issue": "2",
"journal_pages": "63-73",
"pub_year": "1998",
"pubmed_id": "10645443"
},
{
"title": "Genome structure of mycobacteriophage D29: implications for phage evolution.",
"abstract": "Mycobacteriophage D29 is a lytic phage that infects both fast and slow-growing mycobacterial species. The complete genome sequence of D29 reveals that it is a close relative of the temperate mycobacteriophage L5, whose sequence has been described previously. The overall organization of the D29 genome is similar to that of L5, although a 3.6 kb deletion removing the repressor gene accounts for the inability of D29 to form lysogens. Comparison of the two genomes shows that they are punctuated by a large number of insertions, deletions, and substitutions of genes, consistent with the genetic mosaicism of lambdoid phages.",
"full_author_list": "M E Ford, G J Sarkis, A E Belanger, R W Hendrix, G F Hatfull",
"short_author_list": "Ford ME et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9636706",
"journal": "Journal of molecular biology",
"journal_volume": "279",
"journal_issue": "1",
"journal_pages": "143-64",
"pub_year": "1998",
"pubmed_id": "9636706"
},
{
"title": "The site-specific recombination locus of mycobacteriophage Ms6 determines DNA integration at the tRNA(Ala) gene of Mycobacterium spp.",
"abstract": "Genetic determinants of the temperate mycobacteriophage Ms6 required for chromosomal integration were identified. DNA sequence analysis of an attP-containing fragment revealed an ORF encoding a protein of 372 amino acid residues with a C-terminus similar to other conserved C-terminal regions typical of the phage integrase family. Comparison of the sequences of attP, attB and bacteria-prophage junctions attL and attR showed a 26 bp common core sequence, where recombination takes place, near the 5' end of the integrase gene. Nucleotide sequence analysis of the attB chromosomal region showed that the core site overlaps the 3' end of the tRNA(Ala) gene. An integration-proficient plasmid vector was constructed and efficiently inserted at the tRNA(Ala) gene of Mycobacterium smegmatis, Mycobacterium vaccae, Mycobacterium bovis BCG and Mycobacterium tuberculosis H37Ra. It was demonstrated that Ms6 and D29 integrative systems can be used in conjunction for inserting genes at multiple loci. The site-specific integration system of mycobacteriophage Ms6 is a new tool for mycobacterial genetic analysis and is poorly related to those of the L5 bacteriophage family.",
"full_author_list": "A Freitas-Vieira, E Anes, J Moniz-Pereira",
"short_author_list": "Freitas-Vieira A, Anes E, Moniz-Pereira J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9884232",
"journal": "Microbiology (Reading, England)",
"journal_volume": "144 ( Pt 12)",
"journal_issue": "",
"journal_pages": "3397-406",
"pub_year": "1998",
"pubmed_id": "9884232"
},
{
"title": "Inactivation of mycobacteriophage D29 using ferrous ammonium sulphate as a tool for the detection of viable Mycobacterium smegmatis and M. tuberculosis.",
"abstract": "There is still an urgent requirement for more sensitive, cost-effective methods for detection and susceptibility testing of mycobacteria in clinical samples. We have been investigating a simple bacteriophage-based system which could be used for both purposes. As this depends upon the detection of phages which have successfully infected cells, a key step is the efficient removal or inactivation of phages remaining free in the culture medium. We demonstrate here the use of ferrous ammonium sulphate as an effective agent for the inactivation of mycobacteriophage D29 without impairing phage replication in previously infected host bacteria. Using this property, we report the detection of viable Mycobacterium smegmatis, M. bovis BCG and M. tuberculosis using simple low-cost technology. The method is highly sensitive, since it is able to detect 10 colony-forming units of M. smegmatis. It is also rapid, with the detection of M. tuberculosis in sputum specimens within 48 h.",
"full_author_list": "R McNerney, S M Wilson, A M Sidhu, V S Harley, Z al Suwaidi, P M Nye, T Parish, N G Stoker",
"short_author_list": "McNerney R et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9766200",
"journal": "Research in microbiology",
"journal_volume": "149",
"journal_issue": "7",
"journal_pages": "487-95",
"pub_year": "1998",
"pubmed_id": "9766200"
},
{
"title": "Isolation of recombinant phage clones expressing mycobacterial T cell antigens by screening a recombinant DNA library with human CD4+ Th1 clones.",
"abstract": "A lambda gt11 recombinant DNA library of Mycobacterium leprae was screened to isolate recombinant phage clones expressing mycobacterial antigens important for T cell reactivity. The library was plated on a lawn of Escherichia coli Y1090 and recombinant antigens were expressed from isolated phage clones in 96-well plates. Pools of recombinant antigens from 12 wells were tested in T cell proliferation assays with MHC class II restricted human CD4+ Th1 clones secreting interferon-gamma and cytotoxic for antigen pulsed antigen presenting cells. By screening 1750 pools of recombinant antigens with a mixture of eight Th1 clones, we identified two recombinant phage clones that expressed recombinant mycobacterial antigens stimulatory for T cells. MHC restriction analysis and reactivity to a battery of mycobacterial antigens suggested that the two responding Th1 clones recognized mycobacterial antigens/epitopes with different MHC class II (HLA-DR) restriction requirements. Our results suggest that the methodology described in this paper is suited to isolate recombinant phage clones expressing mycobacterial recombinant antigens stimulatory for T cells of protective phenotype. Such antigens may be useful in designing new vaccines and diagnostic reagents against mycobacterial diseases.",
"full_author_list": "A S Mustafa, K E Lundin, F Oftung",
"short_author_list": "Mustafa AS, Lundin KE, Oftung F",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9848681",
"journal": "FEMS immunology and medical microbiology",
"journal_volume": "22",
"journal_issue": "3",
"journal_pages": "205-16",
"pub_year": "1998",
"pubmed_id": "9848681"
},
{
"title": "Characterization of the mIHF gene of Mycobacterium smegmatis.",
"abstract": "Integration of mycobacteriophage L5 requires the mycobacterial integration host factor (mIHF) in vitro. mIHF is a 105-residue heat-stable polypeptide that is not obviously related to HU or any other small DNA-binding proteins. mIHF is most abundant just prior to entry into stationary phase and is essential for the viability of Mycobacterium smegmatis.",
"full_author_list": "M L Pedulla, G F Hatfull",
"short_author_list": "Pedulla ML, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9765584",
"journal": "Journal of bacteriology",
"journal_volume": "180",
"journal_issue": "20",
"journal_pages": "5473-7",
"pub_year": "1998",
"pubmed_id": "9765584"
},
{
"title": "The role of supercoiling in mycobacteriophage L5 integrative recombination.",
"abstract": "The genome of temperate mycobacteriophage L5 integrates into the chromosomes of its hosts, including Mycobacterium smegmatis , Mycobacterium tuberculosis and bacille Calmette-Guérin. This integrase-mediated site-specific recombination reaction occurs between the phage attP site and the mycobacterial attB site and requires the mycobacterial integration host factor. Here we examine the role of supercoiling in this reaction and show that integration is stimulated by DNA supercoiling but that supercoiling of either the attP or the attB substrate enhances recombination. Supercoiling thus facilitates a post-synaptic recombination event. We also show that, while supercoiling is not required for the production of a recombinagenic intasome, a mutant attP DNA deficient in binding of the host factor acquires a dependence on supercoiling for intasome formation and recombination.",
"full_author_list": "C E Peña, J M Kahlenberg, G F Hatfull",
"short_author_list": "Peña CE, Kahlenberg JM, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9705513",
"journal": "Nucleic acids research",
"journal_volume": "26",
"journal_issue": "17",
"journal_pages": "4012-8",
"pub_year": "1998",
"pubmed_id": "9705513"
},
{
"title": "Mycobacteriophage D29 integrase-mediated recombination: specificity of mycobacteriophage integration.",
"abstract": "Mycobacteriophage D29 is a lytic phage that infects both fast- and slow-growing species of the mycobacteria. D29 forms clear plaques on lawns of Mycobacterium smegmatis and Mycobacterium bovis bacille Calmette-Guérin (BCG) in which a very high proportion of infected cells are killed. However, genomic analysis of D29 demonstrates that it is a close relative of the temperate mycobacteriophage L5, and is presumably a non-temperate derivative of a temperate parent. The D29 genome encodes a putative integrase protein with a primary amino acid sequence similar to that of the L5 integrase; the corresponding int genes fall in colinear positions within the D29 and L5 genomes, immediately flanking and transcribed away from their associated attP sites. We show here that the D29 integrase is functional and catalyzes integrative recombination between the D29 attP site and the M. smegmatis attB site in vitro in an mIHF-dependent manner. D29 integrase also mediates recombination between the L5 attP site and attB DNA and, reciprocally, L5 integrase catalyzes recombination with D29 attP DNA. However, in both in-vitro and in-vivo assays, the D29-encoded integrase recombines the D29 attP more efficiently than the L5 attP, and vice versa, suggesting that each integration system has evolved a degree of specificity of attP recognition. We also present the sequences of the putative attP site and integrase protein of the cryptic prophage-like element phiRv2, and compare them to those of mycobacteriophages L5 and D29.",
"full_author_list": "C E Peña, J Stoner, G F Hatfull",
"short_author_list": "Peña CE, Stoner J, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9931474",
"journal": "Gene",
"journal_volume": "225",
"journal_issue": "1-2",
"journal_pages": "143-51",
"pub_year": "1998",
"pubmed_id": "9931474"
},
{
"title": "New method churns out TB mutants.",
"abstract": "",
"full_author_list": "C Potera",
"short_author_list": "Potera C",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9634412",
"journal": "Science (New York, N.Y.)",
"journal_volume": "280",
"journal_issue": "5368",
"journal_pages": "1350-1",
"pub_year": "1998",
"pubmed_id": "9634412"
},
{
"title": "The use of luciferase-reporter phage for antibiotic-susceptibility testing of mycobacteria.",
"abstract": "",
"full_author_list": "P F Riska, W R Jacobs",
"short_author_list": "Riska PF, Jacobs WR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9921495",
"journal": "Methods in molecular biology (Clifton, N.J.)",
"journal_volume": "101",
"journal_issue": "",
"journal_pages": "431-55",
"pub_year": "1998",
"pubmed_id": "9921495"
},
{
"title": "Mycobacteriophages.",
"abstract": "",
"full_author_list": "G J Sarkis, G F Hatfull",
"short_author_list": "Sarkis GJ, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9921476",
"journal": "Methods in molecular biology (Clifton, N.J.)",
"journal_volume": "101",
"journal_issue": "",
"journal_pages": "145-73",
"pub_year": "1998",
"pubmed_id": "9921476"
},
{
"title": "Prokaryotes: the unseen majority",
"abstract": "The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4–6 × 1030 cells and 350–550 Pg of C (1 Pg = 1015 g), respectively. Thus, the total amount of prokaryotic carbon is 60–100% of the estimated total carbon in plants, and inclusion of prokaryotic carbon in global models will almost double estimates of the amount of carbon stored in living organisms. In addition, the earth’s prokaryotes contain 85–130 Pg of N and 9–14 Pg of P, or about 10-fold more of these nutrients than do plants, and represent the largest pool of these nutrients in living organisms. Most of the earth’s prokaryotes occur in the open ocean, in soil, and in oceanic and terrestrial subsurfaces, where the numbers of cells are 1.2 × 1029, 2.6 × 1029, 3.5 × 1030, and 0.25–2.5 × 1030, respectively. The numbers of heterotrophic prokaryotes in the upper 200 m of the open ocean, the ocean below 200 m, and soil are consistent with average turnover times of 6–25 days, 0.8 yr, and 2.5 yr, respectively. Although subject to a great deal of uncertainty, the estimate for the average turnover time of prokaryotes in the subsurface is on the order of 1–2 × 103 yr. The cellular production rate for all prokaryotes on earth is estimated at 1.7 × 1030 cells/yr and is highest in the open ocean. The large population size and rapid growth of prokaryotes provides an enormous capacity for genetic diversity.",
"full_author_list": "William B. Whitman, David C. Coleman, and William J. Wiebe",
"short_author_list": "W. Whitman, D. Coleman, W. Wiebe",
"article_url": "http://www.pnas.org/content/95/12/6578.full.pdf",
"journal": "Proc Natl Acad Sci U S A",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "1998",
"pubmed_id": "9618454"
},
{
"title": "Comparison of three molecular assays for rapid detection of rifampin resistance in Mycobacterium tuberculosis.",
"abstract": "Multidrug-resistant Mycobacterium tuberculosis (MDR-TB) is an emerging problem of great importance to public health, with higher mortality rates than drug-sensitive TB, particularly in immunocompromised patients. MDR-TB patients require treatment with more-toxic second-line drugs and remain infectious for longer than patients infected with drug-sensitive strains, incurring higher costs due to prolonged hospitalization. It is estimated that 90% of United Kingdom rifampin-resistant isolates are also resistant to isoniazid, making rifampin resistance a useful surrogate marker for multidrug resistance and indicating that second- and third-line drugs to which these isolates are susceptible are urgently required. Resistance in approximately 95% of rifampin-resistant isolates is due to mutations in a 69-bp region of the rpoB gene, making this a good target for molecular genotypic diagnostic methods. Two molecular assays, INNO-LiPA Rif.TB (Innogenetics, Zwijndrecht, Belgium) and MisMatch Detect II (Ambion, Austin, Tex.), were performed on primary specimens and cultures to predict rifampin resistance, and these methods were compared with the resistance ratio method. A third method, the phenotypic PhaB assay, was also evaluated in comparison to cultures in parallel with the genotypic assays. In an initial evaluation 16 of 16, 15 of 16, and 16 of 16 rifampin-resistant cultures (100, 93.8, and 100%, respectively), were correctly identified by line probe assay (LiPA), mismatch assay, and PhaB assay, respectively. Subsequently 38 sputa and bronchealveolar lavage specimens and 21 isolates were received from clinicians for molecular analysis. For the 38 primary specimens the LiPA and mismatch assay correlated with culture and subsequent identification and susceptibility tests in 36 and 38 specimens (94.7 and 100%), respectively. For the 21 isolates submitted by clinicians, both assays correlated 100% with routine testing.",
"full_author_list": "S A Watterson, S M Wilson, M D Yates, F A Drobniewski",
"short_author_list": "Watterson SA et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9650946",
"journal": "Journal of clinical microbiology",
"journal_volume": "36",
"journal_issue": "7",
"journal_pages": "1969-73",
"pub_year": "1998",
"pubmed_id": "9650946"
},
{
"title": "[Study of the interaction of MTPN11 mycobacteriophage with host cells based on electron microscopy, fluorimetry, and electro-oriented spectroscopy]",
"abstract": "According to electron-microscopic data, various cells in the M. smegmatis ATCC607 population interact differently with phage MTPH11. Fluorometric studies of phage-host interactions were performed using a membranotropic fluorescent probe, 8-anilino-1-naphthalene sulfonate (ANS). Changes in the electric characteristics of mycobacterial cells infected with the phage were studied by electro-orientational (EO) spectroscopy. The problem of the employment of fluorometry and EO spectroscopy for rapid phage typing of mycobacteria is discussed.",
"full_author_list": "E L Zhilenkov, I G Shemiakin, V M Fomchenkov, A Iu Ivanov, A V Gavriushkin, M V Oborotov",
"short_author_list": "Zhilenkov EL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9891297",
"journal": "Mikrobiologiia",
"journal_volume": "67",
"journal_issue": "5",
"journal_pages": "666-71",
"pub_year": "1998",
"pubmed_id": "9891297"
},
{
"title": "[Properties of MTPN11 mycobacteriophage]",
"abstract": "Some characteristics of the poorly studied phage MTPH11, which is used for identification of mycobacteria, are presented. The phage has an isometric head and a long noncontractile tail (B1 morphotype). The attachment apparatus of this phage includes a basal plate composed of two joint disks and a single tail fiber. The constant of phage adsorption on Mycobacterium smegmatis ATCC607 cells is 6.6 x 10(-9) ml/min. The latent infection period in the MTPH11-host strain 607 system in 65 min; phage progeny ranges from 30 to 40 virions per one cell. The constant of phage inactivation with a homologous antiserum is 50 min-1. The buoyant density of intact MTPH11 virion in CsCl amounts to 1.520 g/cm3. The phage is susceptible to chloroform, retains lytic activity within a pH range of 5 to 9, and is resistant to inactivating agents. The G + C content of the phage DNA is 63 mol%.",
"full_author_list": "E L Zhilenkov, I G Shemiakin, V N Stepanshina, O V Korobova, M V Oborotov, I R Dorozhkova",
"short_author_list": "Zhilenkov EL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9891296",
"journal": "Mikrobiologiia",
"journal_volume": "67",
"journal_issue": "5",
"journal_pages": "660-5",
"pub_year": "1998",
"pubmed_id": "9891296"
},
{
"title": "Conditionally replicating mycobacteriophages: a system for transposon delivery to Mycobacterium tuberculosis.",
"abstract": "Transposon mutagenesis provides a direct selection for mutants and is an extremely powerful technique to analyze genetic functions in a variety of prokaryotes. Transposon mutagenesis of Mycobacterium tuberculosis has been limited in part because of the inefficiency of the delivery systems. This report describes the development of conditionally replicating shuttle phasmids from the mycobacteriophages D29 and TM4 that enable efficient delivery of transposons into both fast- and slow-growing mycobacteria. These shuttle phasmids consist of an Escherichia coli cosmid vector containing either a mini-Tn10(kan) or Tn5367 inserted into a nonessential region of the phage genome. Thermosensitive mutations were created in the mycobacteriophage genome that allow replication at 30 degrees C but not at 37 degrees C (TM4) or 38.5 degrees C (D29). Infection of mycobacteria at the nonpermissive temperature results in highly efficient transposon delivery to the entire population of mycobacterial cells. Transposition of mini-Tn10(kan) occurred in a site-specific fashion in M. smegmatis whereas Tn5367 transposed apparently randomly in M. phlei, Bacille Calmette-Guérin (BCG), and M. tuberculosis. Sequence analysis of the M. tuberculosis and BCG chromosomal regions adjacent to Tn5367 insertions, in combination with M. tuberculosis genomic sequence and physical map data, indicates that the transpositions have occurred randomly in diverse genes in every quadrant of the genome. Using this system, it has been readily possible to generate libraries containing thousands of independent mutants of M. phlei, BCG, and M. tuberculosis.",
"full_author_list": "S Bardarov, J Kriakov, C Carriere, S Yu, C Vaamonde, R A McAdam, B R Bloom, G F Hatfull, W R Jacobs",
"short_author_list": "Bardarov S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9380742",
"journal": "Proceedings of the National Academy of Sciences of the United States of America",
"journal_volume": "94",
"journal_issue": "20",
"journal_pages": "10961-6",
"pub_year": "1997",
"pubmed_id": "9380742"
},
{
"title": "A putative ABC-transport operon of Mycobacterium smegmatis.",
"abstract": "We have recently described the mpr gene of Mycobacterium smegmatis whose product confers resistance to mycobacteriophages L5 and D29 when overproduced (Barsom and Hatfull (1996) Mol. Microbiol. 21, 159-170). We have determined the nt sequence of approximately 3.5 kb immediately adjacent to mpr which appears to encode components of an ATP-binding cassette (ABC) transport system. Four closely-spaced open reading frames (ORF) were identified although two of these may cooperate to produce an integral membrane component of the transport system via a programmed translational frameshift. Another putative protein is also predicted to be an integral membrane protein, while the third is an ABC-transporter protein. We propose that these three putative proteins form a mycobacterial membrane-bound complex involved in protein-dependent transport. This is the first ABC-transport system to be described in mycobacteria.",
"full_author_list": "E K Barsom, G F Hatfull",
"short_author_list": "Barsom EK, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9034323",
"journal": "Gene",
"journal_volume": "185",
"journal_issue": "1",
"journal_pages": "127-32",
"pub_year": "1997",
"pubmed_id": "9034323"
},
{
"title": "Transcriptional silencing by the mycobacteriophage L5 repressor.",
"abstract": "The success of a temperate bacteriophage is dependent upon its ability to completely shut down expression of its lytic genes during lysogenic growth. Mycobacteriophage L5 accomplishes this by an atypical phage repressor, gp71, which binds to multiple asymmetric DNA sites. L5 gp71 regulates transcription initiation at an early lytic promoter, Pleft, but also affects downstream gene expression at 'stoperator' sites in the phage genome. The L5 genome is replete with stoperator sites located within short intergenic spaces in both the early and late lytic operons and oriented specifically with respect to transcription. Binding of gp71 to these sites results in a strong orientation-dependent polar effect on downstream gene expression and global silencing of prophage gene expression.",
"full_author_list": "K L Brown, G J Sarkis, C Wadsworth, G F Hatfull",
"short_author_list": "Brown KL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9312049",
"journal": "The EMBO journal",
"journal_volume": "16",
"journal_issue": "19",
"journal_pages": "5914-21",
"pub_year": "1997",
"pubmed_id": "9312049"
},
{
"title": "Conditionally replicating luciferase reporter phages: improved sensitivity for rapid detection and assessment of drug susceptibility of Mycobacterium tuberculosis.",
"abstract": "TM4 is a lytic mycobacteriophage which infects mycobacteria of clinical importance. A luciferase reporter phage, phAE40, has been constructed from TM4 and was previously shown to be useful for the rapid detection and drug susceptibility testing of Mycobacterium tuberculosis. However, the lytic nature of the phage results in a loss of detectable light output and limits the sensitivity of detection. We describe several strategies aimed at improving the luciferase activity generated by TM4 luciferase phages, including (i) varying the position of the luciferase gene in the phage genome, (ii) isolating host-range mutants of the phage, and (iii) introducing temperature-sensitive mutations in the phage such that it will not replicate at the infecting temperature. Several new phages generated by these methods show increased intensity of luciferase production compared to the first-generation reporter phage phAE40, and one phage, phAE88, also demonstrates an enhanced duration of luciferase activity. This has allowed the detection of as few as 120 BCG cells and the determination of drug susceptibilities of M. tuberculosis in as little as 1 day.",
"full_author_list": "C Carrière, P F Riska, O Zimhony, J Kriakov, S Bardarov, J Burns, J Chan, W R Jacobs",
"short_author_list": "Carrière C et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9399525",
"journal": "Journal of clinical microbiology",
"journal_volume": "35",
"journal_issue": "12",
"journal_pages": "3232-9",
"pub_year": "1997",
"pubmed_id": "9399525"
},
{
"title": "Mycobacteriophage L5 infection of Mycobacterium bovis BCG: implications for phage genetics in the slow-growing mycobacteria.",
"abstract": "Mycobacteriophage L5 is a well-characterized temperate phage that forms stable lysogens in Mycobacterium smegmatis. The host range of L5 is, however, unclear because previous reports suggested that it does not infect slow-growing mycobacteria such as Mycobacterium tuberculosis and bacille Calmette-Guerin (BCG). Moreover, luciferase reporter phage derivatives of L5 failed to produce light from BCG, suggesting that infection is blocked at or before the stage of DNA injection. In this study, we demonstrate that L5 infection of slow growing mycobacteria specifically requires a high concentration of Ca2+, conditions that differs from those required for infection of M. smegmatis by L5 and for infection of BCG by the closely related phage D29. In addition, we show that there are specific genetic determinants of L5 that confer the ability to infect slow growing mycobacteria, without altering infection of M. smegmatis. These observations extend the use of phage L5 for the diagnosis and analysis of tuberculosis and other mycobacterial diseases.",
"full_author_list": "K J Fullner, G F Hatfull",
"short_author_list": "Fullner KJ, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9427405",
"journal": "Molecular microbiology",
"journal_volume": "26",
"journal_issue": "4",
"journal_pages": "755-66",
"pub_year": "1997",
"pubmed_id": "9427405"
},
{
"title": "A Mycobacterium smegmatis mutant with a defective inositol monophosphate phosphatase gene homolog has altered cell envelope permeability.",
"abstract": "A bacteriophage infection mutant (strain LIMP7) of Mycobacterium smegmatis was isolated following transposon mutagenesis. The mutant showed an unusual phenotype, in that all phages tested produced larger plaques on this strain compared to the parent strain. Other phenotypic characteristics of the mutant were slower growth, increased clumping in liquid culture, increased resistance to chloramphenicol and erythromycin, and increased sensitivity to isoniazid and several beta-lactam antibiotics. Permeability studies showed decreases in the accumulation of lipophilic molecules (norfloxacin and chenodeoxycholate) and a small increase with hydrophilic molecules (cephaloridine); taken together, these characteristics indicate an altered cell envelope. The DNA adjacent to the transposon in LIMP7 was cloned and was shown to be highly similar to genes encoding bacterial and mammalian inositol monophosphate phosphatases. Inositol is important in mycobacteria as a component of the major thiol mycothiol and also in the cell wall, with phosphatidylinositol anchoring lipoarabinomannan (LAM) in the cell envelope. In LIMP7, levels of phosphatidylinositol dimannoside, the precursor of LAM, were less than half of those in the wild-type strain, confirming that the mutation had affected the synthesis of inositol-containing molecules. The impA gene is located within the histidine biosynthesis operon in both M. smegmatis and Mycobacterium tuberculosis, lying between the hisA and hisF genes.",
"full_author_list": "T Parish, J Liu, H Nikaido, N G Stoker",
"short_author_list": "Parish T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9401044",
"journal": "Journal of bacteriology",
"journal_volume": "179",
"journal_issue": "24",
"journal_pages": "7827-33",
"pub_year": "1997",
"pubmed_id": "9401044"
},
{
"title": "Characterization of the mycobacteriophage L5 attachment site, attP.",
"abstract": "Lysogenization of mycobacteriophage L5 involves integration of the phage genome into the Mycobacterium smegmatis chromosome. Integration occurs by a site-specific recombination event between a phage attachment site, attP, and a bacterial attachment site, attB, which is catalyzed by the phage-encoded integrase protein. DNase I footprinting reveals that L5 integrase binds to two types of sites within attP which span an unexpectedly large region of 413 bp: seven arm-type sites (P1 to P7) each of which correspond to a consensus sequence 5'-TGCaaCtcYy, and core-type sites at the points of strand exchange. Mutational analyses indicate that not all of the arm-type sites are required for integration, and that the P3 site and the rightmost pair of sites (P6 and P7) are dispensable for integration. We show that a 252 bp segment of attP DNA is sufficient for efficient integrative recombination and that int can be provided in trans for simple and efficient transformation of the mycobacteria.",
"full_author_list": "C E Peña, M H Lee, M L Pedulla, G F Hatfull",
"short_author_list": "Peña CE et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9054972",
"journal": "Journal of molecular biology",
"journal_volume": "266",
"journal_issue": "1",
"journal_pages": "76-92",
"pub_year": "1997",
"pubmed_id": "9054972"
},
{
"title": "Mycobacteriophage D29 contains an integration system similar to that of the temperate mycobacteriophage L5.",
"abstract": "A mycobacteriophage D29 DNA fragment cloned in pRM64, a shuttle plasmid that transforms Mycobacterium smegmatis, was sequenced. The determined sequence was 2592 nucleotides long and had a mean G+C content of 63.7 mol%, similar to that of mycobacterial DNA. Four ORFs were identified: one with strong homology to dCMP deaminase genes; one homologous to mycobacteriophage L5 gene 36, whose function is unknown; one encoding a possible excisase; and one encoding an integrase. The intergenic region between the putative excisase gene and the integrase gene had a lower than average G+C content and showed the presence of the same attP core sequence as mycobacteriophage L5. Transformation experiments using subclones of pRM64 indicated that the integrase gene and all the intergenic region were essential for stable transformation. A subclone containing the integrase gene and the core attP sequence was able to transform but recombinants were highly unstable. Southern analysis of total DNA from cells transformed with pRM64 and its derivatives showed that all the plasmids were integrated at one specific site of the bacterial chromosome. A recombinant exhibiting a high level of resistance to the selective drug kanamycin had two plasmids integrated at different sites. These results demonstrated that the D29 sequences contained in pRM64 were integrative, indicating that the generally hold view of D29 as a virulent phage must be reviewed.",
"full_author_list": "G Ribeiro, M Viveiros, H L David, J V Costa",
"short_author_list": "Ribeiro G et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9274023",
"journal": "Microbiology (Reading, England)",
"journal_volume": "143 ( Pt 8)",
"journal_issue": "",
"journal_pages": "2701-8",
"pub_year": "1997",
"pubmed_id": "9274023"
},
{
"title": "Specific identification of Mycobacterium tuberculosis with the luciferase reporter mycobacteriophage: use of p-nitro-alpha-acetylamino-beta-hydroxy propiophenone.",
"abstract": "We have previously described a luciferase reporter mycobacteriophage (LRP) assay that can detect Mycobacterium tuberculosis and characterize mycobacterial drug susceptibility patterns within 24 to 48 h in positive cultures. One drawback of this LRP protocol is the ability of the recombinant mycobacteriophage phAE40 to infect a variety of Mycobacterium species, thus limiting its specificity for the detection of M. tuberculosis. In this study, we have (i) explored the host range of phAE40, (ii) developed a modified LRP assay that exploits the selective inhibitory effect of the compound p-nitro-alpha-acetylamino-beta-hydroxy propiophenone (NAP) against members of the M. tuberculosis complex to differentiate between the tubercle bacillus and other mycobacterial species, and (iii) tested over 300 samples, including primary clinical isolates and drug-resistant strains of M. tuberculosis, demonstrating the ability of the NAP-modified LRP assay to identify M. tuberculosis complex organisms with high degrees of sensitivity and specificity.",
"full_author_list": "P F Riska, W R Jacobs, B R Bloom, J McKitrick, J Chan",
"short_author_list": "Riska PF et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9399524",
"journal": "Journal of clinical microbiology",
"journal_volume": "35",
"journal_issue": "12",
"journal_pages": "3225-31",
"pub_year": "1997",
"pubmed_id": "9399524"
},
{
"title": "Evaluation of a new rapid bacteriophage-based method for the drug susceptibility testing of Mycobacterium tuberculosis.",
"abstract": "",
"full_author_list": "S M Wilson, Z al-Suwaidi, R McNerney, J Porter, F Drobniewski",
"short_author_list": "Wilson SM et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/9095184",
"journal": "Nature medicine",
"journal_volume": "3",
"journal_issue": "4",
"journal_pages": "465-8",
"pub_year": "1997",
"pubmed_id": "9095184"
},
{
"title": "Characterization of Mycobacterium smegmatis gene that confers resistance to phages L5 and D29 when overexpressed.",
"abstract": "Bacteriophage infection requires a specific interaction with the outer surface of a bacterial host followed by interaction with the cell membrane and phage DNA injection. Phages of the mycobacteria encounter a cell wall that is rich in unusual lipid- and sugar-containing components which form a formidable barrier that must be passed to gain access to the membrane. We describe here a gene of Mycobacterium smegmatis that confers resistance to mycobacteriophages L5 and D29. The phage-resistance phenotype results not from mutation but from elevated expression of a wild-type gene. It appears that the product of this multicopy phage-resistance (mpr) gene may alter the structure of the host cell wall or membrane, thereby inhibiting productive phage DNA injection.",
"full_author_list": "E K Barsom, G F Hatfull",
"short_author_list": "Barsom EK, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8843442",
"journal": "Molecular microbiology",
"journal_volume": "21",
"journal_issue": "1",
"journal_pages": "159-70",
"pub_year": "1996",
"pubmed_id": "8843442"
},
{
"title": "The biology of the genus Mycobacterium.",
"abstract": "",
"full_author_list": "J M Grange",
"short_author_list": "Grange JM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8972114",
"journal": "Society for Applied Bacteriology symposium series",
"journal_volume": "25",
"journal_issue": "",
"journal_pages": "1S-9S",
"pub_year": "1996",
"pubmed_id": "8972114"
},
{
"title": "The molecular genetics of Mycobacterium tuberculosis.",
"abstract": "",
"full_author_list": "G F Hatfull",
"short_author_list": "Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8791708",
"journal": "Current topics in microbiology and immunology",
"journal_volume": "215",
"journal_issue": "",
"journal_pages": "29-47",
"pub_year": "1996",
"pubmed_id": "8791708"
},
{
"title": "Chemistry of the lyxose-containing mycobacteriophage receptors of Mycobacterium phlei/Mycobacterium smegmatis.",
"abstract": "Mycobacterium phlei (strain Timothy) (Mycobacterium smegmatis ATCC 19249) is characterized by the presence of a family of alkali-labile glycolipids, reminiscent of the trehalose-containing lipooligosaccharide class of antigens but lacking the nonreducing trehalose core. Through a combination of methylation analyses, 1H and 13C NMR, two-dimensional 1H/1H and 1H/13C NMR, fast atom bombardment-mass spectrometry, gas chromatography-mass spectrometry, and other analytical techniques, these new structures were shown to possess three distinct features. Firstly, they contained the pentose D-lyxose (Lyx), rarely found in biology, but an epimer of D-arabinose, a key component of the mycobacterial cell wall arabinogalactan and lipoarabinomannnan. Thus, it was apparent that these glycolipids are the same as those described by Bisso et al. and attributed with phage receptor properties [Bisso, G., Castelnuovo, G., Nardelli, M.-G., Orefici, G., Arancia, G., Lanéelle, G., Asselineau, C., & Asselineau, J. (1976) Biochemie 58, 87-97]. Secondly, the complex oligosaccharides within the glycolipids contain the repeating units Lyxn(6-O-CH3-Glc)m and Lyxn(6-O-CH3-Glc)mMan1, where n+m equal to approximately 16 glycosyl residues. Thirdly, the M. phlei glycolipids were found to be heavily O-acylated, such that every D-Lyx residue invariably possesses an acyl function at position -2 and, in some instances, at both positions -2 and -4. The chemical characterization of these glycolipids, not feasible 20 years ago, clearly demonstrates that they are distinct from the type- and species-specific glycopeptidolipids, lipooligosaccharides, phenolic glycolipids, and the genus-specific phosphatidylinositol-based lipoglycans of mycobacteria. This present and previous studies begin to define the precise structural requirements responsible for the attachment of mycobacteriophage to the host cell wall.",
"full_author_list": "K H Khoo, R Suzuki, A Dell, H R Morris, M R McNeil, P J Brennan, G S Besra",
"short_author_list": "Khoo KH et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8794763",
"journal": "Biochemistry",
"journal_volume": "35",
"journal_issue": "36",
"journal_pages": "11812-9",
"pub_year": "1996",
"pubmed_id": "8794763"
},
{
"title": "Construction of D29 shuttle phasmids and luciferase reporter phages for detection of mycobacteria.",
"abstract": "Diseases caused by Mycobacterium tuberculosis, M. leprae and M. avium, cause significant morbidity and mortality worldwide. Effective treatments require that the organisms be speciated and that drug susceptibilities for the causative organisms be characterized. Reporter phage technology has been developed as a rapid and convenient method for identifying mycobacterial species and evaluating drug resistance. In this report we describe the construction of luciferase reporter phages from mycobacteriophage D29 DNA. Shuttle phasmids were first constructed with D29 in order to identify non-essential regions of the D29 genomes and to introduce unique cloning sites within that region. Using this approach, we observed that all of the D29 shuttle phasmids had the cosmid vector localized to one area of the phage genome near one cohesive end. These shuttle phasmids had been constructed with a cosmid that could be readily excised from the D29 genome with different sets of restriction enzymes. Luciferase reporter phages were made by substituting the luciferase cassette for the cosmid vector. Recombinant phages with the luciferase cassette fall into two groups. One group produced light and had the expression cassette oriented with the promoter directing transcription away from the cohesive end. In contrast, the other group had the expression cassette in the opposite orientation and failed to produce light during lytic infection, but did produce light in L5 lysogens which are known to repress D29 promoters. These results suggest that a phage promoter of the D29 phage can occlude the expression of a promoter introduced into this region. D29 luciferase reporter phages are capable of detecting low numbers of L5 lysogens like L5 luciferase phages. However, unlike L5 luciferase phages, D29 luciferase phages can readily infect M. tuberculosis and M. bovis BCG, demonstrating that these phages can be used to evaluate drug susceptibilities of many types of mycobacteria.",
"full_author_list": "R E Pearson, S Jurgensen, G J Sarkis, G F Hatfull, W R Jacobs",
"short_author_list": "Pearson RE et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8996097",
"journal": "Gene",
"journal_volume": "183",
"journal_issue": "1-2",
"journal_pages": "129-36",
"pub_year": "1996",
"pubmed_id": "8996097"
},
{
"title": "A novel host factor for integration of mycobacteriophage L5.",
"abstract": "Bacterial integration host factors (IHFs) play central roles in the cellular processes of recombination, DNA replication, transcription, and bacterial pathogenesis. We describe here a novel mycobacterial IHF (mIHF) of Mycobacterium smegmatis and Mycobacterium tuberculosis that stimulates integration of mycobacteriophage L5. mIHF is the product of a single gene and is unrelated at the sequence level to other integration host factors. By itself, mIHF does not bind preferentially to attP DNA, although it significantly alters the pattern of integrase (Int) binding, promoting the formation of specific integrase-mIHF-attP intasome complexes.",
"full_author_list": "M L Pedulla, M H Lee, D C Lever, G F Hatfull",
"short_author_list": "Pedulla ML et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8986825",
"journal": "Proceedings of the National Academy of Sciences of the United States of America",
"journal_volume": "93",
"journal_issue": "26",
"journal_pages": "15411-6",
"pub_year": "1996",
"pubmed_id": "8986825"
},
{
"title": "Positions of strand exchange in mycobacteriophage L5 integration and characterization of the attB site.",
"abstract": "Mycobacteriophage L5 integrates into the genome of Mycobacterium smegmatis via site-specific recombination between the phage attP site and the bacterial attB site. These two sites have a 43-bp common core sequence within which strand exchange occurs and which overlaps a tRNAGly gene at attB. We show here that a 29-bp segment of DNA is necessary and sufficient for attB function and identify the positions of strand exchange.",
"full_author_list": "C E Peña, J E Stoner, G F Hatfull",
"short_author_list": "Peña CE, Stoner JE, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8808947",
"journal": "Journal of bacteriology",
"journal_volume": "178",
"journal_issue": "18",
"journal_pages": "5533-6",
"pub_year": "1996",
"pubmed_id": "8808947"
},
{
"title": "Cloning and characterization of mycobacteriophage I3 promoters.",
"abstract": "",
"full_author_list": "G R Ramesh, K P Gopinathan",
"short_author_list": "Ramesh GR, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8744840",
"journal": "Indian journal of biochemistry & biophysics",
"journal_volume": "33",
"journal_issue": "1",
"journal_pages": "83",
"pub_year": "1996",
"pubmed_id": "8744840"
},
{
"title": "Phage infection, transfection and transformation of Mycobacterium avium complex and Mycobacterium paratuberculosis.",
"abstract": "Mycobacterium avium complex strains and Mycobacterium paratuberculosis are closely related intracellular pathogens affecting humans and animals. M. avium complex infections are a leading cause of morbidity and mortality in AIDS patients, and M. paratuberculosis is the agent of Johne's disease in ruminants. Genetic manipulation of these micro-organisms would facilitate the understanding of their pathogenesis, the construction of attenuated vaccine strains and the development of new drugs and treatment methods. This paper describes the replication of mycobacterial shuttle phasmids and plasmids, and the expression of the firefly luciferase reporter gene in M. avium complex and M. paratuberculosis. The mycobacteriophage TM4 propagated on M. smegmatis or M. paratuberculosis plaqued at the same efficiency on these two mycobacterial hosts. Screening of M. avium complex and M. paratuberculosis clinical isolates with TM4-derived luciferase reporter phages demonstrated that the majority of these isolates were susceptible to TM4. Conditions for introduction of DNA were determined by transfection of M. paratuberculosis with TM4 DNA and applied to isolate kanamycin-resistant transformants of M. avium complex and M. paratuberculosis with Escherichia coli-Mycobacterium shuttle plasmids. Recombinant plasmids were recovered from transformants without apparent loss of DNA sequences. These results provide the basis for the genetic manipulation of these pathogenic mycobacterial species.",
"full_author_list": "E M Foley-Thomas, D L Whipple, L E Bermudez, R G Barletta",
"short_author_list": "Foley-Thomas EM et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7773411",
"journal": "Microbiology (Reading, England)",
"journal_volume": "141 ( Pt 5)",
"journal_issue": "",
"journal_pages": "1173-81",
"pub_year": "1995",
"pubmed_id": "7773411"
},
{
"title": "Progress on development of the live BCG recombinant vaccine vehicle for combined vaccine delivery.",
"abstract": "BCG, the current vaccine for tuberculosis, has been administered to approximately three billion people. This live vaccine has a low incidence of serious side effects and can be given at birth. Within the past six years, systems for the manipulation and expression of foreign genes in mycobacteria have been developed, allowing the evaluation of rBCG as a vaccine delivery vehicle for heterologous antigens. Recent studies from our group have shown that rBCG expressing outer surface protein A of Borrelia burgdorferi can completely protect mice from an intradermal challenge with this organism. Immune responses protective against Streptococcus pneumoniae challenge have also been achieved by immunization of mice with rBCG expressing PspA. The simplest means of administering multiple vaccine antigens in a rBCG vehicle would be to coexpress these simultaneously in the same BCG recombinant. Currently two general classes of vectors exist for the expression of foreign proteins in BCG: shuttle plasmid vectors, which replicate extrachromosomally in mycobacteria, and shuttle \"phasmid\" vectors, which integrate as a single copy into the mycobacterial chromosome by means of vector-encoded integration functions of the lysogenic mycobacteriophage L5. The genetic capacity of the multicopy plasmid vectors may be 20 kb or more, while the potential exists for stable integration of much larger amounts of DNA into the mycobacterial genome (L5 itself is 52 kb). Additionally, these two expression systems can have the compatibility to coexist in a single BCG cell. Otitis media is caused by infections of the middle ear chiefly with either S. pneumoniae or H. influenzae. Thus, an effective vaccine would necessarily include antigens from both these pathogens. Our initial attempt at construction of a BCG multivaccine vehicle was to express proteins from each of these pathogens from the same multicopy plasmid. We have recently succeeded in coexpressing the S. pneumoniae PspA and H. influenzae PAL proteins in BCG. Future work will address how the biochemical characterization of and immune responses to the recombinant antigens of the \"bivalent\" rBCG:PspA/PAL vaccine compare to those of the respective \"monovalent\" rBCG vaccines.",
"full_author_list": "M S Hanson, C V Lapcevich, S L Haun",
"short_author_list": "Hanson MS, Lapcevich CV, Haun SL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7625654",
"journal": "Annals of the New York Academy of Sciences",
"journal_volume": "754",
"journal_issue": "",
"journal_pages": "214-21",
"pub_year": "1995",
"pubmed_id": "7625654"
},
{
"title": "Transcriptional regulation of repressor synthesis in mycobacteriophage L5.",
"abstract": "Mycobacteriophage L5 is a temperate phage of the mycobacteria that forms stable lysogens in Mycobacterium smegmatis. Lysogeny is maintained by the putative repressor, the gene 71 product, which also mediates immunity to superinfection. We show here that there are three promoters located upstream of gene 71 which are active in an L5 lysogen but which do not require any phage-encoded proteins. In early lytic growth, gene 71 is also transcribed from a promoter, Pleft, located at the right end of the genome and which appears to be a target of gp71 regulation. A model is given for the regulation of L5 life cycles.",
"full_author_list": "C E Nesbit, M E Levin, M K Donnelly-Wu, G F Hatfull",
"short_author_list": "Nesbit CE et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8594325",
"journal": "Molecular microbiology",
"journal_volume": "17",
"journal_issue": "6",
"journal_pages": "1045-56",
"pub_year": "1995",
"pubmed_id": "8594325"
},
{
"title": "L5 luciferase reporter mycobacteriophages: a sensitive tool for the detection and assay of live mycobacteria.",
"abstract": "Recombinant bacteriophages provide efficient delivery systems for introducing reporter genes into specific bacterial hosts. We have constructed mycobacteriophage L5 recombinants carrying the firefly luciferase gene inserted into the tRNA region of the phage genome. Infection of Mycobacterium smegmatis by these phages results in expression of the luciferase gene and light emission. Fortuitously, the luciferase gene is expressed continuously in lysogens surviving infection. Synthesis of luciferase from a mycobacterial promoter created by cloning enables the detection of extremely small numbers of M. smegmatis cells. These reporter phages can be used to discriminate between drug-sensitive and drug-resistant strains of M. smegmatis, and may provide tools for the rapid identification and classification of antimycobacterial agents.",
"full_author_list": "G J Sarkis, W R Jacobs, G F Hatfull",
"short_author_list": "Sarkis GJ, Jacobs WR, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7623662",
"journal": "Molecular microbiology",
"journal_volume": "15",
"journal_issue": "6",
"journal_pages": "1055-67",
"pub_year": "1995",
"pubmed_id": "7623662"
},
{
"title": "Tail length determination in bacteriophage T4",
"abstract": "This report identifies a protein that regulates tail length in bacteriophage T4. Earlier work (Duda et al., 1990) suggested that the gene 29 protein could be involved in T4 tail length determination as a \"template\" or \"tape-measure\", similar to that proposed for the gene H protein in bacteriophage lambda. We have altered the length of a recombinant gene 29 by constructing deletions and duplications in different parts of the gene. Each of these constructs was incorporated into the high-level expression vector, pET-11d. Seven plasmids with different lengths of gene 29 were made and used in complementation studies. We have found that the length of the tail can be decreased by deleting the C-terminal part of gene 29 or increased by forming duplications in different parts of this gene, and that the length of the tail can be proportional to the size of the engineered protein. Unlike phage lambda, plasmids with deletions in the middle of gene 29 or from the N-terminal end produced correspondingly smaller but inactive gene 29 protein and no viable phage were formed. Our results show that alterations in the length of gene 29 protein proportionately alters tail length, and argue strongly for a scheme in which 29 protein is a ruler or template that determines tail length during tail assembly.\r\n",
"full_author_list": "Abuladze NK, Gingery M, Tsai J, Eiserling FA.\r\n",
"short_author_list": "Abuladze NK, Gingery M, Tsai J, Eiserling FA.",
"article_url": "",
"journal": "Virology",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "1994",
"pubmed_id": "8122363"
},
{
"title": "New pyruvylated, glycosylated acyltrehaloses from Mycobacterium smegmatis strains, and their implications for phage resistance in mycobacteria.",
"abstract": "Phage resistance and apparent lysogenization of Mycobacterium smegmatis due to infection with mycobacteriophage D29 results in the emergence of new variations of the pyruvylated, acylated trehaloses described by Saadat and Ballou, J. Biol. Chem. 258 (1983) 1813-1818. Thin-layer chromatography of the glycolipids from two strains of phage-resistant M. smegmatis (mc(2)22 and mc(2)11) and comparison with those from phage-sensitive strains revealed a new, more mobile glycolipid in each case. The structures of these acyltrehalose-containing lipooligosaccharides were elucidated by a combination of gas-liquid chromatography-mass spectrometry, methylation analysis, 1H and 13C NMR spectroscopy, and fast-atom bombardment mass spectrometry. The glycolipid from M. smegmatis mc(2)22 is beta-D-Glcp-(1-->3)-4,6-O-(1-methoxycarbonylethylidene)-beta-D-Glc p-(1-->4)- beta-D-Glcp-(1-->6)-2-O-acyl-alpha-D-Glcp-(<==>1)-3,4-O-acyl-alpha-D-Glc p and that from M. smegmatis mc(2)11 is 4,6-O-(1-methoxycarbonylethylidene)-3-O-Me-beta-D-Glcp-(1-->3)-4,6 -O- (1-methoxycarbonylethylidene)-beta-D-Glcp-(1-->4)-beta-D-Glcp-(1-- >6)-2-O-acyl- alpha-D-Glcp-(1<==>1)-3,4-di-O-acyl-alpha-D-Glcp. These differ from the original pyruvylated glycolipids of Saadat and Ballou in the extent of their O-acylation and O-methylation. The findings are the first example of the definition of a chemical basis for phage resistance and presumed lysogeny in mycobacteria, and show parallels to related changes in gram-negative enteric bacteria.",
"full_author_list": "G S Besra, K H Khoo, J T Belisle, M R McNeil, H R Morris, A Dell, P J Brennan",
"short_author_list": "Besra GS et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8149383",
"journal": "Carbohydrate research",
"journal_volume": "251",
"journal_issue": "",
"journal_pages": "99-114",
"pub_year": "1994",
"pubmed_id": "8149383"
},
{
"title": "New technologies in the diagnosis of tuberculosis.",
"abstract": "Classic methods for laboratory diagnosis of tuberculosis are time consuming, and resulting delays can adversely affect patient care and tuberculosis control. Newer radiometric culture methods can significantly reduce the time required for detection of Mycobacterium tuberculosis. DNA probe assays and high-performance liquid chromatography of mycolic acids allow identification of isolates in a few hours, and use of these methods is strongly encouraged. A new generation of rapid methods based on techniques of molecular biology will eventually allow direct detection and identification of mycobacteria in clinical samples. These methods use rapid nucleic acid amplification techniques, such as the polymerase chain reaction (PCR), rather than growth of cultures to increase the sensitivity of detection. Assays of this type are currently being evaluated in formal trails. Recent analysis of the mechanisms of drug resistance in M tuberculosis may allow the development of assays for direct detection of drug resistant strains at the genetic level. A luciferase reporter mycobacteriophage assay offers an alternate means for rapidly assessing drug resistance. This assay measures the activity of the drug rather than the genetic basis for resistance. DNA fingerprinting methods have provided the means for distinguishing strains for epidemiological purposes. These new approaches will have a dramatic impact on our ability to rapidly and accurately diagnose tuberculosis.",
"full_author_list": "J T Crawford",
"short_author_list": "Crawford JT",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7973172",
"journal": "Seminars in respiratory infections",
"journal_volume": "9",
"journal_issue": "2",
"journal_pages": "62-70",
"pub_year": "1994",
"pubmed_id": "7973172"
},
{
"title": "Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis.",
"abstract": "An invertible DNA element of 6.8 kb, designated the hsd1 locus, was identified in the chromosome of Mycoplasma pulmonis. Infection of host cells with mycoplasma virus P1 revealed that the organism's restriction and modification (R-M) properties are controlled by inversion of hsd1. The nucleotide sequence of hsd1 revealed several genes, the predicted amino acids of which bear striking similarity to the subunits of the type I R-M enzymes previously found only in enteric bacteria.",
"full_author_list": "K Dybvig, H Yu",
"short_author_list": "Dybvig K, Yu H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7934878",
"journal": "Molecular microbiology",
"journal_volume": "12",
"journal_issue": "4",
"journal_pages": "547-60",
"pub_year": "1994",
"pubmed_id": "7934878"
},
{
"title": "Bacteriophages as tools for vaccine development.",
"abstract": "The construction of live recombinant bacterial vaccines requires a reasonably sophisticated genetic system for the introduction, stabilization and expression of foreign antigen genes. Bacteriophages offer a rich collection of tools that can be used for vaccine construction, including site-specific integration-proficient vectors, non-antibiotic selectable markers and signals for efficient transcription and translation of foreign genes. We describe the characterization of a temperate phage of the mycobacteria, mycobacteriophage L5, and application of these phage studies for the construction of recombinant BCG vaccines.",
"full_author_list": "G F Hatfull, L Barsom, L Chang, M Donnelly-Wu, M H Lee, M Levin, C Nesbit, G J Sarkis",
"short_author_list": "Hatfull GF et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7958482",
"journal": "Developments in biological standardization",
"journal_volume": "82",
"journal_issue": "",
"journal_pages": "43-7",
"pub_year": "1994",
"pubmed_id": "7958482"
},
{
"title": "Structural proteins of mycobacteriophage I3: cloning, expression and sequence analysis of a gene encoding a 70-kDa structural protein.",
"abstract": "The structural proteins of mycobacteriophage I3 have been analysed by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis (SDS-PAGE), radioiodination and immunoblotting. Based on their abundance the 34- and 70-kDa bands appeared to represent the major structural proteins. Successful cloning and expression of the 70-kDa protein-encoding gene of phage I3 in Escherichia coli and its complete nucleotide sequence determination have been accomplished. A second (partial) open reading frame following the stop codon for the 70-kDa protein was also identified within the cloned fragment. The deduced amino-acid sequence of the 70-kDa protein and the codon usage patterns indicated the preponderance of codons, as predicted from the high G+C content of the genomic DNA of phage I3.",
"full_author_list": "G R Ramesh, K P Gopinathan",
"short_author_list": "Ramesh GR, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8200544",
"journal": "Gene",
"journal_volume": "143",
"journal_issue": "1",
"journal_pages": "95-100",
"pub_year": "1994",
"pubmed_id": "8200544"
},
{
"title": "Isolation, characterization, and mapping of temperature-sensitive mutations in the genes essential for lysogenic and lytic growth of the mycobacteriophage L1.",
"abstract": "Forty temperature-sensitive mutations affecting lytic growth and eight affecting both establishment and maintenance of lysogeny of the temperate mycobacteriophage L1 have been isolated. All of the latter mutations form one complementation group and map within a very short region around the 15% coordinate of the L1 genome; these affect a single gene, cl, coding for the L1 repressor. The former 40 mutations form 28 complementation groups, identifying 28 different genes, G1-G28, essential for the lytic growth of L1. These genes have been mapped using the Gts mutations. Of the 28 Gts mutants, 14 are defective in host lysis at 42 degrees but not at 32 degrees while the other 14 can lyse the host at both temperatures. Among the former 14 Gts mutants, 6 are also defective in L1 DNA synthesis at 42 degrees, and they map in two different clusters, 4 around 65% and 2 around 84% of the L1 genome.",
"full_author_list": "B Chaudhuri, S Sau, H J Datta, N C Mandal",
"short_author_list": "Chaudhuri B et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8480419",
"journal": "Virology",
"journal_volume": "194",
"journal_issue": "1",
"journal_pages": "166-72",
"pub_year": "1993",
"pubmed_id": "8480419"
},
{
"title": "Comparative analysis of the genomes of mycobacteriophages infecting saprophytic and pathogenic mycobacteria.",
"abstract": "The genomes of a series of mycobacteriophages have been analyzed to disclose possible relationships between genetic characteristics and host range. The percent guanine-plus-cytosine in the DNA of 14 phages was found to be 34.4 to 47.5, as determined by a double-labelling procedure, which is unaffected by the presence of modified bases. The DNA of few mycobacteriophages yielded discordant values when the G + C content was estimated by buoyant density determination and by the double labelling procedure. This observation suggests the possible presence of modified bases in these genomes. The reduced susceptibility of viral DNAs to several restriction endonucleases is suggestive of the occurrence of both methyladenine and methylcytosine in the genome of all the mycobacteriophages studied. Heterologous annealing among the 14 DNAs analyzed yielded 6 hybridization groups. Within one group, the homology level among viral genomes was estimated by comparing the electrophoretic mobilities of restriction fragments: values of 0.8 to 1.3% base substitution have thus been found. A comparison of the genomic characteristics and host range of the mycobacteriophages analyzed suggests a possible relationship between restriction pattern, G + C content, crosshybridization level and host range.",
"full_author_list": "M Coene, M De Kesel, N T Hong, A Gheysen, A Jezierska-Anczukow, C Cocito",
"short_author_list": "Coene M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8240016",
"journal": "Archives of virology",
"journal_volume": "133",
"journal_issue": "1-2",
"journal_pages": "39-49",
"pub_year": "1993",
"pubmed_id": "8240016"
},
{
"title": "Superinfection immunity of mycobacteriophage L5: applications for genetic transformation of mycobacteria.",
"abstract": "Mycobacteriophage L5 is a temperate phage of the mycobacteria that forms stable lysogens in Mycobacterium smegmatis. We show here that the 183-amino-acid product of L5 gene 71 confers immunity to L5 superinfection, is required for maintenance of the lysogenic state and contains a helix-turn-helix DNA-binding motif--properties associated with repressors of temperate phages. We have utilized these observations to demonstrate the use of L5 gene 71 as a selectable marker for genetic transformation of the mycobacteria. Significantly, the use of L5 gene 71 as a selectable gene avoids the requirement for antibiotic-resistance genes providing an important tool for manipulation of the pathogens Mycobacterium tuberculosis and Mycobacterium avium, and for the construction of recombinant BCG vaccines.",
"full_author_list": "M K Donnelly-Wu, W R Jacobs, G F Hatfull",
"short_author_list": "Donnelly-Wu MK, Jacobs WR, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8459767",
"journal": "Molecular microbiology",
"journal_volume": "7",
"journal_issue": "3",
"journal_pages": "407-17",
"pub_year": "1993",
"pubmed_id": "8459767"
},
{
"title": "Stable integration and expression of the Plasmodium falciparum circumsporozoite protein coding sequence in mycobacteria.",
"abstract": "The DNA coding for the circumsporozoite protein of Plasmodium falciparum (CSP; aa 1-412) has been placed under the control of the mycobacterial promoter derived from the gene encoding the 64-kDa antigen of Mycobacterium bovis-BCG. This expression cassette was cloned into pJRD184, an Escherichia coli multicloning site vector, together with the kanamycin resistance gene from Tn903 and the attachment site and integrase gene from the temperate mycobacteriophage FRAT1. One of the resulting plasmids, pNIV2173, introduced by electroporation into both Mycobacterium smegmatis and M. bovis-BCG, integrated at a specific site in the genome of each recipient. Recombinants expressed immunoreactive polypeptides, ranging in size from 62 to 43 kDa, at a level of about 1% of total soluble proteins. Part of this material was present in the culture medium indicating that mycobacterial recombinants were able to secrete the CSP. The M. smegmatis and M. bovis-BCG recombinants, transformed with pNIV2173 and grown in absence of antibiotic, were followed for more than 400 and 50 generations respectively. Over this time span, neither DNA rearrangement nor loss of expression was observed. Inoculation of the recombinant BCG to mice did not induce humoral response to CSP nor proliferative response to CSP Th2R CD4+ T lymphocyte epitope.",
"full_author_list": "F Haeseleer, J F Pollet, M Haumont, A Bollen, P Jacobs",
"short_author_list": "Haeseleer F et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8426607",
"journal": "Molecular and biochemical parasitology",
"journal_volume": "57",
"journal_issue": "1",
"journal_pages": "117-26",
"pub_year": "1993",
"pubmed_id": "8426607"
},
{
"title": "DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics.",
"abstract": "Genetic studies of Mycobacterium tuberculosis and other mycobacterial pathogens have suffered from the lack of a sophisticated genetic system. To address this issue we have developed a viral system through a detailed characterization of mycobacteriophage L5, a temperate phage that infects both fast- and slow-growing mycobacteria. We describe here the complete DNA sequence of the L5 genome and initial characterization of L5 virion structure and gene expression. In addition to providing a genetic 'tool-box' for the mycobacteria we find that L5 offers a new paradigm for dsDNA phages, being phenotypically temperate but employing genetic strategies for phage growth usually associated with lytic bacteriophages.",
"full_author_list": "G F Hatfull, G J Sarkis",
"short_author_list": "Hatfull GF, Sarkis GJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8459766",
"journal": "Molecular microbiology",
"journal_volume": "7",
"journal_issue": "3",
"journal_pages": "395-405",
"pub_year": "1993",
"pubmed_id": "8459766"
},
{
"title": "Rapid assessment of drug susceptibilities of Mycobacterium tuberculosis by means of luciferase reporter phages.",
"abstract": "Effective chemotherapy of tuberculosis requires rapid assessment of drug sensitivity because of the emergence of multidrug-resistant Mycobacterium tuberculosis. Drug susceptibility was assessed by a simple method based on the efficient production of photons by viable mycobacteria infected with specific reporter phages expressing the firefly luciferase gene. Light production was dependent on phage infection, expression of the luciferase gene, and the level of cellular adenosine triphosphate. Signals could be detected within minutes after infection of virulent M. tuberculosis with reporter phages. Culture of conventional strains with antituberculosis drugs, including isoniazid or rifampicin, resulted in extinction of light production. In contrast, light signals after luciferase reporter phage infection of drug-resistant strains continued to be produced. Luciferase reporter phages may help to reduce the time required for establishing antibiotic sensitivity of M. tuberculosis strains from weeks to days and to accelerate screening for new antituberculosis drugs.",
"full_author_list": "W R Jacobs, R G Barletta, R Udani, J Chan, G Kalkut, G Sosne, T Kieser, G J Sarkis, G F Hatfull, B R Bloom",
"short_author_list": "Jacobs WR et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8484123",
"journal": "Science (New York, N.Y.)",
"journal_volume": "260",
"journal_issue": "5109",
"journal_pages": "819-22",
"pub_year": "1993",
"pubmed_id": "8484123"
},
{
"title": "Mycobacteriophage L5 integrase-mediated site-specific integration in vitro.",
"abstract": "Mycobacteriophage L5, a temperate phage of the mycobacteria, forms stable lysogens in Mycobacterium smegmatis via site-specific integration of the phage genome. Recombination occurs within specific phage and bacterial attachment sites and is catalyzed by the phage-encoded integrase protein in vivo. We describe here the overexpression and purification of L5 integrase and its ability to mediate integrative recombination in vitro. We find that L5 integrase-mediated recombination is greatly stimulated by extracts of M. smegmatis but not by Escherichia coli extracts, purified E. coli integration host factor, or purified HU, indicating the presence of a novel mycobacterial integration host factor.",
"full_author_list": "M H Lee, G F Hatfull",
"short_author_list": "Lee MH, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8226625",
"journal": "Journal of bacteriology",
"journal_volume": "175",
"journal_issue": "21",
"journal_pages": "6836-41",
"pub_year": "1993",
"pubmed_id": "8226625"
},
{
"title": "Genetics of tuberculosis.",
"abstract": "Molecular methods for identifying organisms, strain typing, and determining drug susceptibilities are extremely valuable for pathogens that are impossible to grow on artificial media, slow growing on artificial media, or exceptionally hazardous to grow in a clinical microbiology laboratory. DNA hybridization probes and RFLP analysis are currently being used to facilitate the diagnosis and evaluation of mycobacterial disease. PCR is rapidly progressing to the point at which it will become routine in the clinical microbiology laboratory. LCR clearly has a future role in mycobacteriology but requires further understanding of mycobacterial genetics and physiology. The mycobacteriophage reporter-gene assay is an exciting future option that may allow us to obtain critical treatment related information in a much more timely fashion. The technologies mentioned in this article do not include all of the possibilities for the future; however, it can already be imagined that the isolation, identification, and drug-resistance properties of mycobacteria can be determined directly from clinical specimens and the results made available in a matter of days rather than weeks to months. What about the cost? These are expensive methods currently; however, the cost of conventional culture, drug susceptibility determinations, unnecessary periods of isolation for infection control, delays in recognition of resistant isolates, and deaths before the availability of laboratory information are high prices to pay. Only through further investigation can we clarify the most efficient and cost-effective tuberculosis treatment and control program. The dual epidemics of the human immunodeficiency virus and TB will continue to press the scientific community to develop cost-effective approaches, both for developed and developing nations, to a wide array of pathogens. If we do not characterize existing and future organisms at the molecular level, we will be forced to deal with them on their terms and at their leisure.",
"full_author_list": "G L Marks",
"short_author_list": "Marks GL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7901461",
"journal": "The Medical clinics of North America",
"journal_volume": "77",
"journal_issue": "6",
"journal_pages": "1219-34",
"pub_year": "1993",
"pubmed_id": "7901461"
},
{
"title": "[Progress and application of molecular genetics in the research of Mycobacterium tuberculosis]",
"abstract": "In the last decade, a great deal of advances in the genetics of Mycobacterium tuberculosis have been made by the introduction of new genetic technologies. In this review, a brief discussion of the progress in mycobacterial genetics, especially, gene cloning, development of host-vector systems, structural analysis of chromosomal DNA, plasmid DNA and mycobacteriophage DNA, IS element, and drug resistance mechanism was presented.",
"full_author_list": "Y Mizuguchi",
"short_author_list": "Mizuguchi Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8264127",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "68",
"journal_issue": "11",
"journal_pages": "709-14",
"pub_year": "1993",
"pubmed_id": "8264127"
},
{
"title": "Low temperature protocol for efficient transformation of Mycobacterium smegmatis spheroplasts.",
"abstract": "Spheroplasts of Mycobacterium smegmatis LM15, strain 607, were prepared by a combined treatment with glycine and lysozyme. The spheroplasts were tested for ability to take up and express purified mycobacteriophage DNA. Exposure of 1.0 x 10(8) to 1.0 x 10(9) spheroplasts to saturating DNA (1 microgram) for 15 min at 5 degrees C resulted in a transfection efficiency of approximately 0.009% . The transfer of the beta-lactamase marker with DNA purified from strain LM15 to spheroplasts of a beta-lactamase-negative mutant, strain LM144, was achieved. The DNA-treated cultures, after reversion to the bacillary form, contained 20-fold more penicillin-resistant cells than the nontreated control culture. Approximately 80% of the penicillin-resistant colonies from the DNA-treated cells were positive for beta-lactamase Cell-free extracts of penicillin-resistant transformants contained beta-lactamase activity that ranged from 0.046 to 0.134 micromol of benzylpenicillin hydrolyzed/min per mg protein. This low temperature procedure is recommended for high efficiency transformation of M. smegmatis.",
"full_author_list": "S A Naser, C M McCarthy, G B Smith, A K Tupponce",
"short_author_list": "Naser SA et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7764135",
"journal": "Current microbiology",
"journal_volume": "27",
"journal_issue": "3",
"journal_pages": "153-6",
"pub_year": "1993",
"pubmed_id": "7764135"
},
{
"title": "Comparison of restriction fragment length polymorphism of Mycobacterium tuberculosis isolated from cerebrospinal fluid and sputum: a preliminary report.",
"abstract": "Strain characterization of Mycobacterium tuberculosis has been based mainly on mycobacteriophage typing or chromosomal DNA restriction fragment analysis. In this study 10 randomly selected EcoRI chromosomal DNA fragments of M. tuberculosis H37RV were labelled with digoxigenin and used to probe the Southern blot preparation of EcoRI or BstEII digested chromosomal DNA of clinical isolates of M. tuberculosis. 2 probes were able to reveal restriction fragment length polymorphism. Each of the probes divided 15 pulmonary and 6 cerebrospinal fluid (CSF) isolates of M. tuberculosis into 3 groups and combination of both probes divided them into 4 groups. All of the 6 CSF isolates belonged to 1 group while only 5 of the 15 pulmonary isolates belonged to the same group. Work is continuing in order to characterize the nature of the probe and confirm the results in a larger population.",
"full_author_list": "P Palittapongarnpim, S Rienthong, W Panbangred",
"short_author_list": "Palittapongarnpim P, Rienthong S, Panbangred W",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/8103686",
"journal": "Tubercle and lung disease : the official journal of the International Union against Tuberculosis and",
"journal_volume": "74",
"journal_issue": "3",
"journal_pages": "204-7",
"pub_year": "1993",
"pubmed_id": "8103686"
},
{
"title": "Insertion into the Mycobacterium smegmatis genome of the aph gene through lysogenization with the temperate mycobacteriophage Ms6.",
"abstract": "A derivative of the temperate mycobacteriophage Ms6 containing the aph gene from transposon Tn5 was constructed. In the transductants the aph gene was integrated in the bacterial genome. The aph gene is stably maintained in the absence of positive selection after more than 150 generations. The results presented in this report show that Ms6 can be used as a vehicle for the integration of foreign DNA into the Mycobacterium smegmatis genome.",
"full_author_list": "E Anes, I Portugal, J Moniz-Pereira",
"short_author_list": "Anes E, Portugal I, Moniz-Pereira J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1325383",
"journal": "FEMS microbiology letters",
"journal_volume": "74",
"journal_issue": "1",
"journal_pages": "21-5",
"pub_year": "1992",
"pubmed_id": "1325383"
},
{
"title": "Identification of expression signals of the mycobacteriophages Bxb1, L1 and TM4 using the Escherichia-Mycobacterium shuttle plasmids pYUB75 and pYUB76 designed to create translational fusions to the lacZ gene.",
"abstract": "Mycobacterial expression signals were cloned using specially constructed gene fusion shuttle plasmid probes carrying a truncated Escherichia coli lacZ (beta-galactosidase) gene which lacked a promoter, a ribosome binding site, and an ATG start codon. Libraries of mycobacteriophage Bxb1, L1 and TM4 DNAs were constructed, and introduced by electroporation into Mycobacterium smegmatis and the 'bacille Calmette-Guérin' (BCG). Clones carrying mycobacterial expression sequences were detected by their blue colour or characteristic fluorescence when plated on media containing chromogenic or fluorogenic substrates. Varying degrees of beta-galactosidase expression were observed, and one Bxb1 expression signal was identified where beta-galactosidase expression is repressed in phage lysogens.",
"full_author_list": "R G Barletta, D D Kim, S B Snapper, B R Bloom, W R Jacobs",
"short_author_list": "Barletta RG et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1556552",
"journal": "Journal of general microbiology",
"journal_volume": "138",
"journal_issue": "1",
"journal_pages": "23-30",
"pub_year": "1992",
"pubmed_id": "1556552"
},
{
"title": "A stable Escherichia coli-Mycobacterium smegmatis plasmid shuttle vector containing the mycobacteriophage D29 origin.",
"abstract": "A plasmid shuttle vector for Escherichia coli and mycobacteria was constructed from an E. coli plasmid containing the ColE1 origin, a 2.6-kb PstI fragment from bacteriophage D29 that grows in numerous mycobacterial species, and the kanamycin resistance gene either of Tn903 or of Tn5. The resultant plasmid is 7.63 kb and can be introduced via transformation into Mycobacterium smegmatis with high efficiency. In M. smegmatis the plasmid is stable and apparently present in multiple copies. Bioluminescence (luxA and luxB of Vibrio harveyi and fischeri) has been expressed in M. smegmatis from the aminoglycoside transferase promoter of Tn5. The D29 fragment should carry an origin of replication and some associated genes that act on it since various mutations destroy the ability of this fragment to replicate in M. smegmatis. The fragment was localized on the D29 genome map.",
"full_author_list": "M David, S Lubinsky-Mink, A Ben-Zvi, S Ulitzur, J Kuhn, M Suissa",
"short_author_list": "David M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1334270",
"journal": "Plasmid",
"journal_volume": "28",
"journal_issue": "3",
"journal_pages": "267-71",
"pub_year": "1992",
"pubmed_id": "1334270"
},
{
"title": "Molecular cloning and sequencing of the attachment site and integrase gene of the temperate mycobacteriophage FRAT1.",
"abstract": "",
"full_author_list": "F Haeseleer, J F Pollet, A Bollen, P Jacobs",
"short_author_list": "Haeseleer F et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1561099",
"journal": "Nucleic acids research",
"journal_volume": "20",
"journal_issue": "6",
"journal_pages": "1420",
"pub_year": "1992",
"pubmed_id": "1561099"
},
{
"title": "The cohesive ends of mycobacteriophage L5 DNA.",
"abstract": "",
"full_author_list": "M Oyaski, G F Hatfull",
"short_author_list": "Oyaski M, Hatfull GF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1620623",
"journal": "Nucleic acids research",
"journal_volume": "20",
"journal_issue": "12",
"journal_pages": "3251",
"pub_year": "1992",
"pubmed_id": "1620623"
},
{
"title": "A novel transposon trap for mycobacteria: isolation and characterization of IS1096.",
"abstract": "In the course of developing strategies to obtain a mutation in the aspartate semialdehyde dehydrogenase (asd) gene of Mycobacterium smegmatis, an efficient transposon trap was constructed which may be generally useful for the identification of transposable elements in mycobacteria. A DNA fragment containing the asd gene was replaced with an aminoglycoside phosphotransferase gene (aph) to generate a delta asd::aph allele. Attempts to replace the wild-type asd gene with the delta asd::aph allele were unsuccessful, suggesting that this deletion was lethal to the growth of M. smegmatis. The plasmid, pYUB215, which contains beta-galactosidase expressed from a mycobacteriophage promoter and delta asd::aph, was integrated into the chromosome of M. smegmatis by a homologous, single-crossover, recombination event. Visual screening for inactivation of the beta-galactosidase gene in the resulting strain allowed the isolation of a novel mycobacterial insertion element from M. smegmatis. This insertion element, which is unique to M. smegmatis, was designated IS1096 and transposes at a frequency of 7.2 x 10(-5) per cell in an apparently random fashion. IS1096 is 2,275 bp in length and contains two open reading frames which are predicted to encode proteins involved in transposition. This insertion element exhibits several characteristics that suggest it may be a useful tool for genetic analysis of mycobacteria, possibly including the study of mechanisms of pathogenesis.",
"full_author_list": "J D Cirillo, R G Barletta, B R Bloom, W R Jacobs",
"short_author_list": "Cirillo JD et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1660454",
"journal": "Journal of bacteriology",
"journal_volume": "173",
"journal_issue": "24",
"journal_pages": "7772-80",
"pub_year": "1991",
"pubmed_id": "1660454"
},
{
"title": "Development of BCG as a live recombinant vector system: potential use as an HIV vaccine.",
"abstract": "Bacille Calmette-Guèrin (BCG), a live attenuated tubercle bacillus, is currently the most widely used vaccine in the world. Because of its unique characteristics, including low toxicity, adjuvant potential, and long-lasting immunity, BCG represents a novel vaccine vehicle with which to deliver protective antigens of multiple pathogens. We have developed episomal and integrative expression vectors employing regulatory sequences of major BCG heat shock proteins for stable maintenance and expression of foreign antigens in BCG vaccine strains (22). Shuttle plasmids capable of autonomous replication in Escherichia coli and BCG were constructed with a DNA cassette containing a minimal replicon derived from the Mycobacterium fortuitum plasmid pAL5000. Efficient and stable chromosomal integration of recombinant plasmids into BCG was achieved using a DNA segment containing the mycobacteriophage L5 attachment site and integrase coding sequence. Using the BCG hsp60 and hsp70 stress gene promoters, we were able to express Escherchia coli beta-galactosidase to levels in excess of 10% of total cell protein. The major antigens of HIV-1 gag, pol, and env were also stably expressed using our vector systems. The recombinant BCG elicited long-lasting humoral and cellular immune responses to these antigens in mice. Antibody responses to beta-galactosidase using as few as 200 colony-forming units were detected 6 weeks after immunization, and titers (1:30,000) were sustained for more than 10 weeks. Cellular immune responses, of both cytotoxic T cell (CTL) and helper T lymphocytes, were detected to beta-galactosidase. CTL responses were also induced to the HIV-1 envelope protein. Thus, we have demonstrated stable recombinant antigen expression, processing, and presentation using our recombinant BCG vector system. This live recombinant vector system shows promise as a universally applicable and safe vaccine vehicle for protection against various infectious diseases.",
"full_author_list": "T R Fuerst, C K Stover, V F de la Cruz",
"short_author_list": "Fuerst TR, Stover CK, de la Cruz VF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1845119",
"journal": "Biotechnology therapeutics",
"journal_volume": "2",
"journal_issue": "1-2",
"journal_pages": "159-78",
"pub_year": "1991",
"pubmed_id": "1845119"
},
{
"title": "Characterization of the DNF15S2 locus on human chromosome 3: identification of a gene coding for four kringle domains with homology to hepatocyte growth factor.",
"abstract": "A human genomic DNA library was screened by using conditions of reduced stringency with a bovine cDNA probe coding for the kringle domains in prothrombin in order to isolate the human prothrombin gene. Twelve positives were identified, three of which coded for prothrombin (Degen & Davie, 1987). Phage L5 was characterized in more detail because of its strong hybridization to the cDNA probe and its unique restriction map compared to the gene coding for human prothrombin. The gene in L5 was sequenced and found to code for a kringle-containing protein. A human liver cDNA library was screened by using a genomic probe from the gene in L5. cDNAs were isolated that contained sequence identical with regions in the gene in L5. Comparison of the cDNA with the gene indicated that the gene in L5 was composed of 18 exons separated by 17 intervening sequences and is 4690 bp in length. Exons ranged in size from 36 to 242 bp in length while intervening sequences ranged from 77 to 697 bp in length. The putative protein encoded by the gene in L5 contains four kringle domains followed by a serine protease-like domain. This domain structure is identical with that found in hepatocyte growth factor (HGF), although the two proteins are only about 50% identical. On the basis of the similarity of the protein encoded by L5 and HGF, we propose that the putative L5 protein be tentatively called HGF-like protein until a function is identified. The DNA sequence of the gene and cDNA and its translated amino acid sequence were compared against GenBank and NBRF databases. Sequences homologous to DNF15S1 and DNF15S2, human DNF15S2 lung mRNA, and rat acyl-peptide hydrolase were identified in exon 17 to the 3' end of the characterized sequence for the gene. From our results, it is apparent that the gene coding for human HGF-like protein is located at the DNF15S2 locus on human chromosome 3 (3p21). The gene for acyl-peptide hydrolase is 444 bp downstream of the gene coding for HGF-like protein, but on the complementary strand. The DNF15S2 locus has been proposed to code for one or more tumor suppressor genes since this locus is deleted in DNA from small cell lung carcinoma, other lung cancers, renal cell carcinoma, and von Hippel-Lindau syndrome.",
"full_author_list": "S Han, L A Stuart, S J Degen",
"short_author_list": "Han S, Stuart LA, Degen SJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1655021",
"journal": "Biochemistry",
"journal_volume": "30",
"journal_issue": "40",
"journal_pages": "9768-80",
"pub_year": "1991",
"pubmed_id": "1655021"
},
{
"title": "Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guérin.",
"abstract": "Mycobacteriophage L5, a temperate phage of mycobacteria, integrates site-specifically into the Mycobacterium smegmatis chromosome. We have identified the int gene and attP site of L5, characterized the chromosomal attachment site (attB), and constructed plasmid vectors that efficiently transform M. smegmatis through stable site-specific integration of the plasmid into the bacterial genome. These integration-proficient plasmids also efficiently transform slow-growing mycobacteria such as the pathogen Mycobacterium tuberculosis and the vaccine strain bacille Calmette-Guérin (BCG). The ability to easily generate stable recombinants in these slow-growing mycobacteria without the requirement for continual selection is of particular importance for the construction of recombinant BCG vaccines and for the isolation and characterization of mycobacterial pathogenic determinants in animal model systems. Integration vectors of this type should be of general use in a number of additional bacterial systems where temperate phages have been identified.",
"full_author_list": "M H Lee, L Pascopella, W R Jacobs, G F Hatfull",
"short_author_list": "Lee MH et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1901654",
"journal": "Proceedings of the National Academy of Sciences of the United States of America",
"journal_volume": "88",
"journal_issue": "8",
"journal_pages": "3111-5",
"pub_year": "1991",
"pubmed_id": "1901654"
},
{
"title": "Isolation and characterization of temperature sensitive mutants of the F5 deletion mutant of mycobacteriophage D29.",
"abstract": "Seven thermosensitive mutants of the F5 deletion mutant of the mycobacteriophage D29 were described. The mutants were obtained using N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) mutagenesis, and were characterized using temperature shift assays, complementation and recombination tests, electron microscopy of infected host bacteria at non-permissive temperature, and serum blocking power. Mutants deficient in tail assembly, and mutants deficient in head and tail assembly were described. Mutants deficient in head assembly but capable of assembling tails were not isolated during this study. From the data, 3 provisional linkage map of the phage F5 was proposed.",
"full_author_list": "S Sérès, R Lazraq, H Ohayon",
"short_author_list": "Sérès S, Lazraq R, Ohayon H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1930565",
"journal": "Zentralblatt für Bakteriologie : international journal of medical microbiology",
"journal_volume": "275",
"journal_issue": "1",
"journal_pages": "54-62",
"pub_year": "1991",
"pubmed_id": "1930565"
},
{
"title": "[Pathomorphological assessment of the therapeutic effect of mycobacteriophages in tuberculosis]",
"abstract": "The effect of DS6A mycophage was studied in comparison with that of isoniazid on 30 guinea pigs with disseminated tuberculous infection in order to reveal the therapeutic effect of the mycobacteriophage and tissue reactions caused by it. The mycophage was found to have therapeutic properties in disseminated tuberculosis in guinea pigs but its action is less pronounced than in isoniazid monotherapy. Study of the special features of tissue reactions in mycophage monotherapy has demonstrated that with the mycophage phagocytosis remains incomplete and granulomatous processes that gradually lose morphological signs of tuberculous inflammation and acquire typical features of sarcoidosis develop in the animal organs.",
"full_author_list": "Z S Zemskova, I R Dorozhkova",
"short_author_list": "Zemskova ZS, Dorozhkova IR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1775467",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "11",
"journal_pages": "63-6",
"pub_year": "1991",
"pubmed_id": "1775467"
},
{
"title": "Recombinant BCG as a candidate oral vaccine vector.",
"abstract": "Bacille Calmette-Guerin (BCG), currently the most widely used vaccine in the world, was originally administered for many years as an oral vaccine. The low frequency of serious complications, inexpensive production, and adjuvanticity make BCG an ideal candidate for a recombinant vaccine vehicle. Although mycobacteria are slow growing and not yet well characterized genetically, we have recently developed technology for the genetic manipulation of BCG and other mycobacteria. Phage and plasmid systems based on a shuttle strategy to manipulate DNA in Escherichia coli and transfer it to mycobacteria have been developed. We have established that the aminoglycoside phosphotransferase gene can be used as an effective selectable marker in the mycobacteria and that a foreign antigen from Mycobacterium leprae can be expressed in BCG. Furthermore, a thorough analysis of mycobacterial expression sequences has been undertaken to optimize the expression of foreign antigens in BCG. We constructed an expression probe shuttle plasmid with beta-galactosidase as reporter gene, and have used it successfully to identify multiple mycobacteriophage DNA sequences with varying levels of constitutive or regulable promoter activity. Further genetic advances required for development of recombinant BCG into an effective recombinant vaccine vehicle, including possibilities for oral administration, are adumbrated.",
"full_author_list": "R G Barletta, B Snapper, J D Cirillo, N D Connell, D D Kim, W R Jacobs, B R Bloom",
"short_author_list": "Barletta RG et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2101484",
"journal": "Research in microbiology",
"journal_volume": "141",
"journal_issue": "7-8",
"journal_pages": "931-9",
"pub_year": "1990",
"pubmed_id": "2101484"
},
{
"title": "Development of BCG as a recombinant vaccine vehicle.",
"abstract": "",
"full_author_list": "W R Jacobs, S B Snapper, L Lugosi, B R Bloom",
"short_author_list": "Jacobs WR et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2407431",
"journal": "Current topics in microbiology and immunology",
"journal_volume": "155",
"journal_issue": "",
"journal_pages": "153-60",
"pub_year": "1990",
"pubmed_id": "2407431"
},
{
"title": "[Phage typing of Mycobacterium tuberculosis strains coming from Nicaragua (preliminary report)]",
"abstract": "Fifty Nicaraguan strains of Mycobacterium tuberculosis were classified with a scheme of 9 specific phages. A preliminary distribution of characteristic phagotypes of the area is reported, with prevalence of phagotype I (intermedial) (66%), presence of phagotype A (34%) and absence of the rest of the types. Inclusions of phagotypes Bo4 and F-o-WJ within the classification scheme, as well as practical usefulness of the technique in studies directed to disease control, are valued.",
"full_author_list": "C A Jiménez Misas, J A Valdivia Alvarez, D Mazón Zamora",
"short_author_list": "Jiménez Misas CA, Valdivia Alvarez JA, Mazón Zamora D",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2124368",
"journal": "Revista cubana de medicina tropical",
"journal_volume": "42",
"journal_issue": "1",
"journal_pages": "19-24",
"pub_year": "1990",
"pubmed_id": "2124368"
},
{
"title": "Geographic distribution of phage types among cultures of Mycobacterium tuberculosis. II. Cultures from India and South Africa.",
"abstract": "Mycobacterium tuberculosis cultures obtained from India and South Africa were phage-typed to determine distribution patterns according to phage type in these two geographic locations. Of the 74 Indian strains, 14.9% were type 1, 32.4% were type 2, 28.4 were type 7, and 24.3% were type 8, whereas of the 78 South African strains, 20.5% were type 1, 47.5% were type 2, 1.3% were type 4, 11.5% were type 7, 19.2% were type 8. The phage types were then subdivided according to the lytic patterns produced by the six auxillary phages. The phage type distribution in the Indian and South African strains was compared with the type distribution in cultures from the United States and Southeast Asia, and differences were found in the four widely separated geographic areas.",
"full_author_list": "W D Jones",
"short_author_list": "Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2122783",
"journal": "The American review of respiratory disease",
"journal_volume": "142",
"journal_issue": "5",
"journal_pages": "1000-3",
"pub_year": "1990",
"pubmed_id": "2122783"
},
{
"title": "Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis.",
"abstract": "Recent development of vectors and methodologies to introduce recombinant DNA into members of the genus Mycobacterium has provided new approaches for investigating these important bacteria. While most pathogenic mycobacteria are slow-growing, Mycobacterium smegmatis is a fast-growing, non-pathogenic species that has been used for many years as a host for mycobacteriophage propagation and, recently, as a host for the introduction of recombinant DNA. Its use as a cloning host for the analysis of mycobacterial genes has been limited by its inability to be efficiently transformed with plasmid vectors. This work describes the isolation and characterization of mutants of M. smegmatis that can be transformed, using electroporation, at efficiencies 10(4) to 10(5) times greater than those of the parent strain, yielding more than 10(5) transformants per microgram of plasmid DNA. The mutations conferring this efficient plasmid transformation (Ept) phenotype do not affect phage transfection or the integration of DNA into the M. smegmatis chromosome, but seem to be specific for plasmid transformation. Such Ept mutants have been used to characterize plasmid DNA sequences essential for replication of the Mycobacterium fortuitum plasmid pAL5000 in mycobacteria by permitting the transformation of a library of hybrid plasmid constructs. Efficient plasmid transformation of M. smegmatis will facilitate the analysis of mycobacterial gene function, expression and replication and thus aid in the development of BCG as a multivalent recombinant vaccine vector and in the genetic analysis of the virulence determinants of pathogenic mycobacteria.",
"full_author_list": "S B Snapper, R E Melton, S Mustafa, T Kieser, W R Jacobs",
"short_author_list": "Snapper SB et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2082148",
"journal": "Molecular microbiology",
"journal_volume": "4",
"journal_issue": "11",
"journal_pages": "1911-9",
"pub_year": "1990",
"pubmed_id": "2082148"
},
{
"title": "New strategies for leprosy and tuberculosis and for development of bacillus Calmette-Guérin into a multivaccine vehicle.",
"abstract": "",
"full_author_list": "B R Bloom, W R Jacobs",
"short_author_list": "Bloom BR, Jacobs WR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2516995",
"journal": "Annals of the New York Academy of Sciences",
"journal_volume": "569",
"journal_issue": "",
"journal_pages": "155-73",
"pub_year": "1989",
"pubmed_id": "2516995"
},
{
"title": "The modern mycobacteriology laboratory. How it can help the clinician.",
"abstract": "The mycobacteriology laboratory provides the information necessary to diagnose mycobacteriosis and to suggest proper patient management. When the definite diagnosis of disease due to M. tuberculosis is made on the basis of the laboratory result, contact follow-up studies should continue and the patient may be considered infectious if the bacilli were isolated from the sputum. A report of another Mycobacterium species suggests that a contact follow-up is not necessary, that the patient need not be isolated, and that a therapeutic regimen should be based on the results of drug-susceptibility tests with the isolate. Techniques of molecular biology are being used in the laboratory to provide the necessary information quickly for patient management. BACTEC has been accepted into most clinical laboratories to speed reporting of results. Other methods such as genetic and immunologic probes are under development. New DNA probes have been marketed by GenProbe for the identification of cultures of M. tuberculosis, M. avium, and M. intracellulare. HPLC and GLC have been used for the identification of cultures based on unique mycolic acid patterns of the species. Immunologic probes may eventually be the most specific and sensitive, but additional development is necessary. Mycobacteriophage typing of M. tuberculosis isolates has been developed as a tool to aid in epidemiologic studies. These and other technologies are essential in the support of programs for the elimination of tuberculosis.",
"full_author_list": "R C Good, T D Mastro",
"short_author_list": "Good RC, Mastro TD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2505961",
"journal": "Clinics in chest medicine",
"journal_volume": "10",
"journal_issue": "3",
"journal_pages": "315-22",
"pub_year": "1989",
"pubmed_id": "2505961"
},
{
"title": "Isolation and first characterization of a temperate phage growing on Mycobacterium smegmatis and M. bovis-BCG.",
"abstract": "",
"full_author_list": "F Haeseler, J Timm, P Jacobs",
"short_author_list": "Haeseler F, Timm J, Jacobs P",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2503997",
"journal": "Acta leprologica",
"journal_volume": "7 Suppl 1",
"journal_issue": "",
"journal_pages": "252-3",
"pub_year": "1989",
"pubmed_id": "2503997"
},
{
"title": "Mycobacteriophage vector systems.",
"abstract": "Successful application of molecular genetic approaches to the study of mycobacteria necessitates the introduction of recombinant DNA molecules into mycobacterial cells. Efficient methods of introducing DNA into Mycobacterium smegmatis protoplasts have been developed, and the construction of mycobacteriophage recombinant DNA vectors has been initiated. Novel Escherichia coli-Mycobacterium shuttle vectors, termed shuttle phasmids, have been constructed. These vectors were constructed by inserting E. coli cosmids into nonessential regions of mycobacteriophage DNAs. Shuttle phasmids are multifunctional vectors that replicate in E. coli as plasmids and replicate in mycobacteria as phage. The presence of the bacteriophage lambda cos sequences permits the use of the lambda in vitro packaging system for efficient cloning of additional genes into these vectors. Temperate shuttle phasmids have been constructed that can infect and lyse mycobacterial cells or lysogenize mycobacterial cells to stably integrate and express cloned DNA into mycobacterial genomes. Shuttle phasmids can be transduced into a wide variety of mycobacterial species and thus should permit the development of molecular genetic systems for the mycobacteria.",
"full_author_list": "W R Jacobs, S B Snapper, M Tuckman, B R Bloom",
"short_author_list": "Jacobs WR et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2652256",
"journal": "Reviews of infectious diseases",
"journal_volume": "11 Suppl 2",
"journal_issue": "",
"journal_pages": "S404-10",
"pub_year": "1989",
"pubmed_id": "2652256"
},
{
"title": "Development of genetic systems for the mycobacteria.",
"abstract": "Requisite to a detailed understanding of the molecular basis of bacterial pathogenesis is a genetic system which allows for the transfer, mutation, and expression of specific genes. Genetic analysis of mycobacteria has been exceedingly difficult since the mycobacteria grow slowly and no natural efficient method of gene transfer within the pathogenic has thus far been found. Using a molecular genetic approach, we have developed both the vectors and the methodology for efficient gene transfer in the mycobacteria. Initially, a novel of type of mycobacteriophage vector was developed, termed a shuttle phasmid. This hybrid shuttle vector replicates in Escherichia coli as a plasmid and in mycobacteria as a phage, capable of introducing foreign DNA into a wide variety of mycobacterial species. A set of shuttle phasmids, constructed from a temperate mycobacteriophage, retained their ability to lysogenize their mycobacterial hosts and could thus introduce foreign DNA stably into mycobacterial cells. An E. coli gene conferring kanamycin-resistance was cloned into these vectors and shown to express in the mycobacteria, thus providing the first selectable marker gene for subsequent genetic studies. Using kanamycin-resistance gene as a selection, the M. fortuitum plasmid pAL5000 replicon, and electroporation; a plasmid transformation system has been developed for both M. smegmatis and BCG. We now plan to use these phage and plasmid systems to analyze, genetically, the virulence attributes of the pathogenic mycobacteria. In addition, by introducing and expressing foreign antigens in BCG, we hope to develop a novel recombinant multi-vaccine vehicle capable of conferring immunity to a variety of bacterial, viral, and parasitic pathogens.",
"full_author_list": "W R Jacobs, S B Snapper, L Lugosi, A Jekkel, R E Melton, T Kieser, B R Bloom",
"short_author_list": "Jacobs WR et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2503991",
"journal": "Acta leprologica",
"journal_volume": "7 Suppl 1",
"journal_issue": "",
"journal_pages": "203-7",
"pub_year": "1989",
"pubmed_id": "2503991"
},
{
"title": "[Study using phagetype markers of Mycobacterium tuberculosis strains from Ethiopia. A preliminary study]",
"abstract": "Twenty strains of Mycobacterium tuberculosis from Addis Ababa (Ethiopia) are studied by means of the phage typing technique in mycobacteria. The results obtained show the preliminary distribution of phage types belonging to type I (intermediate) and absence of the remaining types. The lysis pattern of autochthonous M. tuberculosis is characterized by a prevalence of sensitivity to phages DS6A, GS4E, BG1, and D34. The early results of sensitivity obtained with phage Bo4 and its assessment within the current scheme for M. tuberculosis classification.",
"full_author_list": "C A Jiménez Misas, J A Valdivia Alvarez, D Mazón Zamora",
"short_author_list": "Jiménez Misas CA, Valdivia Alvarez JA, Mazón Zamora D",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2518596",
"journal": "Revista cubana de medicina tropical",
"journal_volume": "41",
"journal_issue": "2",
"journal_pages": "192-9",
"pub_year": "1989",
"pubmed_id": "2518596"
},
{
"title": "Phage typing of Micobacterium tuberculosis in Cuba.",
"abstract": "",
"full_author_list": "C A Jimenez Misas, J A Valdivia Alvarez, D M Mazon Zamora",
"short_author_list": "Jimenez Misas CA, Valdivia Alvarez JA, Mazon Zamora DM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2517568",
"journal": "Memórias do Instituto Oswaldo Cruz",
"journal_volume": "84",
"journal_issue": "2",
"journal_pages": "271",
"pub_year": "1989",
"pubmed_id": "2517568"
},
{
"title": "Restriction map of mycobacteriophage D29 and its deletion mutant F5.",
"abstract": "A physical map of mycobacteriophage D29 was constructed, including positions for 25 restriction sites for 9 endunocleasic enzymes. D29 DNA contains about 48 150 bp. Analysis of a deletion mutant (F5) has allowed to determine the location of two non essential regions in the genome, allowing further insertion of foreign genes and construction of cosmids.",
"full_author_list": "R Lazraq, J Moniz-Pereira, S Clavel-Sérès, F Clément, H L David",
"short_author_list": "Lazraq R et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2503994",
"journal": "Acta leprologica",
"journal_volume": "7 Suppl 1",
"journal_issue": "",
"journal_pages": "234-8",
"pub_year": "1989",
"pubmed_id": "2503994"
},
{
"title": "Temperate mycobacteriophage from M. smegmatis.",
"abstract": "",
"full_author_list": "I Portugal, E Anes, J Moniz-Pereira",
"short_author_list": "Portugal I, Anes E, Moniz-Pereira J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2503995",
"journal": "Acta leprologica",
"journal_volume": "7 Suppl 1",
"journal_issue": "",
"journal_pages": "243-4",
"pub_year": "1989",
"pubmed_id": "2503995"
},
{
"title": "[Distribution of bacteriophage types of Mycobacterium tuberculosis in France]",
"abstract": "The bacteriophage typing of M. tuberculosis enables separation of the strains of the species according to their sensitivity to certain bacteriophages. A relationship has been observed between the geographical origin of patients and the distribution of the phage types of their strains. This study related to a sample of 450 strains isolated between 1978 and 1987 in patients of French origin coming from different regions in France. An analysis of the data provided by the study indicates that the distribution of the 5 phage types, A, AX, I, B, and C is relatively homogenous in the different regions with a predominance of the phage type A and B. The mean percentage of the lysotypes A, AX, I, B and C in the country as a whole are 43%, 15%, 7%, 30% and 5% respectively. Only in region 3 (Haute and Basse Normandie), 8 (Provence-Côte-d'Azur) and 9 (Rhône-Alpes) is there any perceptible deviation from this distribution. This study also underlines the contribution that can be provided by this type of information in the epidemiology of tuberculosis.",
"full_author_list": "S Clavel-Sérès, F Clément, C Jimenez-Misas",
"short_author_list": "Clavel-Sérès S, Clément F, Jimenez-Misas C",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3146114",
"journal": "Revue des maladies respiratoires",
"journal_volume": "5",
"journal_issue": "6",
"journal_pages": "577-81",
"pub_year": "1988",
"pubmed_id": "3146114"
},
{
"title": "Bacteriophage typing of Mycobacterium tuberculosis cultures from incidents of suspected laboratory cross-contamination.",
"abstract": "Bacteriophage typing was performed on 235 Mycobacterium tuberculosis cultures submitted from 31 laboratories. In each instance, either the attending physician questioned the misdiagnosis of tuberculosis or the laboratory supervisor suspected that laboratory cross-contamination had occurred. Phage typing data confirmed these suspicions. Phage typing is a useful adjunct in the investigation of suspected cross-contamination of laboratory cultures of M. tuberculosis.",
"full_author_list": "W D Jones",
"short_author_list": "Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3140459",
"journal": "Tubercle",
"journal_volume": "69",
"journal_issue": "1",
"journal_pages": "43-6",
"pub_year": "1988",
"pubmed_id": "3140459"
},
{
"title": "Lysogeny and transformation in mycobacteria: stable expression of foreign genes.",
"abstract": "Requisite to a detailed understanding of the molecular basis of bacterial pathogenesis is a genetic system that allows for the transfer, mutation, and expression of specific genes. Because of the continuing importance of tuberculosis and leprosy worldwide, we initiated studies to develop a genetic system in mycobacteria and here report the use of two complementary strategies to introduce and express selectable genetic markers. First, an Escherichia coli cosmid was inserted into the temperate mycobacteriophage L1, generating shuttle phasmids replicating as plasmids in E. coli and phage capable of lysogenizing the mycobacterial host. These temperate shuttle phasmids form turbid plaques on Mycobacterium smegmatis and, upon lysogenization, confer resistance to superinfection and integrate within the mycobacterial chromosome. When an L1 shuttle phasmid containing a cloned gene conferring kanamycin resistance in E. coli was introduced into M. smegmatis, stable kanamycin-resistant colonies--i.e., lysogens--were obtained. Second, to develop a plasmid transformation system in mycobacteria, M. fortuitum/E. coli hybrid plasmids containing mycobacterial and E. coli replicons and a kanamycin-resistance gene were constructed. When introduced into M. smegmatis or BCG (Mycobacterium tuberculosis typus bovinus var. Bacille-Calmette-Guérin) by electroporation, these shuttle plasmids conferred stable kanamycin resistance upon transformants. These systems should facilitate genetic analyses of mycobacterial pathogenesis and the development of recombinant mycobacterial vaccines.",
"full_author_list": "S B Snapper, L Lugosi, A Jekkel, R E Melton, T Kieser, B R Bloom, W R Jacobs",
"short_author_list": "Snapper SB et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/2842799",
"journal": "Proceedings of the National Academy of Sciences of the United States of America",
"journal_volume": "85",
"journal_issue": "18",
"journal_pages": "6987-91",
"pub_year": "1988",
"pubmed_id": "2842799"
},
{
"title": "Studies on clofazimine-resistance in mycobacteria: is the inability to isolate drug-resistance mutants related to its mode of action?",
"abstract": "This study showed that clofazimine was not radiomimetic, it was not a mutagenic compound, it was not an inducer of prophage-lambda, and it did not eliminate plasmids from appropriate host bacteria. The drug caused an effective inhibition of the growth of Mycobacterium aurum, and also inhibited the growth cycle of the mycobacteriophage D29. Cross-resistance between clofazimine, streptomycin and rifampicin could not be demonstrated. Drug-resistance mutants towards clofazimine could not be isolated, and it was found that the existing clofazimine-resistant strains of Mycobacterium tuberculosis were rather susceptible organisms requiring clofazimine in their growth medium to maintain their drug-resistance. Ultrastructural studies showed that clofazimine did not act by cell wall lysis, nor did it act on bacterial ribosomes. Higher concentrations of the drug resulted in bacterial plasmolysis. These findings are discussed in the light of its known properties and proposed mode of action.",
"full_author_list": "H L David, N Rastogi, S Clavel-Sérès, F Clément",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3122464",
"journal": "Zentralblatt für Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectio",
"journal_volume": "266",
"journal_issue": "1-2",
"journal_pages": "292-304",
"pub_year": "1987",
"pubmed_id": "3122464"
},
{
"title": "Introduction of foreign DNA into mycobacteria using a shuttle phasmid.",
"abstract": "Mycobacteria are major pathogens of man and animals. There are approximately 10 million cases of tuberculosis world wide with an annual mortality of three million people. Leprosy, caused by Mycobacterium leprae, afflicts over ten million people, primarily in developing countries. M. tuberculosis and mycobacteria of the M. avium-intracellulare-scrofulaceum (MAIS) group are major opportunistic pathogens of patients with acquired immune deficiency syndrome (AIDS). M. paratuberculosis is the cause of Jöhne's disease in cattle. Yet, BCG (Bacille Calmette-Guerin), an avirulent strain of M. bovis, is the most widely used human vaccine in the world, having been administered to about 2.5 X 10(9) people since 1948 (ref. 4). BCG was highly protective against tuberculosis in England, but has been found not to be effective in preventing pulmonary tuberculosis in adults in Southern India. We have initiated studies to develop the methodology for efficient gene transfer in mycobacteria. We have constructed recombinant shuttle phasmids which are chimaeras containing mycobacteriophage DNA into which an E. coli cosmid is inserted. They can replicate in E. coli as plasmids and in mycobacteria as phages, and transfer DNA across both genera. These shuttle vectors permit for the first time the introduction of foreign DNA by infection into M. smegmatis and BCG. By introducing and ultimately expressing genes for protective antigens for a variety of pathogens, it may be possible to develop cultivatable mycobacteria into useful multivaccine vehicles.",
"full_author_list": "W R Jacobs, M Tuckman, B R Bloom",
"short_author_list": "Jacobs WR, Tuckman M, Bloom BR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3473289",
"journal": "Nature",
"journal_volume": "327",
"journal_issue": "6122",
"journal_pages": "532-5",
"pub_year": "1987",
"pubmed_id": "3473289"
},
{
"title": "[Collective experience with bacteriophage typing and identification of Mycobacterium tuberculosis isolated in the USSR and CSSR]",
"abstract": "",
"full_author_list": "A G Khomenko, I R Dorozhkova, N M Makarevich, I Dubina, M Shlosarek",
"short_author_list": "Khomenko AG et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3125539",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "11",
"journal_pages": "51-6",
"pub_year": "1987",
"pubmed_id": "3125539"
},
{
"title": "Molecular genetics in mycobacteria.",
"abstract": "",
"full_author_list": "A P Pugsley",
"short_author_list": "Pugsley AP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3153607",
"journal": "Microbiological sciences",
"journal_volume": "4",
"journal_issue": "12",
"journal_pages": "366-7",
"pub_year": "1987",
"pubmed_id": "3153607"
},
{
"title": "Characterization of mycobacteriophage I8 and its unrelatedness to mycobacteriophages I1, I3 and I5.",
"abstract": "Homology among the genomes of mycobacteriophages I1, I3, I5 and I8 has been studied. Based on restriction endonuclease cleavage patterns, dot blot hybridization and Southern blot hybridization analysis, the DNAs of phages I1, I3 and I5 have been shown to be homologous and indistinguishable, but entirely different from phage I8. Unlike the others, the I8 genome does not harbour any single-strand interruptions. The DNA is 43 kb in length with limited cyclic permutations and has a G + C content of 54%. The presence of 5-methylcytosine in I8 DNA was indicated from the restriction patterns of MspI and HpaII. The number of sites and fragment sizes for several restriction enzymes on I8 DNA has been determined. Phage I8 has a replication cycle of 300 min, with a latent period of 180 min, a rise period of 120 min and a burst size of 100. The viability of phage I8 is significantly reduced by treatment with organic solvents.",
"full_author_list": "A B Reddy, K P Gopinathan",
"short_author_list": "Reddy AB, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3572361",
"journal": "The Journal of general virology",
"journal_volume": "68 ( Pt 4)",
"journal_issue": "",
"journal_pages": "949-56",
"pub_year": "1987",
"pubmed_id": "3572361"
},
{
"title": "Action of colistin (polymyxin E) on the lytic cycle of the mycobacteriophage D29 in Mycobacterium tuberculosis.",
"abstract": "The antibiotic colistin (polymyxin E) inhibited the lytic cycle of the mycobacteriophage D29 in the tubercle bacilli, but not the D29 adsorption. The protein and nucleic acid synthesis in D29-infected bacteria were not affected significantly. The inhibitory activity was reversed by washing off the antibiotic, and by addition of Ca++, but not in media made iso-osmotic by addition of NaCl or sucrose. Transmission electron microscopy revealed an asymmetric to symmetric transition in the staining profile of the cytoplasmic membrane. Though no mature phage particles were ever observed in colistin-treated, D29-infected tubercle bacilli, loosely arranged aggregates resembling phage proheads were occasionally found. Judging from the above data, it was concluded that colistin inhibited D29 lytic cycle by causing molecular displacements in the inner leaflet of the cytoplasmic membrane, and consequently, the binding sites for D29 structural proteins were not available.",
"full_author_list": "H L David, N Rastogi, S Clavel-Sérès, F Clément",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3097989",
"journal": "Zentralblatt für Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectio",
"journal_volume": "262",
"journal_issue": "3",
"journal_pages": "321-34",
"pub_year": "1986",
"pubmed_id": "3097989"
},
{
"title": "Haptenic oligosaccharides in antigenic variants of mycobacterial C-mycosides antagonize lipid receptor activity for mycobacteriophage D4 by masking a methylated rhamnose.",
"abstract": "The simple apolar C-mycosides, i.e., structurally well-defined hydrophobic glycopeptidolipids of several Mycobacterium species (see diagram below), were earlier shown to behave as receptors for adsorption of mycobacteriophage D4. This phage is usually virulent for Mycobacterium smegmatis. More complex, polar C-mycosides with additional carbohydrate substituents attached solely to the deoxytalose have recently been described. They are the highly specific serotyping antigens discovered by W. B. Schaefer--lipids which characterize members of the Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum (MAIS) complex. Both kinds are depicted in the structure below: (Formula: see text) where X equals H (for simple, apolar C-mycosides) and X equals small oligosaccharides (for antigenic forms; more complex, polar C-mycosides). The present investigations showed that the purified polar antigenic lipids exhibit considerably less adsorptive activity for D4 than do the apolar C-mycosides. Thus, the haptenic oligosaccharides are believed to shield the site in the molecule that the phage recognizes, and the blocking is reinforced by the specific antibodies that the antigens elicit. Although the MAIS serovars usually also produce the phage-reactive apolar C-mycosides, they are not permissive hosts for D4, nor do whole cells adsorb the phage. We suggest that in these species the apolar forms are probably \"covered\" at the cell surface by the antigenic lipids. Therefore, these antigenic mycosides may play a putative role in virulence of the MAIS members by protecting these mycobacteria from their own potential pathogen. The results of chemical transformations at specific sites of the mycoside core coupled with studies of simple synthetic lipid glycosides indicated that the principal phage receptor activity resides in the terminal methylated rhamnose (see diagram). It is this sugar which is evidently masked by the (seemingly remote) haptenic oligosaccharides.",
"full_author_list": "K R Dhariwal, A Liav, A E Vatter, G Dhariwal, M B Goren",
"short_author_list": "Dhariwal KR et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3759906",
"journal": "Journal of bacteriology",
"journal_volume": "168",
"journal_issue": "1",
"journal_pages": "283-93",
"pub_year": "1986",
"pubmed_id": "3759906"
},
{
"title": "Preliminary studies on bacteriophage typing of Mycobacterium tuberculosis strains isolated in Salamanca (Spain).",
"abstract": "A phage typing of 202 strains of Mycobacterium tuberculosis isolated in Central and Northwest Spain was carried out. The commonest phage type was A (64%) and within this type A (45%). This was followed in frequency by phage type B (26%) and in last place type I (10%). No relationship was observed between the phage type and the geographical or anatomical origin of the strains.",
"full_author_list": "J A Garcia-Rodriguez, A C Gomez-Garcia, J Aguero",
"short_author_list": "Garcia-Rodriguez JA, Gomez-Garcia AC, Aguero J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3098576",
"journal": "European journal of epidemiology",
"journal_volume": "2",
"journal_issue": "3",
"journal_pages": "178-81",
"pub_year": "1986",
"pubmed_id": "3098576"
},
{
"title": "Effect of heat treatment on phage susceptibility of a Mycobacterium smegmatis strain.",
"abstract": "Plating efficiency of mycobacteriophage butyricum (By) proved to be 10(-4)-10(-3) on Mycobacterium smegmatis strain Rabinowitz (M. sm. R.) cells being in the logarithmic phase. This increased to 10(-2)-10(-1) when the cells were held at 50-57 degrees C for 2 h before infection. After replacing the cells to 37 degrees C, plating efficiency of the phages returned to the starting values. This phenomenon could be inhibited by nalidixic acid (150 micrograms/ml) and chloramphenicol (10 micrograms/ml) but not by mitomycin C (0.05 microgram/ml). No return to the starting plating efficiency values were observed, if incubation of cells at 37 degrees C after heat treatment has been performed in buffer. The data suggest that By phage propagation in M. sm. R. cells is inhibited by a thermosensitive protein.",
"full_author_list": "K J Háber, I Földes",
"short_author_list": "Háber KJ, Földes I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3105227",
"journal": "Acta microbiologica Hungarica",
"journal_volume": "33",
"journal_issue": "3",
"journal_pages": "257-62",
"pub_year": "1986",
"pubmed_id": "3105227"
},
{
"title": "[Classification of Mycobacterium tuberculosis by phage typing markers in the City of Havana province]",
"abstract": "",
"full_author_list": "C A Jiménez Misas, J A Valdivia Alvarez, D Mazón Zamora",
"short_author_list": "Jiménez Misas CA, Valdivia Alvarez JA, Mazón Zamora D",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3105006",
"journal": "Revista cubana de medicina tropical",
"journal_volume": "38",
"journal_issue": "2",
"journal_pages": "141-5",
"pub_year": "1986",
"pubmed_id": "3105006"
},
{
"title": "Presence of random single-strand gaps in mycobacteriophage I3 DNA.",
"abstract": "The genomic double-stranded DNA of mycobacteriophage I3, when denatured with alkali, heat, formamide or dimethylsulfoxide, breaks down to heterogeneous-sized single-strand (ss) fragments smaller than the expected intact unit genome length suggesting the presence of random ss interruptions on both the strands. The occurrence of the interruptions at random is also demonstrated by two-dimensional gel electrophoresis of the restriction fragments of I3 DNA. These interruptions have no adverse effect on the phage infectivity or DNA transfectivity. Studies with nuclease BAL 31 and end-labeling analysis confirm the presence of random interruptions. Detailed analysis using T4 DNA ligase, nuclease S1 and DNA polymerase I Klenow fragment revealed that the interruptions are in the form of small gaps rather than single phosphodiester bond breaks. The average length of the gap is about 10 nucleotides long and there are 13 to 14 such gaps per DNA molecule.",
"full_author_list": "A B Reddy, K P Gopinathan",
"short_author_list": "Reddy AB, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3781246",
"journal": "Gene",
"journal_volume": "44",
"journal_issue": "2-3",
"journal_pages": "227-34",
"pub_year": "1986",
"pubmed_id": "3781246"
},
{
"title": "Presence of mycobacteriophage I3-like DNA sequences in the genome of its host Mycobacterium smegmatis.",
"abstract": "The genomes of phage I3 and its host Mycobacterium smegmatis have been compared. From thermal melting studies the GC contents of DNA from mycobacteriophage I3 and its host M. smegmatis were found to be 66%. A new method, based only on the initial rates of reassociation, has been developed for calculating the DNA homology. Analysis of DNA reassociation kinetics suggested the presence of one equivalent of the phage I3 genome within the M. smegmatis genome. Southern analysis revealed the presence of almost all of the phage I3 specific sequences within the host genome.",
"full_author_list": "C Sadhu, S Dutta, K P Gopinathan",
"short_author_list": "Sadhu C, Dutta S, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3800555",
"journal": "Archives of microbiology",
"journal_volume": "146",
"journal_issue": "2",
"journal_pages": "166-9",
"pub_year": "1986",
"pubmed_id": "3800555"
},
{
"title": "[The transmission of mycobacteria through the fiberoptic bronchoscope]",
"abstract": "Transmission of Mycobacterium tuberculosis by the flexible fiberoptic bronchoscope was suspected in two patients with positive cultures from bronchial washings but with negative cultures from sputum specimens and no clinical or radiological evidence of active tuberculosis, In both cases, a patient with sputum smear-positive pulmonary tuberculosis had been examined with the same bronchoscope the day before. In one case, mycobacteriophage typing of the cultures of the consecutively examined patients revealed the same phage type in both patients, suggesting transmission by the fiber bronchoscope. In the other case, however, transmission was ruled out by different phage types. Among the few previously reported cases of transmission of Mycobacterium tuberculosis by the flexible fiberoptic bronchoscope, one case of tuberculin conversion occurred. Without antituberculous therapy our patient had negative sputum cultures and no evidence of tuberculosis one year after bronchoscopy. Transmission of other microorganisms and possible causes of transmission by the fiberoptic bronchoscope are reviewed and discussed.",
"full_author_list": "R Bezel, M Salfinger, O Brändli",
"short_author_list": "Bezel R, Salfinger M, Brändli O",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3934749",
"journal": "Schweizerische medizinische Wochenschrift",
"journal_volume": "115",
"journal_issue": "39",
"journal_pages": "1360-5",
"pub_year": "1985",
"pubmed_id": "3934749"
},
{
"title": "Phage typing of the Mycobacterium avium-intracellulare-scrofulaceum complex. A study of strains of diverse geographic and host origin.",
"abstract": "A total of 339 strains of the Mycobacterium avium-intracellulare-scrofulaceum complex were phage typed using our previously described technique and 11 typing phages. These included 235 strains of human origin obtained from state health laboratories in Virginia, Georgia, Florida, and Arkansas, 26 strains isolated from persons with AIDS, 38 strains isolated from animals, and 40 environmental isolates. A phage-typing scheme was developed that denotes sensitivity to 8 primary typing phages: the JF group (JF1, JF2, JF3, and JF4), phage D302, and the AN group (AN3, AN9, and AN1-8). The 3 auxiliary phages (VC3, VA6, and D32) define subgroups of the strains sensitive to the AN phages. A total of 99 strains were sensitive to at least 1 phage. Of 31 serotype 1 or 2 strains from animals, 13 were sensitive to AN phages but resistant to JF phages. In contrast, 7/33 serotype 4 or 8 strains from animals or from persons with AIDS were sensitive to JF phages but not to the AN phages. Of the clinical isolates not associated with AIDS, 78/235 were phage sensitive. These strains could be divided roughly into 4 groups: sensitive to AN phages, sensitive to JF phages, sensitive to phage D302, and sensitive to multiple phages. Only 1 of the environmental isolates was phage sensitive. The results indicate that phage typing can subdivide this heterogeneous group of organisms and is a useful tool for epidemiological studies.",
"full_author_list": "J T Crawford, J H Bates",
"short_author_list": "Crawford JT, Bates JH",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4026062",
"journal": "The American review of respiratory disease",
"journal_volume": "132",
"journal_issue": "2",
"journal_pages": "386-9",
"pub_year": "1985",
"pubmed_id": "4026062"
},
{
"title": "[Physicochemical properties of temperate phage DNA and its possible effect on the variability of Mycobacterium lacticolum]",
"abstract": "The temperate phage 104 S was isolated from the S variant of Mycobacterium lacticolum, strain 104, and some of its characteristics were studied. The content of GC pairs in the phage DNA was 77 mole% as was calculated from the melting profile or 65 mole% as was calculated from the value of buoyant density in CsCl. The DNA was shown to be composed of 18,000 nucleotide pairs. DNA restriction fragments of M. lacticolum R, S and M variants were subjected for the first time to molecular hybridization with [32P]DNA of the temperate phage. The genome of the three M. lacticolum variants and the genome of a non-dissociating S variant clone were shown to contain sequences homologous to the DNA sequence of phage 104 S. Differences are found among the variants in the hybridizing DNA fragments. These data indicate that the phage DNA may actively be involved in the variability of the culture. Its participation can be realized by the different mode of prophage incorporation into the genome of the variants.",
"full_author_list": "N A Obukhova, A A Kolesnikov, D A Maslov, L A Rezenkina, E S Mal'ko",
"short_author_list": "Obukhova NA et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4058328",
"journal": "Mikrobiologiia",
"journal_volume": "54",
"journal_issue": "4",
"journal_pages": "641-6",
"pub_year": "1985",
"pubmed_id": "4058328"
},
{
"title": "Effects of nonionic detergents on mycobacteriophage Bo 20 and some characterization of the phage adsorption to Mycobacterium diernhoferi.",
"abstract": "",
"full_author_list": "H Saito, T Watanabe",
"short_author_list": "Saito H, Watanabe T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4066396",
"journal": "Hiroshima journal of medical sciences",
"journal_volume": "34",
"journal_issue": "3",
"journal_pages": "297-302",
"pub_year": "1985",
"pubmed_id": "4066396"
},
{
"title": "The \"atypical\" mycobacteria: recognition and disease association.",
"abstract": "Although techniques based on immunologic or chromatographic analyses have been described for identifying mycobacteria in clinical laboratories, most microbiologists continue to rely on a series of specialized physiological and biochemical tests for this purpose. The recognition of additional significant species over the past decade has required the addition of more tests to the battery used for mycobacterial identification. This paper will review briefly the taxonomic status of species likely to be encountered in clinical specimens and the most useful tests for characterizing them. Strategies will be presented for using these tests in the most efficient way to provide optimal resolution of taxa without use of an unreasonably large battery of tests. A brief survey of techniques that may become more practical in the future will also be included.",
"full_author_list": "L G Wayne",
"short_author_list": "Wayne LG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/3905261",
"journal": "Critical reviews in microbiology",
"journal_volume": "12",
"journal_issue": "3",
"journal_pages": "185-222",
"pub_year": "1985",
"pubmed_id": "3905261"
},
{
"title": "Abortive infection of Mycobacterium leprae by the mycobacteriophage D29.",
"abstract": "The interactions of mycobacteriophage D29 and Mycobacterium leprae were examined. It was demonstrated that after adsorption D29 injected its DNA in M. leprae. While the synthesis of host proteins and lipids were inhibited in M. tuberculosis and in M. smegmatis during infection by D29, the results were inconclusive in the case of M. leprae because these bacteria did not incorporate the appropriate substrates.",
"full_author_list": "H L David, F Clément, S Clavel-Sérès, N Rastogi",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6399068",
"journal": "International journal of leprosy and other mycobacterial diseases : official organ of the Internatio",
"journal_volume": "52",
"journal_issue": "4",
"journal_pages": "515-23",
"pub_year": "1984",
"pubmed_id": "6399068"
},
{
"title": "Further observations on the mycobacteriophage D29-mycobacterial interactions.",
"abstract": "",
"full_author_list": "H L David, S Sérès-Clavel, F Clément, N Rastogi",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6442822",
"journal": "Acta leprologica",
"journal_volume": "2",
"journal_issue": "2-4",
"journal_pages": "359-67",
"pub_year": "1984",
"pubmed_id": "6442822"
},
{
"title": "Phage-typing and drug-resistance patterns as tools in mycobacterial epidemiology.",
"abstract": "Phage-typing by itself was not sufficient to delineate the boundaries of a mini-epidemic of tuberculosis in upstate New York. Drug-resistance patterns were needed as well. In a small upstate community, 79% of 14 isolates tested were resistant to one or more of the antituberculosis drugs. Of 15 isolates with phage types determined, 47% were type 1(13), 27% were type 7(7, 13), and 27% were type 1(7, 12, 13). By combining phage-typing and sensitivity testing, we were able to demonstrate that 4 or possibly 5 of the 7 phage-type 1(13) strains are epidemiologically related.",
"full_author_list": "H Gruft, R Johnson, R Claflin, A Loder",
"short_author_list": "Gruft H et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6430139",
"journal": "The American review of respiratory disease",
"journal_volume": "130",
"journal_issue": "1",
"journal_pages": "96-7",
"pub_year": "1984",
"pubmed_id": "6430139"
},
{
"title": "Some characteristics of lysogens of Mycobacterium smegmatis.",
"abstract": "By the use of radioactive labelling it was observed that mycobacteriophage butyricum (By) enter Mycobacterium smegmatis strain Rabinowitz (M. sm. R.) cells, lysogenise them but do not form plaques. Mycobacteriophage Rabinowitz (V72) and phage By proved to be heteroimmune; that is, they superinfect lysogens of one another productively. Spontaneous lysis frequencies of two different mycobacterium strains lysogenised by phage By [M. sm. R. (By); M. sm. b. (By)] and that of the double lysogenic M. sm. R. (V72, By) strain were compared. The spontaneous lysis frequency of the two monolysogenic strains was found to be similar (10(-4)-10(-2) indicating that transition into the vegetative replication cycle of By phages occurs also in M. sm. R. cells. Spontaneous lysis frequency of the double lysogenic strain was found to be influenced by the medium used.",
"full_author_list": "K J Háber, I Földes",
"short_author_list": "Háber KJ, Földes I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6464659",
"journal": "Acta microbiologica Hungarica",
"journal_volume": "31",
"journal_issue": "2",
"journal_pages": "135-40",
"pub_year": "1984",
"pubmed_id": "6464659"
},
{
"title": "[Mycobacteriophages. III. (Review article)]",
"abstract": "",
"full_author_list": "C A Jiménez Misas",
"short_author_list": "Jiménez Misas CA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6438734",
"journal": "Revista cubana de medicina tropical",
"journal_volume": "36",
"journal_issue": "1",
"journal_pages": "77-87",
"pub_year": "1984",
"pubmed_id": "6438734"
},
{
"title": "[Phage typing of new mycobacterial species of animal origin]",
"abstract": "",
"full_author_list": "C A Jiménez Misas, J A Valdivia Alvarez, M E Marrero Oteiza",
"short_author_list": "Jiménez Misas CA, Valdivia Alvarez JA, Marrero Oteiza ME",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6399594",
"journal": "Revista cubana de medicina tropical",
"journal_volume": "36",
"journal_issue": "2",
"journal_pages": "146-50",
"pub_year": "1984",
"pubmed_id": "6399594"
},
{
"title": "Length determination in bacteriophage lambda tails",
"abstract": "We have isolated viable mutants of bacteriophage lambda that have in-frame deletions in gene H, which codes for a minor tail protein. They produce correspondingly smaller but active gene H protein products and assemble shorter-tailed phage particles. The deficiency in tail length for each mutant corresponds to the calculated shortening of the gene H protein caused by the deletion. These results show that the H protein determines tail length and argue strongly for a scheme in which the H protein is a ruler or template that measures length during tail assembly.",
"full_author_list": "Katsura I, Hendrix RW.",
"short_author_list": "Katsura I, Hendrix RW.",
"article_url": "",
"journal": "Cell",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "1984",
"pubmed_id": "6096021"
},
{
"title": "Use of S1 nuclease and formamide in combination for the reassociation studies on GC-rich DNA.",
"abstract": "The optimal parameters in the use of nuclease S1 in DNA reassociation kinetics in the presence of formamide have been determined. The conditions are especially suitable for the study of DNA rich in mole percent GC. A 10-fold dilution of the reassociation samples leading to a decrease in both NaCl and formamide concentrations, consequently resulting in a lowering of Tm by only 1.5 degree C, and the S1 digestion at temperatures identical to the reassociation assay in order to retain the stability of the duplex, are two important aspects of this system. Under these conditions, the kinetics of reassociation followed the theoretically predicted pattern, while the earlier reported methods have shown lower values.",
"full_author_list": "C Sadhu, S Datta, K P Gopinathan",
"short_author_list": "Sadhu C, Datta S, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6097143",
"journal": "Analytical biochemistry",
"journal_volume": "142",
"journal_issue": "1",
"journal_pages": "53-7",
"pub_year": "1984",
"pubmed_id": "6097143"
},
{
"title": "The usefulness of phage typing Mycobacterium tuberculosis isolates.",
"abstract": "Mycobacteriophage typing of Mycobacterium tuberculosis isolates was used as an epidemiologic aid in investigating the transmission of tuberculosis in community, industrial, and institutional outbreaks. The technique was also useful in other situations, e.g., documenting congenital transmission of infection and distinguishing exogenous reinfection from endogenous reactivation. Additional studies are indicated to further explore the value of phage typing for tracking the transmission of tuberculosis in the community.",
"full_author_list": "D E Snider, W D Jones, R C Good",
"short_author_list": "Snider DE, Jones WD, Good RC",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6439088",
"journal": "The American review of respiratory disease",
"journal_volume": "130",
"journal_issue": "6",
"journal_pages": "1095-9",
"pub_year": "1984",
"pubmed_id": "6439088"
},
{
"title": "Isolation of mycobacterial phage from the laboratory strain Mycobacterium leprae murium \"Douglas\".",
"abstract": "The colony microstructure of the laboratory strain Mycobacterium leprae murium \"Douglas\" cultivated on Ogawa's egg medium was examined. A bioptical sample from the liver of a white mouse subcutaneously infected and observed for ten months was used as inoculum. The inoculum contained 5.2 X 10(9) acidfast rods. The Ogawa's media were incubated in 5% atmosphere of CO2 at 33 degrees C to 37 degrees C for 6 to 10 months. The outgrown colonies were killed with a formol solution, then embedded into the agarparaffin and cut out with the aid of Reichert's microtom. In thin sections there was an apparent vacuolisation of colonies proving the presence of the temperate phage, which was isolated from the bacterial suspension inoculated on the host non lysogenic strain Mycobacterium smegmatis ATCC 607. On the simple agar medium N-4 the number of 2.4 X 10(9) living particles was achieved, which shows the possible use of this phage for differential diagnostic purposes in the taxonomy studies of mycobacteria.",
"full_author_list": "L Sula, J Sulová, M Mat?jka, J Málková",
"short_author_list": "Sula L et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6389044",
"journal": "Czechoslovak medicine",
"journal_volume": "7",
"journal_issue": "3",
"journal_pages": "174-80",
"pub_year": "1984",
"pubmed_id": "6389044"
},
{
"title": "Lytic potency against various mycobacterial strains of the phage isolated from Mycobacterium leprae murium \"Douglas\".",
"abstract": "The lytic potency of a newly isolated phage Al-1 obtained from the laboratory strain M. leprae murium \"Douglas\" was examined. The phage was multiplied on the laboratory strain M. smegmatis ATCC 607 and for the lytic test 0.1 ml of suspension containing PFU 10(5) was used. In the whole 18 mycobacterial strains both slowly and fast growing multiplied in liquid Sula's medium were tested. For phage lytic tests two simple agar media and standard Redmond's medium RVA-24 were used. The examined slowly growing mycobacteria (H37Rv. M. bovis \"Ravenel\", M. avium \"Kirchberg\", M. kansasii \"Svizenský\", M. tbc INH resist., M. tbc INH, STM, PAS resist.) were resistant to the tested phage similarly as M. phlei from the group of fast growing strains. The results of phage tests on all three used media were characterized by a confluent phage lysis with the exception of the strain M. butyricum \"Rabinovic\", in which even on a very rich media an incomplete lysis with countable plaques was found out. The use of the phage Al-1 for the phage typification also of the strain M. leprae murium is considered on the basis of the inhibition growth tests on Ogawa's egg media.",
"full_author_list": "L Sula, J Sulová",
"short_author_list": "Sula L, Sulová J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6389043",
"journal": "Czechoslovak medicine",
"journal_volume": "7",
"journal_issue": "3",
"journal_pages": "167-73",
"pub_year": "1984",
"pubmed_id": "6389043"
},
{
"title": "Induction of bacteriophage from members of the Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium scrofulaceum serocomplex.",
"abstract": "Bacteriophages have been induced from strains in the Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium scrofulaceum serocomplex by exposure of cultures to UV light or treatment with mitomycin C. One-sixth of the strains examined, representing all but one of the 31 authenticated serotypes, were found to possess phages lytic for a Mycobacterium smegmatis indicator strain. Four single-plaque isolated phages, TM4, TM9, TM10 and TM20, were purified and shown to have a similar morphology on electron micrographs. They had an isometric head of diameter 50-58 nm and a flexible non-contractile tail about 170 nm in length with a terminal bulb. All had an identical buoyant density in CsCl of 1.521 g cm-3 and extreme sensitivity to chloroform. The induced phages differed in host range and possessed the unique ability to lyse other members of the serocomplex. Interest in these phages centres on a possible role in mediating genetic interrelationships between members of the serocomplex.",
"full_author_list": "T L Timme, P J Brennan",
"short_author_list": "Timme TL, Brennan PJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6470677",
"journal": "Journal of general microbiology",
"journal_volume": "130",
"journal_issue": "8",
"journal_pages": "2059-66",
"pub_year": "1984",
"pubmed_id": "6470677"
},
{
"title": "Taxonomy of mycobacterial strains isolated from the tissues of leprosy patients.",
"abstract": "Thirty-six slowly growing mycobacteria isolated from the tissues of leprosy patients were studied using 40 characteristics as well as susceptibility to 27 distinct mycobacteriophages. The composition in mycolic acids of selected strains was also studied. According to the data, the strains formed 5 clusters. Some of the clusters were possibly as yet undescribed species; however, comparison of the data with the known properties of Mycobacterium leprae leads to the conclusion that none of the strains were identical to the leprosy bacillus.",
"full_author_list": "H L David, C Asselineau, M Daffé, M A Lanéelle, F Clément, V Lévy-Frébault",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6372573",
"journal": "Annales de microbiologie",
"journal_volume": "134B",
"journal_issue": "3",
"journal_pages": "367-77",
"pub_year": "1983",
"pubmed_id": "6372573"
},
{
"title": "The bacteriology of Mycobacterium leprae.",
"abstract": "",
"full_author_list": "P Draper",
"short_author_list": "Draper P",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6405519",
"journal": "Tubercle",
"journal_volume": "64",
"journal_issue": "1",
"journal_pages": "43-56",
"pub_year": "1983",
"pubmed_id": "6405519"
},
{
"title": "[Incidence of phagotypes of Mycobacterium tuberculosis in Czechoslovakia and East Germany and of Mycobacterium bovis in Czechoslovakia and Argentina]",
"abstract": "The following study gives review of the results of the phagetyping of M. tuberculosis strains in different localities of Czechoslovakia and German Democratic Republic (165 strains from Czechoslovakia and 102 strains from GDR) and the comparison of the occurrence of phage subgroups of M. bovis strains in two different localities of Czechoslovakia (62 strains) and Argentina (93 strains). The results of the phagetyping of the Czechoslovak M. tuberculosis strains show that this group comprises all the 6 phage subgroups and agree very well in subgroups Ax, A2, B and C with the M. tuberculosis strains from GDR. Both groups of strains differ in subgroups A2 (9) and D. The results with the fresh isolated Argentinian M. bovis strains show that this group has only subgroups Ax and D in comparison with the old laboratory strains of M. bovis which have subgroups Ax, A2(9), and D. The phagetyping of the M. tuberculosis and M. bovis strains was undertaken with the help of 11 international mycobacterial phages. The use of mycobacterial phages in 1 RTD (Routine Test Dilution) and 10 RTD concentrations (in contrary to the 1 RTD and concentrated phage suspensions used previously) decreased the number of the \"unspecific\" reactions.",
"full_author_list": "J Dubina, L Sula, W Käppler, K H Schubert",
"short_author_list": "Dubina J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6410595",
"journal": "Zeitschrift für Erkrankungen der Atmungsorgane",
"journal_volume": "160",
"journal_issue": "3",
"journal_pages": "247-52",
"pub_year": "1983",
"pubmed_id": "6410595"
},
{
"title": "Bacteriophage typing of strains of Mycobacterium tuberculosis from Nepal.",
"abstract": "One hundred strains of Mycobacterium tuberculosis isolated from cases of pulmonary tuberculosis in Nepalese villagers were typed with the World Health Organization set of bacteriophages. The number of strains in the 3 major phage types A, I, and B were 19, 53, and 28 respectively. This distribution is significantly different from those described in other geographical regions. In particular there was a relatively low incidence of type A strains and, in common with South India, there was a high proportion of type I strains. All the strains in this study were resistant to 5-Furan-2 carbonic acid hydrazine and 34 were highly resistant to isoniazid. Representative strains of the 3 phage types, including 4 isoniazid-resistant type I strains, did not differ in their virulence in the guinea pig; thus the type I strains found in Nepal may not be of the same origin as those of this phage type from India which are usually attenuated in the guinea pig. This study provides further evidence for the existence of geographical differences in the types of tubercle bacilli.",
"full_author_list": "D Goode",
"short_author_list": "Goode D",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6405518",
"journal": "Tubercle",
"journal_volume": "64",
"journal_issue": "1",
"journal_pages": "15-21",
"pub_year": "1983",
"pubmed_id": "6405518"
},
{
"title": "[Mycobacteriophages. II. (Review article)]",
"abstract": "",
"full_author_list": "C A Jiménez Misas",
"short_author_list": "Jiménez Misas CA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6764273",
"journal": "Revista cubana de medicina tropical",
"journal_volume": "34",
"journal_issue": "3",
"journal_pages": "289-97",
"pub_year": "1983",
"pubmed_id": "6764273"
},
{
"title": "Phage-type patterns of Mycobacterium tuberculosis from Southeast Asian immigrants.",
"abstract": "Cultures of Mycobacterium tuberculosis isolated from 86 Southeast Asian immigrants were phage typed as type 1 (10.5%), type 2 (57.0%), type 5 (23.2%), and type 8 (9.3%). Strains belonging to types 3, 4, 6, and 7 were not found among the 86 strains tested. The lytic patterns of 6 auxiliary phages further divided the strains into 5 to 14 additional subgroups. The phage-type distribution in the Asian cultures was different from the type distribution in cultures from residents in the United States.",
"full_author_list": "W D Jones, C L Woodley",
"short_author_list": "Jones WD, Woodley CL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6402965",
"journal": "The American review of respiratory disease",
"journal_volume": "127",
"journal_issue": "3",
"journal_pages": "348-9",
"pub_year": "1983",
"pubmed_id": "6402965"
},
{
"title": "Transfection of Mycobacterium smegmatis SN2 with mycobacteriophage I3 DNA.",
"abstract": "Mycobacterium smegmatis SN2 does not exhibit natural competence for the uptake of phage I3 DNA. Competence can artificially be induced by treatment with glycine or CaCl2, and the combination of both is even more effective. The efficiency of transfection can be improved by inclusion of protamine sulphate and heterologous RNA in the system. From 32P DNA uptake studies the major barrier for the entry of DNA has been found to be the complex cell wall. The efficiency of transfection calculated on the basis of fraction of DNA which has entered the cell is comparable to that of other bacterial systems. The phage development takes a longer time (7 h for one cycle) after transfection, as compared to infection (4 h).",
"full_author_list": "S S Karnik, K P Gopinathan",
"short_author_list": "Karnik SS, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6667087",
"journal": "Archives of microbiology",
"journal_volume": "136",
"journal_issue": "4",
"journal_pages": "275-80",
"pub_year": "1983",
"pubmed_id": "6667087"
},
{
"title": "[Comparative study of the chemical composition and properties of the capsule polysaccharides in M-, S- and R-variants of Mycobacterium lacticolum]",
"abstract": "Polysaccharides from the capsules of Mycobacterium lacticolum M, S and R variants were comparatively studied for the first time. The polysaccharides from M and S cells contained galactose, glucose and mannose; however, the polysaccharides must be different since they vary in specific rotation. The capsule polysaccharide from R cells contained also arabinose. Its specific rotation differed considerably from those of M and S cells. The polysaccharides are involved in phage adsorption on mycobacterial cells, and the three variants show differences in this respect. The free exopolysaccharides of M, S and R variants are identical with the corresponding capsule exoglycans, and their proportions differ among the variants.",
"full_author_list": "E S Mil'ko, I V Botvinko, R A Stepanova, N S Egorov",
"short_author_list": "Mil'ko ES et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6621420",
"journal": "Mikrobiologiia",
"journal_volume": "52",
"journal_issue": "3",
"journal_pages": "388-91",
"pub_year": "1983",
"pubmed_id": "6621420"
},
{
"title": "Incorporation of thymine, thymidine, adenine and uracil into nucleic acids of Mycobacterium phlei and its phage.",
"abstract": "Like other prototroph bacteria, Mycobacterium phlei was found to incorporate thymine into its DNA very poorly. As a result of a rapid thymidine-to-thymine conversion, thymidine incorporation also proved to be inefficient. Thymidine incorporation could be somewhat enhanced by pretreatment of the cells with uridine. When radioactive adenine, and particularly uracil, were used as precursors, highly labelled DNA could be obtained from the cells, although the majority of radioactivity was found in the RNA. Uracil was thus found to be the most suitable precursor for labelling phage DNA. On the basis of these findings, uracil is recommended for in vivo labelling of Mycobacterium and mycobacteriophage DNA.",
"full_author_list": "P A Somogyi, I Földes",
"short_author_list": "Somogyi PA, Földes I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6847034",
"journal": "Annales de microbiologie",
"journal_volume": "134A",
"journal_issue": "1",
"journal_pages": "19-28",
"pub_year": "1983",
"pubmed_id": "6847034"
},
{
"title": "Adsorption of mycobacteriophages on Mycobacterium leprae: taxonomic significance.",
"abstract": "The following bacteriophages were shown to adsorb on Mycobacterium leprae: BK1, Clark, Sedge, Baits, Watson and D29. Bacteriophages that did not adsorb on the leprosy bacilli were Bg1, Legendre, Marshall, Panetti, Leo and Wiseman. The taxonomic significance of these findings and some prospective consequences of these investigations are discussed.",
"full_author_list": "H L David, S Clavel, F Clément",
"short_author_list": "David HL, Clavel S, Clément F",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7051934",
"journal": "Annales de microbiologie",
"journal_volume": "133",
"journal_issue": "1",
"journal_pages": "93-7",
"pub_year": "1982",
"pubmed_id": "7051934"
},
{
"title": "Presence of lipids in mycobacteriophage i3.",
"abstract": "The presence of lipids has been demonstrated in mycobacteriophage I3. The total lipid was composed of 69% phospholipids and 31% neutral lipids. More than two-thirds of phospholipids present in the phage were synthesized in the host prior to infection. The fatty acid composition of the phage differed markedly from that of its host, both in chain length and the degree of saturation. The phage lipid was mostly composed of saturated fatty acids of which more than 50% were short chain fatty acids. Changes in growth temperatures reflected variations in fatty acid composition, characteristic of the phage, and which were distinctly different from those of the host. Electron microscopic observations revealed that the phage has a membranous bilayer structure. The presence of lipids may facilitate the phage-host interaction especially in lipid-rich organisms like mycobacteria.",
"full_author_list": "M L Gope, K P Gopinathan",
"short_author_list": "Gope ML, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7069400",
"journal": "The Journal of general virology",
"journal_volume": "59",
"journal_issue": "Pt 1",
"journal_pages": "131-8",
"pub_year": "1982",
"pubmed_id": "7069400"
},
{
"title": "[Biology of the tubercle bacillus]",
"abstract": "",
"full_author_list": "J Grosset, C Truffot-Pernot",
"short_author_list": "Grosset J, Truffot-Pernot C",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6808636",
"journal": "Revue médicale de la Suisse romande",
"journal_volume": "102",
"journal_issue": "3",
"journal_pages": "257-63",
"pub_year": "1982",
"pubmed_id": "6808636"
},
{
"title": "[Mycobacteriophages. I. (Review article)]",
"abstract": "",
"full_author_list": "C A Jiménez Misas",
"short_author_list": "Jiménez Misas CA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6750714",
"journal": "Revista cubana de medicina tropical",
"journal_volume": "34",
"journal_issue": "1",
"journal_pages": "45-53",
"pub_year": "1982",
"pubmed_id": "6750714"
},
{
"title": "Bacteriophage types of Mycobacterium tuberculosis in the United States.",
"abstract": "Strains of Mycobacterium tuberculosis from various geographic areas within the continental United States were typed according to their susceptibility to 4 mycobacteriophages. Of 462 wild isolates studied, 34% were phage type 1 (previously designated A0), 42% were type 2 (A1), 2.6% were type 5 (A4), 13% were type 7 (A6), and 20.1% were type 8 (B). Distribution of types was essentially unaffected by geographic location, sex, age, or ethnic origin of the patient or by resistance of the isolate to antituberculosis drugs. Major types were further divided by susceptibility of the strains to lysis by 8 auxiliary phages, 2 of which were phages newly evaluated in this study. A new numbering system is proposed for designating major phage types of M. tuberculosis.",
"full_author_list": "W D Jones, R C Good, N J Thompson, G D Kelly",
"short_author_list": "Jones WD et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6807151",
"journal": "The American review of respiratory disease",
"journal_volume": "125",
"journal_issue": "6",
"journal_pages": "640-3",
"pub_year": "1982",
"pubmed_id": "6807151"
},
{
"title": "Phage typing of Mycobacterium tuberculosis: a time for standardization.",
"abstract": "",
"full_author_list": "G P Kubica",
"short_author_list": "Kubica GP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6807157",
"journal": "The American review of respiratory disease",
"journal_volume": "126",
"journal_issue": "1",
"journal_pages": "3-4",
"pub_year": "1982",
"pubmed_id": "6807157"
},
{
"title": "[Comparison of the lysogenic properties of the R-, S- and M-variants of Mycobacterium lacticolum]",
"abstract": "",
"full_author_list": "N A Obukhova, N S Egorov, E S Mil'ko, S V Toldaev",
"short_author_list": "Obukhova NA et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6805519",
"journal": "Nauchnye doklady vysshe? shkoly. Biologicheskie nauki",
"journal_volume": "",
"journal_issue": "4",
"journal_pages": "81-5",
"pub_year": "1982",
"pubmed_id": "6805519"
},
{
"title": "Morphology of bacteriophages from Mycobacterium lepraemurium.",
"abstract": "The two phages obtained from mycobacterium lepraemurium strain \"Douglas\" by using M. segmatis ATCC 607 as a non-lysogenic indicator (kindly supplied by L. Sula and named as AL1 and 1/1) were adsorbed on M. Smegmatis ATCC 607 with a P 45'/P0 of 0.046 and 0.01, respectively. Ultrastructural studies showed that these phages could be classified as Bradley type B1.",
"full_author_list": "N Rastogi, H L David",
"short_author_list": "Rastogi N, David HL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6756256",
"journal": "Annales de microbiologie",
"journal_volume": "133",
"journal_issue": "2",
"journal_pages": "303-9",
"pub_year": "1982",
"pubmed_id": "6756256"
},
{
"title": "Methylated nucleic acid bases in Mycobacterium and mycobacteriophage DNA.",
"abstract": "Methylated bases of the DNA of two mycobacteria (Mycobacterium phlei and Mycobacterium smegmatis var. butyricum) and two mycobacteriophages (Phage phlei and Phage butyricum) have been studied. In both the bacterial and the phage DNAs 5-methyl-cytosine and 6-methyl-aminopurine could be detected. Using L-(methyl-H3)-methionine as methyl donor not only the methylated bases of bacterium and phage DNA proved to be radioactive, but also the non-methylated purine residues and thymine. Possible pathways of this phenomenon are discussed.",
"full_author_list": "P A Somogyi, M Maso Bel, I Földes",
"short_author_list": "Somogyi PA, Maso Bel M, Földes I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7168369",
"journal": "Acta microbiologica Academiae Scientiarum Hungaricae",
"journal_volume": "29",
"journal_issue": "3",
"journal_pages": "181-5",
"pub_year": "1982",
"pubmed_id": "7168369"
},
{
"title": "Stimulating effects of a weak constant magnetic field (0.8 Gauss) on the growth of two mycobacterial phages no 308 and 33d.",
"abstract": "A liquid culture of ATCC 607 infected with two mycobacterial phages and exposed to constant magnetic fields 0.8 G for 48 hours was replanted on simple agar media without oleic acidalbumin enrichment. In both phages a pronounced stimulating effect was observed demonstrated in the phage No. 308 by almost confluent lysis in magnetized culture and in the phage 33 D by uncountable lytic plaques. Magnetized phage cultures could be preferably used for preparing rich stock suspensions also from poorly growing phages needed for phage classification of mycobacteria.",
"full_author_list": "L Sula, J Sulová, J Janota",
"short_author_list": "Sula L, Sulová J, Janota J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7142685",
"journal": "Journal of hygiene, epidemiology, microbiology, and immunology",
"journal_volume": "26",
"journal_issue": "3",
"journal_pages": "230-4",
"pub_year": "1982",
"pubmed_id": "7142685"
},
{
"title": "Phage typing of the Mycobacterium avium-intracellulare-scrofulaceum complex.",
"abstract": "Because of the need for additional criteria for characterizing strains of the M. avium-intracellulare-scrofulaceum (MAIS) complex the practicality of phage typing was examined. We developed a satisfactory method for plaque assays with these organisms using the soft-agar overlay technique with Dubos oleic acid-albumen agar. Cells were cultured in 7H9 broth enriched with oleic acid-albumen complex and glycerol. A number of available phages and 2 phages recently isolated from soil were tested for their ability to infect various MAIS strains. Phages AN9, AN3, AN1-8, D302, VA6, VC3, D32, JF1, JF2, JF3, and JF4 were selected for preliminary typing. All of the phages were propagated on M. smegmatis. Sixty-one MAIS strains having 29 different serotypes were tested and 33 were sensitive to at least 1 phage. Of 17 M. avium strains (serotypes 1, 2, and 3), 16 were phage-sensitive. Considerable diversity in patterns of phage lysis was observed, and the patterns of lysis did not coincide with serotype. Although we do not yet have a formal phage typing scheme, our results indicated that the MAIS strains are suitable for phage typing.",
"full_author_list": "J T Crawford, J K Fitzhugh, J H Bates",
"short_author_list": "Crawford JT, Fitzhugh JK, Bates JH",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7305110",
"journal": "The American review of respiratory disease",
"journal_volume": "124",
"journal_issue": "5",
"journal_pages": "559-62",
"pub_year": "1981",
"pubmed_id": "7305110"
},
{
"title": "Phage Typing of the Mycobacterium avium-intracellulare-scrofulaceum Complex",
"abstract": "Because of the need for additional criteria for characterizing strains of the M. avium-intracellulare-scrofulaceum (MAIS) complex the practicality of phage typing was examined. We developed a satisfactory method for plaque assays with these organisms using the soft-agar overlay technique with Dubos oleic acid-albumen agar. Cells were cultured in 7H9 broth enriched with oleic acid-albumen complex and glycerol. A number of available phages and 2 phages recently isolated from soil were tested for their ability to infect various MAIS strains. Phages AN9, AN3, AN1-8, D302, VA6, VC3, D32, JF1, JF2, JF3, and JF4 were selected for preliminary typing. All of the phages were propagated on M. smegmatis. Sixty-one MAIS strains having 29 different serotypes were tested and 33 were sensitive to at least 1 phage. Of 17 M. avium strains (serotypes 1, 2, and 3), 16 were phage-sensitive. Considerable diversity in patterns of phage lysis was observed, and the patterns of lysis did not coincide with serotype. Although we do not yet have a formal phage typing scheme, our results indicated that the MAIS strains are suitable for phage typing.",
"full_author_list": "Crawford JT, Fitzhugh JK, Bates JH.",
"short_author_list": "Crawford JT, Fitzhugh JK, Bates JH.",
"article_url": "",
"journal": "Am Rev Respir Dis.",
"journal_volume": "5",
"journal_issue": "124",
"journal_pages": "559-562",
"pub_year": "1981",
"pubmed_id": ""
},
{
"title": "Paracrystalline inclusions in Mycobacterium leprae.",
"abstract": "The occurrence of paracrystalline inclusions of Mycobacterium leprae infected with the mycobacteriophage D29 or treated with mitomycin C was reported before [5, 6]. In pursuing these studies we have now documented by electron micrography a number of paracrystals we thought sufficient to further describe these inclusions, and to show that they appeared to be formed in association with the intracellular membranous structures of the leprosy bacilli.",
"full_author_list": "H L David, S Clavel, F Clément, M Lesourd",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7020523",
"journal": "Annales de microbiologie",
"journal_volume": "132A",
"journal_issue": "1",
"journal_pages": "41-50",
"pub_year": "1981",
"pubmed_id": "7020523"
},
{
"title": "Double lysogeny of Mycobacterium smegmatis.",
"abstract": "While the plating efficiency of mycobacteriophage butyricum (By) on Mycobacterium smegmatis strain Rabinowitz (M.sm.R.) cells is less than 10(-8), it proved to be 5 X 10(-1) on the lysogenic Mycobacterium smegmatis strain Rabinowitz (M.sm.R. [V72]) cells. Bacteriophage By forms plaques on M.sm.R. cells at a very low frequency; it can, however, adsorb to these cells in the same degree as to its original host. The average burst size of Mycobacterium smegmatis strain butyricum (M.sm.b.) cells infected with mycobacteriophage By is 60, and that of M.sm.R. (V72) superinfected with bacteriophage By is only 6. A double lysognic strain was isolated from M.sm.R. (V72) cells surviving By phage infection.",
"full_author_list": "K J Háber, B P Vajda, I Földes",
"short_author_list": "Háber KJ, Vajda BP, Földes I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7315537",
"journal": "Acta microbiologica Academiae Scientiarum Hungaricae",
"journal_volume": "28",
"journal_issue": "4",
"journal_pages": "407-11",
"pub_year": "1981",
"pubmed_id": "7315537"
},
{
"title": "Presence of nucleoside triphosphates and calcium associated with mycobacteriophage 13.",
"abstract": "The association of nucleoside triphosphate molecules and calcium ions with purified particles of mycobacteriophage 13 has been documented. The content of nucleoside triphosphate has been determined to be 118 molecules per phage particle by equilibrium dialysis against labelled ATP or 148 molecules per phage particle by the direct determination of labelled nucleoside triphosphate. The concentration of bound Ca2+ exhibited a high degree of variation between different batches, which may be due to the nonspecific binding of Ca2+ by the virus particles. However, the tightly bound Ca2+ not removable by dialysis against calcium-specific chelating agent, showed a constant value of 2985 atoms/phage particle.",
"full_author_list": "S S Karnik, K P Gopinathan",
"short_author_list": "Karnik SS, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6796030",
"journal": "Archives of microbiology",
"journal_volume": "130",
"journal_issue": "1",
"journal_pages": "50-3",
"pub_year": "1981",
"pubmed_id": "6796030"
},
{
"title": "[Bacteriophage occurrence in \"Mycobacterium phlei\" (author's transl)]",
"abstract": "Surface growth of synchronized bacteria was obtained by means of a suspension of Mycobacterium phlei cells in pentane, the dispersion of which resulted from passage through glass (Ballotini) column. By using standardized conditions, a series of identical cultures were obtained, suitable for studying their evolution as a function of time. By counting colonies every twenty minutes, during ten hours, two doublings were observed, with a generation time of five hours. At the end of a plateau, just before the next doubling, the curve exhibited a marked decrease. Bacteriophages were found in culture medium at the time corresponding to this decrease. In thin sections of the pellicles collected at this time, condensations resembling DNA from phage heads could be noticed within the bacterial cells, as well as free phages in th close neighbourhood of burst cells. The relations between phage and bacteria, and the possible relation between the presence of the phage and the synthesis of phleates has not been determined.",
"full_author_list": "L Lapchine, C Asselineau",
"short_author_list": "Lapchine L, Asselineau C",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7235453",
"journal": "Annales de microbiologie",
"journal_volume": "132",
"journal_issue": "2",
"journal_pages": "129-39",
"pub_year": "1981",
"pubmed_id": "7235453"
},
{
"title": "Infection in rhesus (Macaca mulatta) and squirrel (Saimiri sciureus) monkeys due to Mycobacterium tuberculosis phage type B. Outbreak in a primate colony.",
"abstract": "",
"full_author_list": "C G Mayhall, V A Lamb, P H Coleman",
"short_author_list": "Mayhall CG, Lamb VA, Coleman PH",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6808137",
"journal": "Journal of medical primatology",
"journal_volume": "10",
"journal_issue": "6",
"journal_pages": "302-11",
"pub_year": "1981",
"pubmed_id": "6808137"
},
{
"title": "Macromolecular synthesis in mycobacteriophage I3 infected cells.",
"abstract": "DNA-, RNA- and protein synthesis have been studied in Mycobacterium smegmatis cells infected with phage I3. The macromolecular synthesis continued until the end of latent period. Early RNA and protein synthesis were necessary prior to the commencement of DNA replication. The infecting phage DNA sedimented as larger than unit length of genome, after initiation of DNA synthesis. Although the host DNA was not degraded, 90 percent of the RNA synthesized after phage infection hybridized to phage DNA.",
"full_author_list": "V Nagaraja, K P Gopinathan",
"short_author_list": "Nagaraja V, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6173740",
"journal": "Molecular biology reports",
"journal_volume": "8",
"journal_issue": "1",
"journal_pages": "11-5",
"pub_year": "1981",
"pubmed_id": "6173740"
},
{
"title": "Involvement of DNA gyrase in the replication and transcription of mycobacteriophage I3 DNA.",
"abstract": "",
"full_author_list": "V Nagaraja, K P Gopinathan",
"short_author_list": "Nagaraja V, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6265282",
"journal": "FEBS letters",
"journal_volume": "127",
"journal_issue": "1",
"journal_pages": "57-62",
"pub_year": "1981",
"pubmed_id": "6265282"
},
{
"title": "[The survival of D-29 and MyF2 P/59-mycobacteriophages in continuous cultures]",
"abstract": "The cultivation technique of two mycobacteriophages (D-29 and MyF2 P/59) in continuous cultures with a simple synthetic medium is described. The ATCC-607-strain (M. smegmatis) was used as a host strain. The medium was exchanged every 24 hours for 14 days, then the whole cultivation equipment including waste bottle was hermetically closed and preserved in a thermostat for seven years. Every six months about 250 ml of new liquid medium was added into the cultivation container after finishing the passage cultivation. Both mycobacteriophages could be found out still after 6 years in the mixture of the mycobacteriophages preserved in the waste bottle and in the culture container even after seven years. The possibility of using the technique of continuous cultivation of phages for preparing fresh 24 hours old suspensions necessary for phage typing of the mycobacteria is discussed.",
"full_author_list": "L Sula, J Sulová, J Janota",
"short_author_list": "Sula L, Sulová J, Janota J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7347952",
"journal": "Zeitschrift für Erkrankungen der Atmungsorgane",
"journal_volume": "157",
"journal_issue": "1",
"journal_pages": "3-9",
"pub_year": "1981",
"pubmed_id": "7347952"
},
{
"title": "Therapy of experimental tuberculosis in guinea pigs with mycobacterial phages DS-6A, GR-21 T, My-327.",
"abstract": "Guinea pigs, weighing 250-350 g, were infected with approximately 5,000 of live germs M- tuberculosis H 37 Rv grown 10 days in deep culture of liquid semisynthetic medium according to Sula. The infection was performed subcutaneously in inquinal region. For the therapy following phages were used: DS-6A, GR-21/T, My-327 injected twice a week subcutaneously in the dose of 10(6)/1 ml of live particles for 10 weeks. The therapeutic effect was expressed by spleen and hilus index. Out of the phages used, phage DS-6A had the highest therapeutic effect with mean spleen index of 0.19, corresponding approximately to the spleen index reached with the most effective tuberculostaticum INH. The exact explanation of the phage therapeutic effect in given experimental conditions, when the phages are not applied locally in order to gain the direct contact with infectious antigens, is not known. It is suggested that there presumably exists an interaction between the released phage nucleic acid and the nucleic acid synthesis needed for the growth of mycobacteria in vivo.",
"full_author_list": "L Sula, J Sulová, M Stolcpartová",
"short_author_list": "Sula L, Sulová J, Stolcpartová M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7327068",
"journal": "Czechoslovak medicine",
"journal_volume": "4",
"journal_issue": "4",
"journal_pages": "209-14",
"pub_year": "1981",
"pubmed_id": "7327068"
},
{
"title": "Phage typing of South Indian M. tuberculosis strains by \"surface\" and \"overlay\" method.",
"abstract": "",
"full_author_list": "L Sula, J Sulová, M Stolcpartová",
"short_author_list": "Sula L, Sulová J, Stolcpartová M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6243075",
"journal": "Czechoslovak medicine",
"journal_volume": "4",
"journal_issue": "4",
"journal_pages": "215-23",
"pub_year": "1981",
"pubmed_id": "6243075"
},
{
"title": "[The susceptibility of in vitro-selected drug-resistant strains of M. tuberculosis to lysis by mycobacteriophage PH (MTPH 9), and the study of a lysogenic mutant isolated from the SM-resistant strain (author's transl)]",
"abstract": "",
"full_author_list": "K Sushida, M Yayoshi, H Nakano, M Kono, M Wakai",
"short_author_list": "Sushida K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6799688",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "56",
"journal_issue": "12",
"journal_pages": "561-6",
"pub_year": "1981",
"pubmed_id": "6799688"
},
{
"title": "Spontaneous release of mycophages from lysogenic bovine strains.",
"abstract": "Mycophages were successfully isolated from lysogenic bovine strains without previous exposure to physical or chemical agents. These mycophages were exposed to 53 mycobacterial strains using ATCC 607 as an indicator strain. These strains included rapidly growing strains, human, bovine, avian, murine and BCG strains of different geographical origin. Mycophages PM/90/69 produced lysis of human bovine, murine, BCG strains and most of the rapidly growing strains; whereas Mycophage V24 was sensitive to some rapidly growing strains only. Avian strains were resistant to both mycophages.",
"full_author_list": "M H Tageldin, A M El Hassan, I E Mustafa",
"short_author_list": "Tageldin MH, El Hassan AM, Mustafa IE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7039057",
"journal": "Tubercle",
"journal_volume": "62",
"journal_issue": "4",
"journal_pages": "263-9",
"pub_year": "1981",
"pubmed_id": "7039057"
},
{
"title": "The tadpole-shaped structures in human non-necrotizing granulomas.",
"abstract": "We scrutinized the secondary lysosomal vesicle of the epitheloid cell from 9 patients whose biopsy specimens show multiple non-necrotizing granulomas by light microscopy (LM). In 4 of the 9 patients, we found tadpole-shaped structures (TSS) approximately tenfold larger than the size of the mycobacteriophage by transmission electron microscopy (TEM). In addition, we used a plasma etching method on epon-embedded tissue and successfully demonstrated the stereoscopic appearance of the TSS by scanning electron microscopy (SEM). The identified TSS were further analyzed with an X-ray energy dispersive spectrometer for their microchemistry. The TSS appeared to be integral structures by TEM and SEM and did not contain any nonbiologic elements when analyzed with the X-ray energy dispersive spectrometer. Their location as well as their morphologic features and microchemistry suggested that the TSS are a microorganism and related to the formation of the granulomas in our 4 patients.",
"full_author_list": "N Wang, D E Schraufnagel, M G Sampson",
"short_author_list": "Wang N, Schraufnagel DE, Sampson MG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7235379",
"journal": "The American review of respiratory disease",
"journal_volume": "123",
"journal_issue": "5",
"journal_pages": "560-4",
"pub_year": "1981",
"pubmed_id": "7235379"
},
{
"title": "Effects of antituberculosis and antileprosy drugs on mycobacteriophage D29 growth.",
"abstract": "The minimal inhibitory concentrations of antituberculosis and antileprosy drugs were determined for Mycobacterium aurum. The concentrations that reduced the final yield of bacteriophage D29R1 by 50% and the time during the replication cycle at which the drugs completely inhibited phage production were estimated. THe 50% inhibitory concentration/minimal inhibitory concentration ratios were close to 1.0 for clofazimine, colistin, rifampin, and streptomycin; these ratios were high for dapsone (diaminodiphenylsulfone) and isoniazid. Ethambutol (minimal inhibitory concentration, 1.0 micrograms/ml) was without effect on viral growth.",
"full_author_list": "H L David, S Clavel, F Clement, J Moniz-Pereira",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7447413",
"journal": "Antimicrobial agents and chemotherapy",
"journal_volume": "18",
"journal_issue": "2",
"journal_pages": "357-9",
"pub_year": "1980",
"pubmed_id": "7447413"
},
{
"title": "Phage typing of Mycobacterium kansasii.",
"abstract": "An improved phage typing scheme of M. kansasii is presented. Ultrasonic treatment of the bacterial suspensions was successfully used in order to obtain homogeneous bacterial growth and to improve the reproducibility of the typing. By means of 9 phages 14 lysis patterns (phage types) could be distinguished. The phage typing was applied to 450 strains of Dutch, British and Czechoslovakian origin. The epidemiological relationships between environmental and clinical isolates of M. kansasii among the strains of Dutch and Czechoslovakian origin was confirmed by the results of phage typing.",
"full_author_list": "H W Engel, L G Berwald, J M Grange, M Kubin",
"short_author_list": "Engel HW et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7368319",
"journal": "Tubercle",
"journal_volume": "61",
"journal_issue": "1",
"journal_pages": "11-9",
"pub_year": "1980",
"pubmed_id": "7368319"
},
{
"title": "Typing Mycobacterium tuberculosis with mycobacteriophage Bo4.",
"abstract": "Mycobacteriophage Bo4 grown on the indicator host strain Mycobacterium fortuitum SN203 was restricted and modified by Mycobacterium tuberculosis H37Rv. Phage Bo4.Rv was restricted and modified by the alternate host SN 203. M. tuberculosis strain Myc 1025 was described as a r-m-isolate. By using the mycobacterial prototype strains for phage typing wild M. tuberculosis isolates, it was demonstrated that only the modified phage Bo4.H37Rv was a potential typing phage.",
"full_author_list": "W D Jones",
"short_author_list": "Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6777457",
"journal": "The Journal of general virology",
"journal_volume": "49",
"journal_issue": "2",
"journal_pages": "319-22",
"pub_year": "1980",
"pubmed_id": "6777457"
},
{
"title": "Possible involvement of a calcium-stimulated ATP-hydrolyzing activity associated with mycobacteriophage I3 in the DNA injection process.",
"abstract": "Ca2+ ions are necessary for the successful propagation of mycobacteriophage I3. An assay for the phage DNA release in the presence of an isolated cell wall preparation from the host was established, and in this system Ca2+ ions also stimulated the release of DNA. The inhibition of phage DNA injection caused by Tween 80 (polyoxyethylene sorbitan monooleate), a nonionic detergent routinely used in mycobacterial cultures, was reversed by Ca2+. The presence of a phage-associated ATP-hydrolyzing activity was demonstrated. This enzyme was stimulated by Ca2+ ions and inhibited by Tween 80. From this and the behavior of the two agents at the level of DNA injection, as well as the fact that phage I3 has a contractile tail structure, we conclude that the phage-associated ATPase is involved in the DNA injection process.",
"full_author_list": "S S Karnik, K P Gopinathan",
"short_author_list": "Karnik SS, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6445012",
"journal": "Journal of virology",
"journal_volume": "33",
"journal_issue": "3",
"journal_pages": "969-75",
"pub_year": "1980",
"pubmed_id": "6445012"
},
{
"title": "[Natural variability of mycobacteria and related organisms]",
"abstract": "",
"full_author_list": "E S Mil'ko, N S Egorov, N A Obukhova",
"short_author_list": "Mil'ko ES, Egorov NS, Obukhova NA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6768404",
"journal": "Nauchnye doklady vysshe? shkoly. Biologicheskie nauki",
"journal_volume": "",
"journal_issue": "3",
"journal_pages": "5-19",
"pub_year": "1980",
"pubmed_id": "6768404"
},
{
"title": "Requirement for calcium ions in mycobacteriophage I3 DNA injection and propagation.",
"abstract": "Ca2+ ions are absolutely necessary for the propagation of mycobacteriophage I3 in synthetic medium. These ions are required for successful infection of the host and during the entire span of the intracellular development of the phage. A direct assay of the phage DNA injection using 32[P] labelled phage, shows that Ca2+ ions are necessary for the injection process. The injection itself is a slow process and takes 15 min to complete at 37 degrees C. The bacteria infected in presence of Ca2+ tend to abort if the ions are subsequently withdrawn from the growth medium. The effect of calcium withdrawal is maximally felt during the early part of the latent period; however, later supplementation of Ca2+ ions salvage phage production and the mature phage progeny appear after a delayed interval, proportional to the time of addition of Ca2+.",
"full_author_list": "V Nagaraja, K P Gopinathan",
"short_author_list": "Nagaraja V, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7369828",
"journal": "Archives of microbiology",
"journal_volume": "124",
"journal_issue": "2-3",
"journal_pages": "249-54",
"pub_year": "1980",
"pubmed_id": "7369828"
},
{
"title": "[Susceptibility test of Mycobacterium lepraemurium against mycobacteriophages (author's transl)]",
"abstract": "",
"full_author_list": "M Nakamura, H Ichimaru",
"short_author_list": "Nakamura M, Ichimaru H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7021520",
"journal": "Nippon Rai Gakkai zasshi",
"journal_volume": "49",
"journal_issue": "3",
"journal_pages": "168-71",
"pub_year": "1980",
"pubmed_id": "7021520"
},
{
"title": "Mycobacteriophage structure and function: a review.",
"abstract": "",
"full_author_list": "T A Rado, J H Bates",
"short_author_list": "Rado TA, Bates JH",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/7395640",
"journal": "Advances in tuberculosis research. Fortschritte der Tuberkuloseforschung. Progrès de l'exploration d",
"journal_volume": "20",
"journal_issue": "",
"journal_pages": "64-91",
"pub_year": "1980",
"pubmed_id": "7395640"
},
{
"title": "Morphological and cytoenzymatic characteristics of peripheral zone of lytic plaques induced by mycobacterial phages.",
"abstract": "Morphology and cytoenzymatic characteristics were studied using potassium tellurite, of peripheral zones of lytic plaques in fast growing mycobacteria (ATCC 607, Redmond No 521, Penso S1P) exposed to various mycobacterial phages and slowly growing M. bovis BCG, H37RV 50 gamma INH resistant strains. The latter revealed on borders of lytic plaques a bright tellurite-negative zone of variable width, macroscopically undemonstrable in culture free from potassium tellurite. Microscopically only single mycobacteria of various shapes, whereas in the tellurite-positive zone typical arrangement of BCG rods in compact, strong acid-fast cords present also in the so-called grey zone contacting the tellurite-negative zone, were found. The said tellurite zonal phenomen is explained by abortive infection with phages under study, which results in killing the mycobacterial cells without phage multiplication. The microscopical examination of surface pellicles by thin section showed the phage abortive infection to form a much broader zone than demonstrable in macroscopical examination, since under the black pellicle containing reduced metallic tellurite another tellurite-negative layer is hidden. The quickly growing mycobacteria in the peripheral zones of lytic plaques were either fully tellurite-positive or showed on the inside of the plaque a very narrow, hardly visible tellurite-negative border, microscopically similar to M. bovis BCG and H37RV. The possible utilization of tellurite cytoenzymatic reaction in differential diagnostics both of mycobacteria and mycobacterial phages is discussed.",
"full_author_list": "L Sula",
"short_author_list": "Sula L",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6998685",
"journal": "Czechoslovak medicine",
"journal_volume": "3",
"journal_issue": "2",
"journal_pages": "132-7",
"pub_year": "1980",
"pubmed_id": "6998685"
},
{
"title": "Comparative studies of the strains PA and PN of Mycobacterium phlei leading to their reclassification: examination of lipids and DNA, biochemical tests and phage typing.",
"abstract": "Study of lipid and DNA, biochemical tests and phage typing performed on the strain PA previously labelled Mycobacterium phlei, lead to the conclusion that this strain belongs to the species M. smegmatis. Parallel studies performed on strain PN, isolated from a culture of strain PA, as well as DNA homology percentage of the two strains, do not support the assumption that strain PN could have resulted from a mutation of strain PA Strain PN produces mycolic acids similar to those found in Rhodococcus bronchialis; the few biological tests applied quite agree with such a classification.",
"full_author_list": "C Asselineau, I Baess, A Kolman, L Lapchine, G Puzo, K Wickmann",
"short_author_list": "Asselineau C et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/539691",
"journal": "Annales de microbiologie",
"journal_volume": "130B",
"journal_issue": "4",
"journal_pages": "385-98",
"pub_year": "1979",
"pubmed_id": "539691"
},
{
"title": "Further studies of mycobacteriophage 33D (Warsaw) for differentiation of BCG from M. bovis and M. tubeculosis.",
"abstract": "Mycobacteriophage 33D (Warsaw) was used to differentiate Bacille Calmette-Guerin (BCG) strains from M. bovis and M. tuberculosis. Known strains as well as clinical strains of BCG were used in the study. Single plaque isolations and adsorption studies demonstrated that phage 33D (Warsaw) did not adsorb to BCG cultures.",
"full_author_list": "W D Jones",
"short_author_list": "Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/109978",
"journal": "Tubercle",
"journal_volume": "60",
"journal_issue": "1",
"journal_pages": "55-8",
"pub_year": "1979",
"pubmed_id": "109978"
},
{
"title": "Interfamilial transfer of amber suppressor gene for the isolation of amber mutants of Mycobacteriophage I3.",
"abstract": "A suppressor-containing strain of Mycobacterium smegmatis SN2 was isolated by transferring an amber suppressor carried on the plasmid of Pseudomonas pseudoalcaligenes ERA through transformation. Amber mutants of mycobacteriophage I3 were isolated.",
"full_author_list": "T Ramakrishnan, M S Shaila",
"short_author_list": "Ramakrishnan T, Shaila MS",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/443992",
"journal": "Archives of microbiology",
"journal_volume": "120",
"journal_issue": "3",
"journal_pages": "301-2",
"pub_year": "1979",
"pubmed_id": "443992"
},
{
"title": "Accidental contamination of diagnostic cultures of mycobacteria and phage identification of the contaminating strain.",
"abstract": "Phage typing of mycobacteria is a new technique not yet widely used for classification and intraspecies differentiation. Systematic long-term studies organized by the WHO have succeeded, using a battery of 11 different mycobacterial phages, in dividing M. tuberculosis into 3 different phage sub-groups, preliminarily labelled as A, B and C. A special case of phage-typing is presented which enabled identification of a virulent mycobacterial strain causing accidental contamination of diagnostic mycobacterial cultures. The strain was an old laboratory one, H37Rv, belonging to phage subgroup B.",
"full_author_list": "L Sula, J Sulová",
"short_author_list": "Sula L, Sulová J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/117577",
"journal": "Tubercle",
"journal_volume": "60",
"journal_issue": "3",
"journal_pages": "159-62",
"pub_year": "1979",
"pubmed_id": "117577"
},
{
"title": "On the mechanism of the antimycobacterial activity of isoniazid + prothionamide + dapsone (Isoprodian).",
"abstract": "Increased antimycobacterial activity of Isoprodian (isoniazid + prothionamide + dapsone) may be due to (i) decreased mutation rate for INH resistance provoked in mycobacteria by DDS (in 2 of 3 strains tested); (ii) leakage of K+, Na+ or Ca++ caused by INH and/or by PTH (in all 3 strains tested), and (iii) indicating damages which may increase the low level penetration of DDS into the cell in sub-MIC concentrations as shown by phage proliferation changes (tested in 1 strain with 1 phage).",
"full_author_list": "R Urbanczik",
"short_author_list": "Urbanczik R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/477453",
"journal": "Chemotherapy",
"journal_volume": "25",
"journal_issue": "5",
"journal_pages": "261-7",
"pub_year": "1979",
"pubmed_id": "477453"
},
{
"title": "[Virulence of H37RV cultures treated with mycobacteriophages]",
"abstract": "",
"full_author_list": "A A Balakleevskaia, L A Kosobutski?",
"short_author_list": "Balakleevskaia AA, Kosobutski? LA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/97663",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "6",
"journal_pages": "77-9",
"pub_year": "1978",
"pubmed_id": "97663"
},
{
"title": "Interaction of Mycobacterium leprae and mycobacteriophage D29.",
"abstract": "This study of the interaction between Mycobacterium leprae and the mycobacteriophage D29 showed that the viruses caused a patchy damage of cell wall structure and the accumulation in the host of internal crystalline structures. Whether the observed ultrastructural alterations were caused by the replication of D29 was not clear. Mitomycin C also caused the accumulation of crystalline structures in M. leprae.",
"full_author_list": "H L David, S Clavel, F Clement, L Meyer, P Draper, I D Burdett",
"short_author_list": "David HL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/382947",
"journal": "Annales de microbiologie",
"journal_volume": "129 B",
"journal_issue": "4",
"journal_pages": "561-70",
"pub_year": "1978",
"pubmed_id": "382947"
},
{
"title": "Adsorption of mycobacteriophage D29 on Mycobacterium leprae.",
"abstract": "",
"full_author_list": "H L David, F Clément, L Meyer",
"short_author_list": "David HL, Clément F, Meyer L",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/358889",
"journal": "Annales de microbiologie",
"journal_volume": "129",
"journal_issue": "4",
"journal_pages": "563-6",
"pub_year": "1978",
"pubmed_id": "358889"
},
{
"title": "Characterisation of mycobacteriophage ATCC 11759. Unusual physiocochemical properties of its DNA.",
"abstract": "Growth conditions and a purification procedure for mycobacteriophage ATCC 11759, a lytic phage for Mycobacterium smegmatis, are described. The phage is a large DNA phage with a very long tail (240 nm). A study of its DNA revealed three interesting features. 1. After denaturation the DNA molecule yields two strands of different buoyant densities. 2. The native DNA has unusual physical properties: its buoyant density in CsC1 is very low (1.654 g/cm3), its sedimentation rate is lower than expected for the molecular weight, its thermal stability at low ionic strength is high. 3. The DNA (in its native form or after reannealing) is resistant to various restriction endonucleases.",
"full_author_list": "J C Drapier, F Quetier, J F Petit",
"short_author_list": "Drapier JC, Quetier F, Petit JF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/720334",
"journal": "European journal of biochemistry / FEBS",
"journal_volume": "91",
"journal_issue": "1",
"journal_pages": "163-70",
"pub_year": "1978",
"pubmed_id": "720334"
},
{
"title": "Mycobacteriophages and phage typing.",
"abstract": "",
"full_author_list": "H W Engel",
"short_author_list": "Engel HW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/418716",
"journal": "Annales de microbiologie",
"journal_volume": "129",
"journal_issue": "1",
"journal_pages": "75-90",
"pub_year": "1978",
"pubmed_id": "418716"
},
{
"title": "Structure of native and chloroform-methanol-treated mycobacteriophage R1.",
"abstract": "The morphologies of native and chloroform-methanol-treated mycobacteriophage R1 were compared by electron microscopy, utilizing three negative stains. R1 was determined to be a complex phage. The head appears as an elongated cylinder with a pointed end (93 +/- 3 by 42 +/- 3 nm) constructed from an orderly arrangement of capsomeres. The phage tail measures 209 +/- 11 by 11 +/- 1 nm and possesses a striated surface with two base plates at its distal end. Treatment of R1 with chloroform-methanol resulted in disruption of both the head and tail structures and was accompanied by loss of infectivity. However, because no likely lipid-containing structure was observed in native phages, there is the possibility that the mechanism of chloroform-methanol inactivation is something other than lipid extraction.",
"full_author_list": "D Fay, B U Bowman",
"short_author_list": "Fay D, Bowman BU",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/691117",
"journal": "Journal of virology",
"journal_volume": "27",
"journal_issue": "2",
"journal_pages": "432-5",
"pub_year": "1978",
"pubmed_id": "691117"
},
{
"title": "Inhibition of DNA injection from mycobacteriophage I3 by Tween-80.",
"abstract": "",
"full_author_list": "R R Gadagkar, K P Gopinathan",
"short_author_list": "Gadagkar RR, Gopinathan KP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/741659",
"journal": "Virology",
"journal_volume": "91",
"journal_issue": "2",
"journal_pages": "487-8",
"pub_year": "1978",
"pubmed_id": "741659"
},
{
"title": "Phage typing of mycobacteria using paper discs.",
"abstract": "The suitability of phage-impregnated paper discs for the phage typing of mycobacteria was studied. The relevance of the routine test dilution, the volume of the phage used, the mode of incubation, and the effect of prolonged storage of phage-impregnated paper discs were considered. By using paper discs, each impregnated with one of 5 different mycobacteriophages (BG1, BK1, G37, CRI-3 and LG) that lyse Mycobacterium smegmatis 607B, it was determined that 100 x the routine test dilution in a volume of at least 20 microliter was required for phage lysis. Soaked and dried paper discs produced larger areas of lysis than those with 20-microliter volumes. Soaked discs were found to be stable even after storage for 8 weeks at 4 degrees C.",
"full_author_list": "P R Gangadharam, C S Simmons, C E Stager",
"short_author_list": "Gangadharam PR, Simmons CS, Stager CE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/354442",
"journal": "The American review of respiratory disease",
"journal_volume": "118",
"journal_issue": "1",
"journal_pages": "148-50",
"pub_year": "1978",
"pubmed_id": "354442"
},
{
"title": "Host-phage relationships in the genus Mycobacterium and their clinical significance.",
"abstract": "Progress made during the last 15 years in the studies on the relationships between mycobacteria and their bacteriophages is reviewed. The basic biology of the phages and the applications of studies on adaptation and host range are discussed in relation to the development of phage typing systems for epidemiological purposes. The nature of lysogeny, its natural occurrence, its experimental establishment, the effect of the lysogenic state on the host bacterium and the evidence that lysogenic mycobacteria are involved in human disease, especially sarcoidosis, is reviewed.",
"full_author_list": "J M Grange",
"short_author_list": "Grange JM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/100919",
"journal": "Tubercle",
"journal_volume": "59",
"journal_issue": "3",
"journal_pages": "203-25",
"pub_year": "1978",
"pubmed_id": "100919"
},
{
"title": "The correlation of bacteriophage types of Mycobacterium tuberculosis with guinea-pig virulence and in vitro-indicators of virulence.",
"abstract": "Among 58 isoniazid-sensitive strains of Mycobacterium tuberculosis from India, Burma and East Africa, 23 were of phage type A, 31 of type I (intermediate), 4 of type B and none of type C. Type I strains differed from type A strains in being attenuated in the guinea-pig, susceptible to H2O2, sensitive to thiophen-2-carboxylic acid hydrazide and resistant to thiacetazone and p-aminosalicylic acid; the content of strongly acidic lipids and of sulphatide lipids was low and the attenuation indicator lipid was present. The pattern of results with the type B strains did not correspond to the patterns for types A or I. Strains of type I appear to be a distinct group within the species M. tuberculosis.",
"full_author_list": "J M Grange, V R Aber, B W Allen, D A Mitchison, M B Goren",
"short_author_list": "Grange JM et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/80440",
"journal": "Journal of general microbiology",
"journal_volume": "108",
"journal_issue": "1",
"journal_pages": "1-7",
"pub_year": "1978",
"pubmed_id": "80440"
},
{
"title": "Lysogeny associated with mucoid variation in Mycobacterium kansasii.",
"abstract": "Ten of 200 strains of Mycobacterium kansasii were found to produce very mucoid growth on Löwenstein-Jensen medium. By electronmicroscopy these 10 strains were found to be lysogenic, whereas no phage was observed in cultures of 30 non-mucoid strains. The cultural and biochemical properties of the lysogenic strains are compared with those of non-lysogenic strains, and the morphology of the phages is described.",
"full_author_list": "J M Grange, R G Bird",
"short_author_list": "Grange JM, Bird RG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/401434",
"journal": "Journal of medical microbiology",
"journal_volume": "11",
"journal_issue": "1",
"journal_pages": "1-6",
"pub_year": "1978",
"pubmed_id": "401434"
},
{
"title": "Resistance relationships in Mycobacterium smegmatis ATCC 607 to phages sensitive or resistant to both chloroform and streptomycin sulphate.",
"abstract": "Four of eight mycobacteriophages did not form plaques after they were exposed to chloroform. Phages sensitive to chloroform did not produce plaques when plated on media containing 1000 microgram/ml of streptomycin sulphate. The same concentration of dihydrostreptomycin sulphate did not interfere with plaque formation. Mutants of Mycobacterium smegmatis resistant to each of the eight phages were isolated. Sensitivity or resistance to chloroform and streptomycin sulphate and phage resistant bacterial mutants may provide a basis for classifying the mycobacteriophages.",
"full_author_list": "W D Jones, J Greenberg",
"short_author_list": "Jones WD, Greenberg J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/77894",
"journal": "The Journal of general virology",
"journal_volume": "39",
"journal_issue": "3",
"journal_pages": "555-7",
"pub_year": "1978",
"pubmed_id": "77894"
},
{
"title": "Modification of methods used in bacteriophage typing of Mycobacterium tuberculosis isolates.",
"abstract": "A procedure in which soft agar overlays were used in bacteriophage-typing Mycobacterium tuberculosis is presented. This safer method uses commercially available media, whereas media presently used must be prepared in the laboratory. Single plaque isolations of the phage BG-1 specifying phage type A and B of M. tuberculosis were readily made by using the modified procedures. This purification and the use of prototype strain Myc 1415 as the indicator host strain have significantly enhanced the ability to discriminate among strains of phage types A and B.",
"full_author_list": "W D Jones, J Greenberg",
"short_author_list": "Jones WD, Greenberg J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/96127",
"journal": "Journal of clinical microbiology",
"journal_volume": "7",
"journal_issue": "5",
"journal_pages": "467-9",
"pub_year": "1978",
"pubmed_id": "96127"
},
{
"title": "[Bacteriophage typing of Mycobacteria of the 1st and 3rd Ranion groups]",
"abstract": "",
"full_author_list": "L A Kosobutski?",
"short_author_list": "Kosobutski? LA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/714910",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "10",
"journal_pages": "62-5",
"pub_year": "1978",
"pubmed_id": "714910"
},
{
"title": "[Mycobacteriophage typing of acid-fast strains isolated from patients in various provinces of Poland]",
"abstract": "",
"full_author_list": "W Manowska, H Rdu?towska, A Jezierska-Anczuków, B Pelczarska",
"short_author_list": "Manowska W et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/103079",
"journal": "Pneumonologia polska",
"journal_volume": "46",
"journal_issue": "12",
"journal_pages": "825-8",
"pub_year": "1978",
"pubmed_id": "103079"
},
{
"title": "Genetic transfers in Mycobacteria.",
"abstract": "",
"full_author_list": "M Slosárek, M Konícková-Radochová, J Konícek",
"short_author_list": "Slosárek M, Konícková-Radochová M, Konícek J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/417980",
"journal": "Folia microbiologica",
"journal_volume": "23",
"journal_issue": "2",
"journal_pages": "140-51",
"pub_year": "1978",
"pubmed_id": "417980"
},
{
"title": "Biochemical and morphological characterization of mycobacteriophage R1.",
"abstract": "Large-scale propagation of mycobacteriophage R1 in broth culture has allowed the isolation of quantities of virus sufficient for characterization of its nucleic acid and lipid components as well as investigation of its ultrastructural attributes. Analysis of R1 DNA indicates that it is double stranded and possesses a molecular weight of 2.5 X 10(7) and a guanine-plus-cytosine content of 65.7 +/- 0.5%. The lipid fraction of R1 accounts for 14% of the total dry weight of the virus, 20% of which was identified as free or esterified sterols. A rapid loss of viral titer occurred after seconds of exposure to organic solvents. This result suggests that the lipid fractions of R1 is essential for its infectivity. Electron microscopic investigation of solvent-extracted R1 showed extensive deterioration of its normal morphology, including nucleocapsid disintegration and base plate separation. Routine phosphotungstate preparations demonstrated a particle with an oval head and a noncontractile tail. Altering the pH of the phosphotungstate negative stain from neutrality damage the viral particles. Uranyl formate-contrasted specimens displayed an elongated hexagonal nucleocapsid with a neck region; the cross-striated tail possessed a starlike base plate.",
"full_author_list": "B L Soloff, T A Rado, B E Henry, J H Bates",
"short_author_list": "Soloff BL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/23439",
"journal": "Journal of virology",
"journal_volume": "25",
"journal_issue": "1",
"journal_pages": "253-62",
"pub_year": "1978",
"pubmed_id": "23439"
},
{
"title": "Comparison of several culture media used for studies on mycobacteriophages.",
"abstract": "The value of RVA, N-1, 7H10, 7H11 and Sauton's media for studies on mycobacteriophage infeciton and lysis of mycobacteria was assessed. Experiments were made with mycobacteriophages BGI, BKI, CRI-3, G37, and LG, all of which lyse Mycobacterium smegmatis strain 607B, and with mycobacteriophage DS6A which lyses Mycobacterium tuberculosis strain H37Rv. The methods involved \"direct lysis\", the measurement of \"routine test dilutions\" and counts of plaque-forming units. It was found that N-1, 7H10 and 7H11 media gave better overall results than RVA medium for M. smegmatis strain 607B and its phages, and that RVA medium was generally the most useful for M. tuberculositems employed.",
"full_author_list": "C E Stager, P R Gangadharam",
"short_author_list": "Stager CE, Gangadharam PR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/96257",
"journal": "Journal of medical microbiology",
"journal_volume": "11",
"journal_issue": "2",
"journal_pages": "187-91",
"pub_year": "1978",
"pubmed_id": "96257"
},
{
"title": "Mycobacterium.",
"abstract": "",
"full_author_list": "L Barksdale, K S Kim",
"short_author_list": "Barksdale L, Kim KS",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/67839",
"journal": "Bacteriological reviews",
"journal_volume": "41",
"journal_issue": "1",
"journal_pages": "217-372",
"pub_year": "1977",
"pubmed_id": "67839"
},
{
"title": "[Infection of mycobacteria with mycobacteriophage. 2. Adsorption-invasion time of mycobacteriophage B-1 strain to 7 strains of myobacteria (author's transl)]",
"abstract": "",
"full_author_list": "Y Hagihara, M Sakata, K Shikada, M Sasaki",
"short_author_list": "Hagihara Y et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/881755",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "52",
"journal_issue": "4",
"journal_pages": "185-8",
"pub_year": "1977",
"pubmed_id": "881755"
},
{
"title": "Host modification and restriction with a mycobacteriophage isolated from a pseudolysogenic Mycobacterium chelonei.",
"abstract": "A pseudolysogenic Mycobacterium chelonei and its phage phi630 are described. Phage phi630 is the first mycobacteriophate reported to be resistant to the nonpolar solvents chloroform, dioxan and diethyl ether. The phage had a latent period of 75 min, a rise period of 90 min and a burst size of 5I. Evidence is presented for host modification and restriction. Phage phi630A, grown on host strain M. chelonei F-630 Rg, plated on the alternative host M. smegmatis ATCC607 with an efficiency of plating (e.o.p.) of 10(-5). Phage phi630B, grown on host M. smegmatis, plated with an e.o.p. of 10(-5) on the alternative host F-630 Rg. Phages phi630A and phi630B absorbed equally well on their alternative hosts and on their indicator host strains. The progeny of plaques from initial platings on the alternative host, when grown in the alternative host, exhibited a marked reduction in e.o.p. on their original host.",
"full_author_list": "W D Jones, J Greenberg",
"short_author_list": "Jones WD, Greenberg J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/874454",
"journal": "Journal of general microbiology",
"journal_volume": "99",
"journal_issue": "2",
"journal_pages": "389-95",
"pub_year": "1977",
"pubmed_id": "874454"
},
{
"title": "Phage types of Mycobacterium bovis, substrains of BCG.",
"abstract": "Nineteen substrains of Mycobacterium bovis, strain bacille Calmette-Guérin (BCG) used in laboratories throughout the world for the preparation of BCG vaccines were phage-typed with a battery of mycobacteriophages. The results revealed differences in their susceptibility to phage lysis that allow subdivision of these strains of BCG into two or more phage types.",
"full_author_list": "E Mankiewicz, M Liivak",
"short_author_list": "Mankiewicz E, Liivak M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/326364",
"journal": "Canadian journal of microbiology",
"journal_volume": "23",
"journal_issue": "6",
"journal_pages": "818-23",
"pub_year": "1977",
"pubmed_id": "326364"
},
{
"title": "Ultrastructural studies of mycobacterial phages isolated from the material of sarcoid patients.",
"abstract": "Mycophages DNAIII, Legendre and Clark, isolated from sarcoid material by Mankiewicz, belongs with respect to their ultrastructural morphology, to the systematic group B according to Bradley or to group IV according to Tikhonenko. These phages contain 2-DNA, their head is a regular icosahedron, the tail consisting of a helix of protein subunits is attached to the head by a narrowed segment and is fixed in it by means of a disc-like structure. It is terminated by a ball-shoped or conical end structure. By their dimensions, these phages belong to the smallest ones in this systematic group. In comparison with other mycobacterial phages, the studied phages exhibit very low mechanical resistance. This characteristic is most pronounced in phage DNAIII. This group of mycophages is also very sensitive lipid solvents and increased temeprature. This phenomenon is also most pronounced in phage DNAIII. The explanation of these findings will be the subject of our further study.",
"full_author_list": "H Mohelská, E Wisingerová",
"short_author_list": "Mohelská H, Wisingerová E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/560406",
"journal": "Journal of hygiene, epidemiology, microbiology, and immunology",
"journal_volume": "21",
"journal_issue": "1",
"journal_pages": "1-8",
"pub_year": "1977",
"pubmed_id": "560406"
},
{
"title": "Chemical and physical properties of mycobacteriophage D29.",
"abstract": "Mycobacteriophage D29 has a head of uniform size (average diameter 65 nm) and regular shape and a tail of variable length. The stability of the bacteriophage is optimal between pH 9 and 10. The virus contain double-stranded DNA and six structural polypeptides, three major and three minor. The molecular weights of these six polypeptides, as determined by polyacrylamide gel electrophoresis in the presence of dodecylsulfate, are 150 000, 138 000, 13 000, 66 000 and 24 000. The virus contains no lipids as shown by (a) the lack of structural changes after inactivation of the bacteriophage with chloroform, (b) the absence of lipids containing [32P]phosphate or [35S]sulfate in labeled virus, and (c) the absence of an electron paramagnetic resonance spectrum in bacteriophage which had been incubated with a nitroxide-containing fatty acid.",
"full_author_list": "R Schäfer, U Huber, R M Franklin",
"short_author_list": "Schäfer R, Huber U, Franklin RM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/837938",
"journal": "European journal of biochemistry / FEBS",
"journal_volume": "73",
"journal_issue": "1",
"journal_pages": "239-46",
"pub_year": "1977",
"pubmed_id": "837938"
},
{
"title": "Phage type of tubercle bacilli isolated from patients with two or more sites of organ involvement.",
"abstract": "To evaluate the possibility of separate pulmonary infections in human beings by different strains of Mycobacterium tuberculosis, a search for multiple phage types within a single host was under-taken. Culture isolates from 2 or more distinct anatomic sites of infection in the same patient were obtained from 87 persons. In 3 subjects, 2 distinct phage types were found. The possible explanations for 2 types in the same patient and the epidemiologic implications are discussed.",
"full_author_list": "J H Bates, W W Stead, T A Rado",
"short_author_list": "Bates JH, Stead WW, Rado TA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/823847",
"journal": "The American review of respiratory disease",
"journal_volume": "114",
"journal_issue": "2",
"journal_pages": "353-8",
"pub_year": "1976",
"pubmed_id": "823847"
},
{
"title": "A study on the receptor for a mycobacteriophage : phage phlei.",
"abstract": "From Mycobacterium phlei, glycolipid fractions have been isolated which inactivate phage Phlei. On the basis of the characteristics of the inactivation (specificity, kinetics, requirement for Ca++) typical of the phage-host cell system, it was concluded that these fractions contain the receptor sites for phage Phlei ; this conclusion was supported by electron microscopic studies. All the active fractions contain four kinds of components : fatty acids, glycerol, sugars (D-lyxose, 6-0-methyl-D-glucose, and low amounts of glucose and mannose), and water-soluble acids. These acids are isolated by degradation of the receptor fractions as oxalic and pyruvic acids. Variations of the ratio oxalic acid/pyruvic acid according to the mode of degradation and the absence of the peak characteristic of the protons of a pyruvic acid residue in the NMR spectrum, suggest that these acids might arise from the splitting of oxaloacetic acid. A tentative structure of the receptor is proposed, in many monoglycerides are linked through keto-acid to a polysaccharide core.",
"full_author_list": "G Bisso, G Castelnuovo, M G Nardelli, G Orefici, G Arancia, G Lanéelle, C Asselineau, J Asselineau",
"short_author_list": "Bisso G et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/953052",
"journal": "Biochimie",
"journal_volume": "58",
"journal_issue": "1-2",
"journal_pages": "87-97",
"pub_year": "1976",
"pubmed_id": "953052"
},
{
"title": "Acid-fastness of Mycobacteri,m tuberculosis H37Rv following infection by mycobacteriophage DS6A.",
"abstract": "Mycobacterium tuberculosis H37Rv demonstrates a loss of acid-fastness following exposure to specific mycobacteriophage DS6A. No effect was seen with another mycobacteriophage GS7 which does not lyse this organism.",
"full_author_list": "P R Gangadharam, C E Stager",
"short_author_list": "Gangadharam PR, Stager CE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/62438",
"journal": "Tubercle",
"journal_volume": "57",
"journal_issue": "3",
"journal_pages": "203-5",
"pub_year": "1976",
"pubmed_id": "62438"
},
{
"title": "Bacteriophage typing of Mycobacterium tuberculosis strains isolated in South East England.",
"abstract": "The species Mycobacterium tuberculosis may be subdivided by its susceptibility to lysis by bacteriophages. In this study 300 strains have been typed with six phages to determine the prevalence of various phage types in South East England. The distribution of the phage types is considered in relation to the patients' racial origins and the clinical presentation of disease, whether pulmonary or extrapulmonary. The technical aspects of phage typing are described and modifications of existing techniques are discussed.",
"full_author_list": "J M Grange, C H Collins, D McSwiggan",
"short_author_list": "Grange JM, Collins CH, McSwiggan D",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/821195",
"journal": "Tubercle",
"journal_volume": "57",
"journal_issue": "1",
"journal_pages": "59-66",
"pub_year": "1976",
"pubmed_id": "821195"
},
{
"title": "Isolation and characterization of nocardia-like variants of Mycobacterium smegmatis.",
"abstract": "Orange-red-pigmented (OR) colonies were isolated from cream-yellow-pigmented Mycobacterium smegmatis after exposure to either mycobacteriophage MC4 or ultraviolet light; these variant strains were designated OR4 and ORuv, respectively. Early subculture of OR-colonies did not show any segregation of parental-type cells. However, colonies resembling the parental strains, possibly representing a back mutant (REV-OR4), were occasionally found during subculture of established OR-colonies or upon treatment with N-nitrose-N'-nitro-N-methylguanidine. The OR-variants were characterized by their lytic response to nocardiophage, but not to mycobacteriophages, presence of alpha-branched, beta-hydroxylated fatty acids of the Nocardia-type, and a guanine plus cytosine value of deoxyribonucleic acid (DNA) between 62 and 64 mol%. They were more resistant to the lethal action of both ultraviolet light and mitomycin C treatment than the parental and back mutant strains. Although the OR-variants in this study possess characteristics common to the genus Nocardia or some of the 'rhodochrous' mycobacteria, evidence is presented that they form a new class of mycobacterial variants.",
"full_author_list": "R J Hawley, T Imaeda, N Mann",
"short_author_list": "Hawley RJ, Imaeda T, Mann N",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/974902",
"journal": "Canadian journal of microbiology",
"journal_volume": "22",
"journal_issue": "10",
"journal_pages": "1480-91",
"pub_year": "1976",
"pubmed_id": "974902"
},
{
"title": "Use of phage F-phi WJ-1 of Mycobacterium fortuitum to discern more phage types of Mycobacterium tuberculosis.",
"abstract": "A total of 125 strains of Mycobacterium tuberculosis from the Southeastern area of the United States was subjected to phage typing. In addition to the five major mycobacteriophages, a new phage, F-phi WJ-1, was used in the study. The results obtained with the five major phages were: type A0, 35.2%; TYPE B, 29.6%, and type C, 4.0%. The remaining 21.2% of the strains phaged typed as subgroups A1 through A6. These percentages were similar to the typing results of earlier studies. The new phage, F-phi WJ-1, subdivided each of the phage types, with the exception of type C, into two subgroups. The possible role of host modification-restriction of the phages used in phage typing of strains of M. tuberculosis is discussed.",
"full_author_list": "W D Jones, J Greenberg",
"short_author_list": "Jones WD, Greenberg J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/818112",
"journal": "Journal of clinical microbiology",
"journal_volume": "3",
"journal_issue": "3",
"journal_pages": "324-6",
"pub_year": "1976",
"pubmed_id": "818112"
},
{
"title": "[Electron microscopic study of the spatial structure of mycobacteriophage butyricum process]",
"abstract": "",
"full_author_list": "A M Mikha?lov, P Somogyi, G V Petrovski?, V B Grigor'ev, A S Kaftanova",
"short_author_list": "Mikha?lov AM et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1009834",
"journal": "Doklady Akademii nauk SSSR",
"journal_volume": "231",
"journal_issue": "3",
"journal_pages": "1472-5",
"pub_year": "1976",
"pubmed_id": "1009834"
},
{
"title": "[Isolation of Mycobacterium phages from the lymph nodes]",
"abstract": "",
"full_author_list": "V A Polkhovski?",
"short_author_list": "Polkhovski? VA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/948837",
"journal": "Veterinariia",
"journal_volume": "",
"journal_issue": "6",
"journal_pages": "98-9",
"pub_year": "1976",
"pubmed_id": "948837"
},
{
"title": "Evidence for host-dependent modification and restriction of bacteriophage DNA in Mycobacterium tuberculosis.",
"abstract": "Wild isolates of Mycobacterium tuberculosis may be divided into the three internationally recognized phage types on the basis of susceptibility to mycobacteriophages DS6A, BK1 and D34. Strains of type A are lysed at high efficiency by DS6A only; type B is lysed by BK1 grown on Mycobacterium smegmatis ATCC607 and DS6A, while type C is lysed additionally by D34 grown on atypical Mycobacterium F130. Propagation of D34 on a C-strain (D34-C) or BK1 on a B-strain (BK1-B) has no effect on viral host-range. D34-C has an efficiency of plating (e.o.p.) of 10(-5) on type B strains and 10(-7) on A strains. BK1-B plates on A strains at an e.o.p. of 10(-5). BK1 recovered from and repropagated on an A strain (BK1-A) has an e.o.p. of 1-0 on strains of all classes. D34-B has an e.o.p. of 1-0 on strains of type B and C, while D34-A plates with high efficiency on types B and C and displayed an e.o.p. of 10(-4) on type A. Repropagation of these viruses on the M. tuberculosis strains originally lysed by them results in the restoration of their previous host range. Variations in plating efficiency cannot be explained by differences in viral absorption alone. These findings suggest that the three phage types of human tubercle bacilli are related by a hierarchical pattern of DNA restriction and modification in which the C pattern is included in the B, and both patterns are included in A-modified DNA. Viruses such as DS6A which are equally virulent for strains of all classes are not susceptible to host dependent restriction.",
"full_author_list": "T A Rado, J H Bates, J K Fitzhugh",
"short_author_list": "Rado TA, Bates JH, Fitzhugh JK",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/812956",
"journal": "The Journal of general virology",
"journal_volume": "30",
"journal_issue": "1",
"journal_pages": "91-7",
"pub_year": "1976",
"pubmed_id": "812956"
},
{
"title": "[A study of the PH phage susceptibility of M. tuberculosis isolated from tuberculosis patients (author's transl)]",
"abstract": "",
"full_author_list": "K Sushida, F Osada",
"short_author_list": "Sushida K, Osada F",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/815709",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "51",
"journal_issue": "1",
"journal_pages": "13-7",
"pub_year": "1976",
"pubmed_id": "815709"
},
{
"title": "Concentration and purification of mycobacteriophages with polyethylene glycol 6000.",
"abstract": "Experiments were performed to concentrate and purify mycobacteriophages with polyethylene glycol 6000; 6, 9, and 8 per cent polyethylene glycol 6,000 proved to be optimal concentrations for precipitating phages of Mycobacterium phlei, Mycobacterium smegmatis strain butyricum, and mycobacterium smegmatis strain Rabinowitz, respectively. Preparative polyethylene glycol reverse gradients were constructed for further concentration and purification of the precipitated phages. With the method described, large amounts of crude phage lysates can be concentrated and purified rapidly.",
"full_author_list": "B P Vajda, K J Háber",
"short_author_list": "Vajda BP, Háber KJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/779553",
"journal": "The American review of respiratory disease",
"journal_volume": "114",
"journal_issue": "1",
"journal_pages": "245-8",
"pub_year": "1976",
"pubmed_id": "779553"
},
{
"title": "Results of typing of \"M. tuberculosis\" with seven known and two adapted phages.",
"abstract": "",
"full_author_list": "I Baess",
"short_author_list": "Baess I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/820283",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "563-7",
"pub_year": "1975",
"pubmed_id": "820283"
},
{
"title": "Inactivation of phages DS6A and D29 by acetone extracts of Mycobacterium tuberculosis and Mycobacterium bovis.",
"abstract": "The adsorption rate constant for mycobacteriophage DS6A on clumped cells of Mycobacterium tuberculosis strain H37Rv was found to be 6.33 x 10(-13) ml per min per colony former. Acetone-extracted cells of H37Rv did not absorb phage DS6A. Acetone extracts of cells of H37Rv and of Mycobacterium bovis strain BCG inhibited plaque formation of mycobacteriophage DS6A and of phage D29. Suspensions of these extracts in heart infusion broth with 0.002 M calcium chloride and 1 per cent dioxane required 20 hours of incubation (activation) at 37 degrees C with stirring before they were capable of inactivating phage DS6A, but did not require activation for inhibition of phage D29. Sonication of water mixtures of these extracts for 45 sec yielded suspensions that were highly active against phage DS6A and independent of the 20-hour lag period. Such preparations were also active against phage D29. The extract prepared from cells of BCG was more active than the extract from cells of H37Rv. Water washing of chloroform solutions of each extract did not remove significant amounts of solid material or reduce the phage-inactivating activites of either extract.",
"full_author_list": "B U Bowman, L J Fisher, D T Witiak, H A Newman",
"short_author_list": "Bowman BU et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/807139",
"journal": "The American review of respiratory disease",
"journal_volume": "112",
"journal_issue": "1",
"journal_pages": "17-22",
"pub_year": "1975",
"pubmed_id": "807139"
},
{
"title": "Isolation of mycobacteriophages from surface water.",
"abstract": "",
"full_author_list": "G Caroli, C M Avio",
"short_author_list": "Caroli G, Avio CM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1230052",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "568-70",
"pub_year": "1975",
"pubmed_id": "1230052"
},
{
"title": "Phage typing of \"Mycobacterium kansasii\", an important aid in studying its epidemiology.",
"abstract": "",
"full_author_list": "H W Engel",
"short_author_list": "Engel HW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1230054",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "583-93",
"pub_year": "1975",
"pubmed_id": "1230054"
},
{
"title": "Phage typing of strains of \"M. tuberculosis\" in the Netherlands.",
"abstract": "",
"full_author_list": "H W Engel",
"short_author_list": "Engel HW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/820284",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "578-83",
"pub_year": "1975",
"pubmed_id": "820284"
},
{
"title": "[Action of mycobacteriophages in experimental tuberculosis]",
"abstract": "",
"full_author_list": "S I Gel'berg, G I Sharov",
"short_author_list": "Gel'berg SI, Sharov GI",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/810793",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "4",
"journal_pages": "70-4",
"pub_year": "1975",
"pubmed_id": "810793"
},
{
"title": "The genetics of mycobacteria and mycobacteriophages - a review.",
"abstract": "The genus Mycobacterium, despite its medical importance, has so far received relatively little attention from bacterial geneticists. Nevertheless examples of the transfer of genes from one strain to another by means of transformation, phage-mediated transduction and direct cellular contact have been reported. The modification of strains by experimental or naturally occurring lysogeny has been studied in some detail and there is evidence that phage may contribute significantly to variation within species. Mycobacteriophages have been the subject of genetic analyses and have proved of value in the study of certain aspects of host-induced phage modification. In addition phages are being used to develop typing systems for use in epidemiological studies. It is evident that much of interest and value awaits discovery by means of genetic analysis of the mycobacteria and their phages and hopefully the next decade or so will bring great advances in this subject.",
"full_author_list": "J M Grange",
"short_author_list": "Grange JM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/814665",
"journal": "Tubercle",
"journal_volume": "56",
"journal_issue": "3",
"journal_pages": "227-38",
"pub_year": "1975",
"pubmed_id": "814665"
},
{
"title": "Pseudolysogeny in Mycobacterium diernhoferi ATCC19341.",
"abstract": "",
"full_author_list": "J M Grange",
"short_author_list": "Grange JM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1176958",
"journal": "Journal of general microbiology",
"journal_volume": "89",
"journal_issue": "2",
"journal_pages": "387-91",
"pub_year": "1975",
"pubmed_id": "1176958"
},
{
"title": "Proceedings: Bacteriophage typing of strains of Mycobacterium tuberculosis isolated in south-east england.",
"abstract": "",
"full_author_list": "J M Grange",
"short_author_list": "Grange JM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/806685",
"journal": "Journal of medical microbiology",
"journal_volume": "8",
"journal_issue": "2",
"journal_pages": "Pix (2)",
"pub_year": "1975",
"pubmed_id": "806685"
},
{
"title": "The nature and incidence of lysogeny in Mycobacterium fortuitum.",
"abstract": "Ten of 28 strain of Mycobacterium fortuitum (ranae) were found to be associated with bacteriophage; three were pseudolysogenic, one liberated a phage that lysed a sensitive indicator strain, two liberated morphologically complete phages that did not lyse any of the strains used in this study and four liberated morphologically defective phages. The lysogenic and defectively lysogenic strains showed anomalies in cultural, biochemical and antigenic properties and in susceptibility to superinfecting phages. In view of the high frequency of lysogeny found in M. fortuitum, the role of bacteriophage in the variation of properties, including pathogenicity, of mycobacteria of greater clinical importance merits further consideration.",
"full_author_list": "J M Grange, R G Bird",
"short_author_list": "Grange JM, Bird RG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1142414",
"journal": "Journal of medical microbiology",
"journal_volume": "8",
"journal_issue": "2",
"journal_pages": "215-23",
"pub_year": "1975",
"pubmed_id": "1142414"
},
{
"title": "Ultrastructure of L-phase variants isolated from a culture of Mycobacterium phlei.",
"abstract": "Relatively stable L-phase colonies were isolated from old cultures of a selected clone of Mycobacterium phlei. The colonies grew at 52 degrees C and were composed of rod-shaped, oval or spherical cells. Large amoeba-like cells were occasionally present. These were usually limited by a double-layered membrane and devoid of normal cell-wall components such as bacteriophage receptors. The large amoeba-like bodies sometimes showed both outer and inner double-layered membranes, especially in pseudopodium-like cellular extensions. An unusual feature of rod-shaped cells was retention of the original shape despite the loss of their cell walls. Two types of walled cells occurred during successive transfers of L colonies. One was the true revertant which had characteristics in common with the wild-type M. phlei, such as growth at 52 degrees C and ultrastructural organisation. The other, designated as the \"atypical-cell-wall variant\", was characterised by growth at 52 degrees C, thick cell walls, and disordered septation. Wild-type M. phlei, L variants, revertants and atypical-cell-wall variants released mycobacteriophage particles. These bacteriophages were almost identical in respect to morphology, host range, and neutralisation by antiserum. The results obtained suggest strongly that all types of cells examined were derived from M. phlei.",
"full_author_list": "T Imaeda",
"short_author_list": "Imaeda T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1177288",
"journal": "Journal of medical microbiology",
"journal_volume": "8",
"journal_issue": "3",
"journal_pages": "389-95",
"pub_year": "1975",
"pubmed_id": "1177288"
},
{
"title": "Phage typing report of 125 strains of \"Mycobacterium tuberculosis\".",
"abstract": "",
"full_author_list": "W D Jones",
"short_author_list": "Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/820285",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "599-604",
"pub_year": "1975",
"pubmed_id": "820285"
},
{
"title": "Differentiation of known strains of BCG from isolates of mycobacterium bovis and Mycobacterium tuberculosis by using mycobacteriophage 33D.",
"abstract": "The use of mycobacteriophage 33D to differentiate strains of BCG from isolates of Mycobacterium bovis was investigated. The procedure was found to be reproducible and, using the commercially available media described, can be recommended for use in mycobacterial reference laboratories.",
"full_author_list": "W D Jones",
"short_author_list": "Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/809476",
"journal": "Journal of clinical microbiology",
"journal_volume": "1",
"journal_issue": "4",
"journal_pages": "391-2",
"pub_year": "1975",
"pubmed_id": "809476"
},
{
"title": "[Effect of mycobacteriophages on the course of experimental tuberculosis in albino mice]",
"abstract": "",
"full_author_list": "B N Koz'min-Sokolov, Vabilin",
"short_author_list": "Koz'min-Sokolov BN, Vabilin ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/810794",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "4",
"journal_pages": "75-9",
"pub_year": "1975",
"pubmed_id": "810794"
},
{
"title": "Phage types of mycobacterium tuberculosis in cultures isolated from Eskimo patients.",
"abstract": "The phage type of each of 3 colonies selected at random from cultures of mycobacterium tuberculosis isolated from 233 Eskimo patients was determined. In 33 cultures, colonies of different phage types were observed. In 22 cases, the differences in phage types paralleled differences in drug susceptibility of the bacteria. A comparative study with cultures of Mycobacterium tuberculosis isolated from while patients did not reveal differences in phage types among 3 colonies from the same culture. This observation suggests that some of the numerous reactivations of the disease in Eskimo patients may be due to exogenous reinfections.",
"full_author_list": "E Mankiewicz, M Liivak",
"short_author_list": "Mankiewicz E, Liivak M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/804287",
"journal": "The American review of respiratory disease",
"journal_volume": "111",
"journal_issue": "3",
"journal_pages": "307-12",
"pub_year": "1975",
"pubmed_id": "804287"
},
{
"title": "[Determination of Mycobacteria strains isolated from pigs by means of Mycobacteriophages and agglutination tests]",
"abstract": "",
"full_author_list": "W Manowska, B Pelczarska, H Rdultowska, B Surmiak",
"short_author_list": "Manowska W et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1116743",
"journal": "Gru?lica i choroby p?uc; tuberculosis et pneumonologia",
"journal_volume": "43",
"journal_issue": "3",
"journal_pages": "233-8",
"pub_year": "1975",
"pubmed_id": "1116743"
},
{
"title": "[Genetics of Mycobacterium]",
"abstract": "",
"full_author_list": "Y Mizuguchi, T Tokunaga",
"short_author_list": "Mizuguchi Y, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/809598",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "30",
"journal_issue": "2",
"journal_pages": "297-313",
"pub_year": "1975",
"pubmed_id": "809598"
},
{
"title": "Morphology of mycophages DNA III. Legendre and Clark.",
"abstract": "",
"full_author_list": "H Mohelská, E Wisingerová",
"short_author_list": "Mohelská H, Wisingerová E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1230057",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "606-14",
"pub_year": "1975",
"pubmed_id": "1230057"
},
{
"title": "Phage typing of Japanese strains of \"M. tuberculosis\".",
"abstract": "",
"full_author_list": "T Murohashi, Y Mizuguchi",
"short_author_list": "Murohashi T, Mizuguchi Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/820286",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "615-7",
"pub_year": "1975",
"pubmed_id": "820286"
},
{
"title": "World Health Organization studies on bacteriophage typing of mycobacteria. Subdivision of the species Mycobacterium tuberculosis.",
"abstract": "The ability of lytic mycobacteriophages to subdivide the species Mycobacterium tuberculosis reliably has been studied using a series of 100 strains isolated from cases of tuberculosis in the Netherlands. Techniques for the propagation and application of the viruses have been standardized, as have the conditions for growth and preparation of bacterial strains. On the basis of lytic results with 11 mycobacteriophages, it is proposed that the species Mycobacterium tuverculosis may be subdivided into at least 3 major phage types, A, B, and C, and into 2 subjects, Ax and A2. The reliability of the individual bacteriophage lytic result has been assessed, and the relationship between phage reliability and the degree of certainty with which a strain may be assigned to a phage type is described. The effect of rigorous standardization of techniques on the reliability of bacteriphage typing is demonstrated, and a standard protocol is proposed.",
"full_author_list": "T A Rado, J H Bates, H W Engel, E Mankiewicz, T Murohashi, Y Mizuguchi, L Sula",
"short_author_list": "Rado TA et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/804840",
"journal": "The American review of respiratory disease",
"journal_volume": "111",
"journal_issue": "4",
"journal_pages": "459-68",
"pub_year": "1975",
"pubmed_id": "804840"
},
{
"title": "Evidence for infection by two distinct strains of Mycobacterium tuberculosis in pulmonary tuberculosis: report of 9 cases.",
"abstract": "The sputum cultures of 26 patients in whom bacteriologic relapse occurred during or after an initial course of treatment with antimicrobial drugs were compared by phage typing with cultures isolated previously from the same patients. Nine (34 per cent) were different in phage type. Whether this indicates exogenous reinfection as the mechanism for the relapse, the presence of two distinct phage types present from the outset, or change in phage type of the original single strain has not been determined. These observations may have implications relating to epidemiology and control of tuberculosis.",
"full_author_list": "J W Raleigh, R H Wichelhausen, T A Rado, J H Bates",
"short_author_list": "Raleigh JW et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/812397",
"journal": "The American review of respiratory disease",
"journal_volume": "112",
"journal_issue": "4",
"journal_pages": "497-503",
"pub_year": "1975",
"pubmed_id": "812397"
},
{
"title": "Phage susceptibilities of \"Mycobacterium bovis\" isolates.",
"abstract": "",
"full_author_list": "W D Richards",
"short_author_list": "Richards WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/779674",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "618-22",
"pub_year": "1975",
"pubmed_id": "779674"
},
{
"title": "[Typing of Mycobacterium tuberculosis with the aid of phages and other methods]",
"abstract": "",
"full_author_list": "G I Sharov, L A Kosobutski?",
"short_author_list": "Sharov GI, Kosobutski? LA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/813213",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "8",
"journal_pages": "73-7",
"pub_year": "1975",
"pubmed_id": "813213"
},
{
"title": "Biophysical properties of mycobacteriophages.",
"abstract": "Biophysical characterization of two mycobacteriophages (Phlei phage and Butyricum phage) was carried out. Biophysical parameters obtained were: (i) buoyant densities in CsCl of I . 51 g/ml for both phages; (ii) sedimentation coefficient of 490 S and 410 S; (iii) DNA content of 42 and 34% and (iv) mol. wt. calculated by electron microscopic dimensions to be 123 x 10(6) and 116 x 10(6) for Butyricum and Phlei phage, respectively.",
"full_author_list": "P A Somogyi, G V Petrovsky, V B Grigorev",
"short_author_list": "Somogyi PA, Petrovsky GV, Grigorev VB",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1052827",
"journal": "The Journal of general virology",
"journal_volume": "29",
"journal_issue": "2",
"journal_pages": "235-8",
"pub_year": "1975",
"pubmed_id": "1052827"
},
{
"title": "[Delineation and modification of mycobacteriophage]",
"abstract": "",
"full_author_list": "K Suga, Y Mizoguchi",
"short_author_list": "Suga K, Mizoguchi Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1240272",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "30",
"journal_issue": "1",
"journal_pages": "248",
"pub_year": "1975",
"pubmed_id": "1240272"
},
{
"title": "Phage typification of 100 strains of \"Mycobacterium tuberculosis\" isolated in Czechoslovakia.",
"abstract": "",
"full_author_list": "L Sula, J Sulová",
"short_author_list": "Sula L, Sulová J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/820287",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "623-8",
"pub_year": "1975",
"pubmed_id": "820287"
},
{
"title": "[Mycobacteriophage]",
"abstract": "",
"full_author_list": "T Tokunaga",
"short_author_list": "Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/1221147",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "50",
"journal_issue": "11",
"journal_pages": "420-2",
"pub_year": "1975",
"pubmed_id": "1221147"
},
{
"title": "Phage susceptibility patterns of \"M. tuberculosis\" strains freshly isolated from Virginia patients.",
"abstract": "",
"full_author_list": "A J Ward, S M Sieg",
"short_author_list": "Ward AJ, Sieg SM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/820288",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "629-33",
"pub_year": "1975",
"pubmed_id": "820288"
},
{
"title": "Inactivation of the mycophage activity by lipid solvents.",
"abstract": "",
"full_author_list": "E Wisingerová, J Sulová, E Sassmannová",
"short_author_list": "Wisingerová E, Sulová J, Sassmannová E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/779675",
"journal": "Annali Sclavo; rivista di microbiologia e di immunologia",
"journal_volume": "17",
"journal_issue": "4",
"journal_pages": "634-40",
"pub_year": "1975",
"pubmed_id": "779675"
},
{
"title": "The preservation of mycobacteriophages by means of freeze drying.",
"abstract": "",
"full_author_list": "H W Engel, L Smith, L G Berwald",
"short_author_list": "Engel HW, Smith L, Berwald LG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4823411",
"journal": "The American review of respiratory disease",
"journal_volume": "109",
"journal_issue": "5",
"journal_pages": "561-6",
"pub_year": "1974",
"pubmed_id": "4823411"
},
{
"title": "Growth inhibitory activity of deoxyribonucleic acid-containing factor(s) isolated from lepromatous lesions.",
"abstract": "Deoxyribonucleic acid-containing factor(s) isolated from Mycobacterium leprae suspensions obtained from lepromas of nine patients showed growth inhibitory activity against Micrococcus and both orange-red-pigmented and coccoid mutants of mycobacteria. No growth inhibition was observed for parent mycobacterial species, Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus epidermidis.",
"full_author_list": "T Imaeda",
"short_author_list": "Imaeda T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4609913",
"journal": "Infection and immunity",
"journal_volume": "10",
"journal_issue": "4",
"journal_pages": "957-9",
"pub_year": "1974",
"pubmed_id": "4609913"
},
{
"title": "Transduction of a streptomycin R-factor from Mycobacterium smegmatis to Mycobacterium tuberculosis H37Rv.",
"abstract": "",
"full_author_list": "W D Jones, R E Beam, H L David",
"short_author_list": "Jones WD, Beam RE, David HL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4220076",
"journal": "Tubercle",
"journal_volume": "55",
"journal_issue": "1",
"journal_pages": "73-80",
"pub_year": "1974",
"pubmed_id": "4220076"
},
{
"title": "Partially carbon coated support films--qualities and application.",
"abstract": "",
"full_author_list": "H Kölbel",
"short_author_list": "Kölbel H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4444773",
"journal": "Mikroskopie",
"journal_volume": "30",
"journal_issue": "7-8",
"journal_pages": "208-14",
"pub_year": "1974",
"pubmed_id": "4444773"
},
{
"title": "[Mycobacterial phages. II. Identification of an additional collection of mycobacteriophages by antigenic properties, morphology and sensitivity to inactivating agents]",
"abstract": "",
"full_author_list": "L A Kosobutski?",
"short_author_list": "Kosobutski? LA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4454811",
"journal": "Zhurnal mikrobiologii, epidemiologii, i immunobiologii",
"journal_volume": "",
"journal_issue": "1",
"journal_pages": "136-7",
"pub_year": "1974",
"pubmed_id": "4454811"
},
{
"title": "[Experimental tuberculous infection produced by the system phage-Mycobacterium]",
"abstract": "",
"full_author_list": "L A Kosobutski?, G I Sharov, A A Balakleevskaia",
"short_author_list": "Kosobutski? LA, Sharov GI, Balakleevskaia AA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4211266",
"journal": "Problemy tuberkuleza",
"journal_volume": "52",
"journal_issue": "5",
"journal_pages": "63-7",
"pub_year": "1974",
"pubmed_id": "4211266"
},
{
"title": "Changes in the lytic spectrum and antigenic properties of mycobacteriophages after passages on Mycobacterium tuberculosis and other mycobacteria.",
"abstract": "",
"full_author_list": "L A Kosobutsky",
"short_author_list": "Kosobutsky LA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4139192",
"journal": "Journal of hygiene, epidemiology, microbiology, and immunology",
"journal_volume": "18",
"journal_issue": "1",
"journal_pages": "42-9",
"pub_year": "1974",
"pubmed_id": "4139192"
},
{
"title": "[Biological properties of mycobacteriophages]",
"abstract": "",
"full_author_list": "B N Koz'min-Sokolov, A Aminov, G P Petrova",
"short_author_list": "Koz'min-Sokolov BN, Aminov A, Petrova GP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4208500",
"journal": "Zhurnal mikrobiologii, epidemiologii, i immunobiologii",
"journal_volume": "51",
"journal_issue": "4",
"journal_pages": "80-5",
"pub_year": "1974",
"pubmed_id": "4208500"
},
{
"title": "The effect of mycobacteriophage particles on cell-mediated immune reactions.",
"abstract": "",
"full_author_list": "E Mankiewicz, V Kurti, H Adomonis",
"short_author_list": "Mankiewicz E, Kurti V, Adomonis H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4419553",
"journal": "Canadian journal of microbiology",
"journal_volume": "20",
"journal_issue": "9",
"journal_pages": "1209-18",
"pub_year": "1974",
"pubmed_id": "4419553"
},
{
"title": "Bacteriophage typing of Mycobacterium ranae (Fortuitum). The use of unadapted and adapted phages in the development of a typing system.",
"abstract": "",
"full_author_list": "G Nordström, J M Grange",
"short_author_list": "Nordström G, Grange JM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4208335",
"journal": "Acta pathologica et microbiologica Scandinavica. Section B: Microbiology and immunology",
"journal_volume": "82",
"journal_issue": "1",
"journal_pages": "87-93",
"pub_year": "1974",
"pubmed_id": "4208335"
},
{
"title": "[Combined application of mycobacteriophages and tubazid in experimental tuberculosis]",
"abstract": "",
"full_author_list": "G I Sharov, S I Gel'berg, V S Peschanski?",
"short_author_list": "Sharov GI, Gel'berg SI, Peschanski? VS",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4445140",
"journal": "Problemy tuberkuleza",
"journal_volume": "",
"journal_issue": "12",
"journal_pages": "67-71",
"pub_year": "1974",
"pubmed_id": "4445140"
},
{
"title": "Properties of mycobacteriophage DS6A. II. Lipid composition.",
"abstract": "",
"full_author_list": "B U Bowman, H A Newman, J M Moritz, R M Koehler",
"short_author_list": "Bowman BU et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4630313",
"journal": "The American review of respiratory disease",
"journal_volume": "107",
"journal_issue": "1",
"journal_pages": "42-9",
"pub_year": "1973",
"pubmed_id": "4630313"
},
{
"title": "Response of Mycobacteria to ultraviolet light radiation.",
"abstract": "",
"full_author_list": "H L David",
"short_author_list": "David HL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4201017",
"journal": "The American review of respiratory disease",
"journal_volume": "108",
"journal_issue": "5",
"journal_pages": "1175-85",
"pub_year": "1973",
"pubmed_id": "4201017"
},
{
"title": "Pathogenicity as the main differentiating character within the avium-intracellulare complex.",
"abstract": "",
"full_author_list": "H W Engel",
"short_author_list": "Engel HW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4198563",
"journal": "Annales de la Société belge de médecine tropicale",
"journal_volume": "53",
"journal_issue": "4",
"journal_pages": "275-86",
"pub_year": "1973",
"pubmed_id": "4198563"
},
{
"title": "Partial characterization of mycobacteriophage R1 particles surviving chloroform treatment.",
"abstract": "",
"full_author_list": "M A Fleer, B U Bowman",
"short_author_list": "Fleer MA, Bowman BU",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4735384",
"journal": "Microbios",
"journal_volume": "7",
"journal_issue": "25",
"journal_pages": "37-44",
"pub_year": "1973",
"pubmed_id": "4735384"
},
{
"title": "Transduction in mycobacterium phlei.",
"abstract": "",
"full_author_list": "S M Gelbart, S E Juhasz",
"short_author_list": "Gelbart SM, Juhasz SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4540257",
"journal": "Antonie van Leeuwenhoek",
"journal_volume": "39",
"journal_issue": "1",
"journal_pages": "1-10",
"pub_year": "1973",
"pubmed_id": "4540257"
},
{
"title": "Intra-specific variation in the mycobacteria. A taxonomic aid.",
"abstract": "",
"full_author_list": "J M Grange",
"short_author_list": "Grange JM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4198568",
"journal": "Annales de la Société belge de médecine tropicale",
"journal_volume": "53",
"journal_issue": "4",
"journal_pages": "339-46",
"pub_year": "1973",
"pubmed_id": "4198568"
},
{
"title": "Bacteriophage typing of Mycobacterium ranae (Fortuitum). The correlation of lysis by mycobacteriophage BK4 and inositol utilisation.",
"abstract": "",
"full_author_list": "J M Grange, G Nordstrom",
"short_author_list": "Grange JM, Nordstrom G",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4203240",
"journal": "Acta pathologica et microbiologica Scandinavica. Section B: Microbiology and immunology",
"journal_volume": "81",
"journal_issue": "4",
"journal_pages": "408-12",
"pub_year": "1973",
"pubmed_id": "4203240"
},
{
"title": "Studies on the bacteriophage of a natural lysogenic Mycobacterium fortuitum.",
"abstract": "",
"full_author_list": "W D Jones",
"short_author_list": "Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4201632",
"journal": "The American review of respiratory disease",
"journal_volume": "108",
"journal_issue": "6",
"journal_pages": "1438-41",
"pub_year": "1973",
"pubmed_id": "4201632"
},
{
"title": "[Studies on the identification of infection source for pulmonary tuberculosis in family using bacteriophage types as a marker. I. Experimental studies on phage typing of M. tuberculosis]",
"abstract": "",
"full_author_list": "K Kitahara",
"short_author_list": "Kitahara K",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4632269",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "48",
"journal_issue": "1",
"journal_pages": "9-15",
"pub_year": "1973",
"pubmed_id": "4632269"
},
{
"title": "Mode of action of kanamycin on Mycobacterium bovis BCG.",
"abstract": "",
"full_author_list": "K Konno, K Oizumi, N Kumano, S Oka",
"short_author_list": "Konno K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4577267",
"journal": "The American review of respiratory disease",
"journal_volume": "108",
"journal_issue": "1",
"journal_pages": "101-7",
"pub_year": "1973",
"pubmed_id": "4577267"
},
{
"title": "[Inactivation of mycobacterial phages by some antineoplastic agents and antibiotics]",
"abstract": "",
"full_author_list": "L A Kosobutski?",
"short_author_list": "Kosobutski? LA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4776409",
"journal": "Antibiotiki",
"journal_volume": "18",
"journal_issue": "8",
"journal_pages": "731-4",
"pub_year": "1973",
"pubmed_id": "4776409"
},
{
"title": "A comparison of three mycobacteriophages.",
"abstract": "",
"full_author_list": "J P Kraiss, S M Gelbart, S E Juhasz",
"short_author_list": "Kraiss JP, Gelbart SM, Juhasz SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4796280",
"journal": "The Journal of general virology",
"journal_volume": "20",
"journal_issue": "1",
"journal_pages": "75-87",
"pub_year": "1973",
"pubmed_id": "4796280"
},
{
"title": "[Comparison of phage susceptibility of Mycobacterium tuberculosis isolated from patients in Japan, Netherland and Ceylon]",
"abstract": "",
"full_author_list": "Y Mizuguchi, Y Maruyama, K Suga, T Murohashi",
"short_author_list": "Mizuguchi Y et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4732084",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "48",
"journal_issue": "6",
"journal_pages": "219-25",
"pub_year": "1973",
"pubmed_id": "4732084"
},
{
"title": "[Determination of mycobacteriophages in manure and sewage]",
"abstract": "",
"full_author_list": "V A Polkhovski?",
"short_author_list": "Polkhovski? VA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4218918",
"journal": "Veterinariia",
"journal_volume": "",
"journal_issue": "4",
"journal_pages": "31-3",
"pub_year": "1973",
"pubmed_id": "4218918"
},
{
"title": "[Methods of isolation of mycobacteriophages]",
"abstract": "",
"full_author_list": "V A Polkhovski?",
"short_author_list": "Polkhovski? VA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4203380",
"journal": "Problemy tuberkuleza",
"journal_volume": "51",
"journal_issue": "7",
"journal_pages": "73-6",
"pub_year": "1973",
"pubmed_id": "4203380"
},
{
"title": "Exogenous reinfection with Mycobacterium tuberculosis confirmed by phage typing.",
"abstract": "",
"full_author_list": "J W Raleigh, R Wichelhausen",
"short_author_list": "Raleigh JW, Wichelhausen R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4200815",
"journal": "The American review of respiratory disease",
"journal_volume": "108",
"journal_issue": "3",
"journal_pages": "639-42",
"pub_year": "1973",
"pubmed_id": "4200815"
},
{
"title": "[Effect of mycobacteriophages on the specific activity of BCG vaccine in an experiment]",
"abstract": "",
"full_author_list": "G I Sharov, S I Gel'berg",
"short_author_list": "Sharov GI, Gel'berg SI",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4584752",
"journal": "Problemy tuberkuleza",
"journal_volume": "51",
"journal_issue": "8",
"journal_pages": "70-3",
"pub_year": "1973",
"pubmed_id": "4584752"
},
{
"title": "Further studies on the inactivation of mycobacteriophage D29 by chloroform.",
"abstract": "",
"full_author_list": "M B Shay, B U Bowman",
"short_author_list": "Shay MB, Bowman BU",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4583540",
"journal": "The American review of respiratory disease",
"journal_volume": "108",
"journal_issue": "5",
"journal_pages": "1248-52",
"pub_year": "1973",
"pubmed_id": "4583540"
},
{
"title": "WHO cooperative studies on the phage-typing of mycobacteria. 1. Phage lysis of Czechoslovak and Italian strains of Mycobacterium tuberculosis.",
"abstract": "",
"full_author_list": "L Sula, W B Redmond, J F Coster, I Baess, J H Bates, G Caroli, E Mankiewicz, T Murohashi, E Vandra",
"short_author_list": "Sula L et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4196836",
"journal": "Bulletin of the World Health Organization",
"journal_volume": "48",
"journal_issue": "1",
"journal_pages": "57-63",
"pub_year": "1973",
"pubmed_id": "4196836"
},
{
"title": "The direct demonstration of phage microlysis in thin sections of colonies of argentinian Mycobacterium bovis strains.",
"abstract": "",
"full_author_list": "L Sula, J Sulová, M Spurná",
"short_author_list": "Sula L, Sulová J, Spurná M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4146828",
"journal": "Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene. Erste Abteilung O",
"journal_volume": "223",
"journal_issue": "4",
"journal_pages": "520-32",
"pub_year": "1973",
"pubmed_id": "4146828"
},
{
"title": "Failure to produce experimental sarcoidosis in guinea pigs with Mycobacterium tuberculosis and mycobacteriophage DS6A.",
"abstract": "",
"full_author_list": "B U Bowman, W T Amos, J C Geer",
"short_author_list": "Bowman BU, Amos WT, Geer JC",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4621424",
"journal": "The American review of respiratory disease",
"journal_volume": "105",
"journal_issue": "1",
"journal_pages": "85-94",
"pub_year": "1972",
"pubmed_id": "4621424"
},
{
"title": "Ultrastructure of some mycobacteriophages.",
"abstract": "",
"full_author_list": "M Buraczewska, B Kwiatkowski, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5007614",
"journal": "The American review of respiratory disease",
"journal_volume": "105",
"journal_issue": "1",
"journal_pages": "22-9",
"pub_year": "1972",
"pubmed_id": "5007614"
},
{
"title": "Nature of the receptor substance of Mycobacterium smegmatis for D4 bacteriophage adsorption.",
"abstract": "The acetone-soluble fraction extracted from lyophilized cells of Mycobacterium smegmatis ATCC 607 inhibited D4, a species-specific phage active against M. smegmatis. Evidence is presented indicating that the D4 inhibition was caused by the phage receptor substance(s) contained in this fraction. A fraction eluted from silicic acid with chloroform-methanol (95:5, v/v) showed the strongest inhibition of D4 phage. This fraction contained sugars and amino acids, and its infrared absorption spectrum was practically identical with those of the mycoside C isolated from the other species of mycobacteria. Further fractionation revealed that the active material was a mixture of several closely related peptidoglycolipids all of which showed, more or less, the phage inhibition. One of the compounds was purified and partially characterized; it contains three different amino acids, allo-threonine, alanine, and phenylalanine, at a molar ratio of 1:1:1, and also three different deoxyhexoses, probably 6-deoxytalose, 3,4-di-o-methylrhamnose, and 2,3,4-tri-o-methylrhamnose. A tentative name of \"mycoside C(sm)\" is proposed for this substance which possesses a slightly different structure from the known types of mycoside C and is probably specific for the species of M. smegmatis. A fraction extracted from the D4-resistant mutant of M. smegmatis ATCC 607 by acetone and then by chloroform-methanol (95:5, v/v) showed no phage inhibition and had no sugar component. In addition, this fraction contained lysine, serine, and a small amount of both glycine and an unidentified amino acid.",
"full_author_list": "A Furuchi, T Tokunaga",
"short_author_list": "Furuchi A, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5053464",
"journal": "Journal of bacteriology",
"journal_volume": "111",
"journal_issue": "2",
"journal_pages": "404-11",
"pub_year": "1972",
"pubmed_id": "5053464"
},
{
"title": "Mycosides C: behavior as receptor site substance for mycobacteriophage D4.",
"abstract": "Interpretation of an earlier published infrared spectrum of Mycobacterium smegmatis lipids with receptor site activity for D4 phage led us to the inference that the active substance is very likely a mycoside C. This hypothesis was confirmed: the well-characterized mycosides C(s) and C(1217) elaborated by the heterologous strains M. scrofulaceum and Mycobacterium species 1217, respectively, are essentially indistinguishable from the smegmatis lipids in their behavior toward D4. Minute quantities adsorb and extensively inactivate the phage on appropriate incubations. In accord with derivative expectations, Mycobacterium species 1217 is a permissive host, attacked and lysed by D4. However, our current strains of M. butyricum, M. avium, and M. scrofulaceum, which reputedly produce various related mycosides C, are neither lysed by nor do they significantly adsorb the phage. Implications of these observations are discussed.",
"full_author_list": "M B Goren, J K McClatchy, B Martens, O Brokl",
"short_author_list": "Goren MB et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4113889",
"journal": "Journal of virology",
"journal_volume": "9",
"journal_issue": "6",
"journal_pages": "999-1003",
"pub_year": "1972",
"pubmed_id": "4113889"
},
{
"title": "Characterization and mycobacteriophage typing of Mycobacterium xenopi.",
"abstract": "",
"full_author_list": "J J Gunnels, J H Bates",
"short_author_list": "Gunnels JJ, Bates JH",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4551828",
"journal": "The American review of respiratory disease",
"journal_volume": "105",
"journal_issue": "3",
"journal_pages": "388-92",
"pub_year": "1972",
"pubmed_id": "4551828"
},
{
"title": "[Bacteriophage typing of Mycobacterium tuberculosis]",
"abstract": "",
"full_author_list": "H Ionesco",
"short_author_list": "Ionesco H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4196469",
"journal": "Revue de tuberculose et de pneumologie",
"journal_volume": "36",
"journal_issue": "6",
"journal_pages": "917-21",
"pub_year": "1972",
"pubmed_id": "4196469"
},
{
"title": "Preliminary observations on the occurrence of a streptomycin R-factor in Mycobacterium smegmatis ATCC 607.",
"abstract": "",
"full_author_list": "W D Jones, H L David",
"short_author_list": "Jones WD, David HL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5038198",
"journal": "Tubercle",
"journal_volume": "53",
"journal_issue": "1",
"journal_pages": "35-42",
"pub_year": "1972",
"pubmed_id": "5038198"
},
{
"title": "[Influence of various support films on image size and contrast of thin-sectioned biological objects in electron microscopy]",
"abstract": "",
"full_author_list": "H K Kölbel",
"short_author_list": "Kölbel HK",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4567572",
"journal": "Mikroskopie",
"journal_volume": "27",
"journal_issue": "7",
"journal_pages": "202-21",
"pub_year": "1972",
"pubmed_id": "4567572"
},
{
"title": "[Isolation of mycobacteriophages from the external environment]",
"abstract": "",
"full_author_list": "B N Koz'min-Sokolov",
"short_author_list": "Koz'min-Sokolov BN",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4124516",
"journal": "Laboratornoe delo",
"journal_volume": "10",
"journal_issue": "",
"journal_pages": "623-4",
"pub_year": "1972",
"pubmed_id": "4124516"
},
{
"title": "Structure of a transducing mycobacteriophage.",
"abstract": "Electron micrographs of the transducing phage I3 for Mycobacterium smegmatis strain SN2 revealed a phage with a contractile tail and a head with isometric symmetry and visible capsomeres.",
"full_author_list": "L M Kozloff, C V Sundar Raj, R N Rao, V A Chapman, S DeLong",
"short_author_list": "Kozloff LM et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5014933",
"journal": "Journal of virology",
"journal_volume": "9",
"journal_issue": "2",
"journal_pages": "390-3",
"pub_year": "1972",
"pubmed_id": "5014933"
},
{
"title": "A co-operative numerical analysis of rapidly growing mycobacteria.",
"abstract": "",
"full_author_list": "G P Kubica, I Baess, R E Gordon, P A Jenkins, J B Kwapinski, C McDurmont, S R Pattyn, H Saito, V Silcox, J L Stanford, K Takeya, M Tsukamura",
"short_author_list": "Kubica GP et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4653958",
"journal": "Journal of general microbiology",
"journal_volume": "73",
"journal_issue": "1",
"journal_pages": "55-70",
"pub_year": "1972",
"pubmed_id": "4653958"
},
{
"title": "Bacteriophage types of mycobacteria.",
"abstract": "",
"full_author_list": "E Mankiewicz",
"short_author_list": "Mankiewicz E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4627149",
"journal": "Canadian journal of public health. Revue canadienne de santé publique",
"journal_volume": "63",
"journal_issue": "4",
"journal_pages": "342-54",
"pub_year": "1972",
"pubmed_id": "4627149"
},
{
"title": "Lysogeny and deoxyribonuclease production in mycobacteria.",
"abstract": "",
"full_author_list": "E Mankiewicz, M G Tamari",
"short_author_list": "Mankiewicz E, Tamari MG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5077781",
"journal": "The American review of respiratory disease",
"journal_volume": "106",
"journal_issue": "4",
"journal_pages": "609-10",
"pub_year": "1972",
"pubmed_id": "5077781"
},
{
"title": "Segregation of unselected markers in mycobacterial recombinants.",
"abstract": "",
"full_author_list": "Y Mizuguchi",
"short_author_list": "Mizuguchi Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4538371",
"journal": "Japanese journal of microbiology",
"journal_volume": "16",
"journal_issue": "2",
"journal_pages": "77-81",
"pub_year": "1972",
"pubmed_id": "4538371"
},
{
"title": "Eagle's basal medium as a defined medium for Mycoplasma studies.",
"abstract": "",
"full_author_list": "D C Quinlan, A Liss, J Maniloff",
"short_author_list": "Quinlan DC, Liss A, Maniloff J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4571002",
"journal": "Microbios",
"journal_volume": "6",
"journal_issue": "22",
"journal_pages": "179-85",
"pub_year": "1972",
"pubmed_id": "4571002"
},
{
"title": "Isolation from media of two bacteriophages, protamylase-H37Rv (PH) active against Mycobacterium tuberculosis.",
"abstract": "",
"full_author_list": "K Sushida, N Hirano",
"short_author_list": "Sushida K, Hirano N",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4626101",
"journal": "The American review of respiratory disease",
"journal_volume": "106",
"journal_issue": "2",
"journal_pages": "269-71",
"pub_year": "1972",
"pubmed_id": "4626101"
},
{
"title": "[Bacteriophage receptor--cell surface structure of the bacteria as the site of gene acceptance]",
"abstract": "",
"full_author_list": "T Tokunaga",
"short_author_list": "Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4265206",
"journal": "Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme",
"journal_volume": "17",
"journal_issue": "9",
"journal_pages": "692-703",
"pub_year": "1972",
"pubmed_id": "4265206"
},
{
"title": "Report on a pseudolysogenic mycobacterium and a review of the literature concerning pseudolysogeny.",
"abstract": "",
"full_author_list": "I Baess",
"short_author_list": "Baess I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5283061",
"journal": "Acta pathologica et microbiologica Scandinavica. Section B: Microbiology and immunology",
"journal_volume": "79",
"journal_issue": "3",
"journal_pages": "428-34",
"pub_year": "1971",
"pubmed_id": "5283061"
},
{
"title": "Further evidence against the concept of decreased phage neutralizing ability of serum of patients with sarcoidosis.",
"abstract": "",
"full_author_list": "B U Bowman, T M Daniel",
"short_author_list": "Bowman BU, Daniel TM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5125591",
"journal": "The American review of respiratory disease",
"journal_volume": "104",
"journal_issue": "6",
"journal_pages": "908-14",
"pub_year": "1971",
"pubmed_id": "5125591"
},
{
"title": "Induction of phages from lysogenic mycobacteria by means of ultraveiolet irradiation.",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5125183",
"journal": "The American review of respiratory disease",
"journal_volume": "104",
"journal_issue": "5",
"journal_pages": "760-2",
"pub_year": "1971",
"pubmed_id": "5125183"
},
{
"title": "Studies on mycobacteriophages. Lytic properties of mycobacterophages 33-D isolated from lysogenic bacilli.",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4995672",
"journal": "Polish medical journal",
"journal_volume": "10",
"journal_issue": "1",
"journal_pages": "92-5",
"pub_year": "1971",
"pubmed_id": "4995672"
},
{
"title": "A quick method for differentiating between virulent bovine and attenuated BCG bacilli.",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4992689",
"journal": "The American review of respiratory disease",
"journal_volume": "103",
"journal_issue": "1",
"journal_pages": "116-7",
"pub_year": "1971",
"pubmed_id": "4992689"
},
{
"title": "Selective mycobacteriophage isolation with membrane filters.",
"abstract": "A simple technique is described whereby mycobacteriophages are selectively isolated by adsorption on mycobacteria layered within membrane filter sandwiches before standard enrichment procedures.",
"full_author_list": "J Grant",
"short_author_list": "Grant J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4998350",
"journal": "Applied microbiology",
"journal_volume": "21",
"journal_issue": "6",
"journal_pages": "1091",
"pub_year": "1971",
"pubmed_id": "4998350"
},
{
"title": "Inhibition by fifampin of mycobacteriophage D29 replication in its drug-resistant host, Mycobacterium smergmatis ATCC 607.",
"abstract": "",
"full_author_list": "W D Jones, H L David",
"short_author_list": "Jones WD, David HL",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5579905",
"journal": "The American review of respiratory disease",
"journal_volume": "103",
"journal_issue": "5",
"journal_pages": "618-24",
"pub_year": "1971",
"pubmed_id": "5579905"
},
{
"title": "[Investigations on the morphological characterization of some mycobacteril phages]",
"abstract": "",
"full_author_list": "H K Kölbel, H Mohelska",
"short_author_list": "Kölbel HK, Mohelska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5572052",
"journal": "Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene. Erste Abteilung O",
"journal_volume": "217",
"journal_issue": "4",
"journal_pages": "507-28",
"pub_year": "1971",
"pubmed_id": "5572052"
},
{
"title": "[Mycobacteriophages. I. Morphology and antigen properties of some mycophages]",
"abstract": "",
"full_author_list": "L A Kosobutski?",
"short_author_list": "Kosobutski? LA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5553631",
"journal": "Zhurnal mikrobiologii, epidemiologii, i immunobiologii",
"journal_volume": "48",
"journal_issue": "1",
"journal_pages": "79-84",
"pub_year": "1971",
"pubmed_id": "5553631"
},
{
"title": "[Detection of mycobacteriophages in tuberculosis and sarcoidosis patients]",
"abstract": "",
"full_author_list": "B N Koz'min-Sokolov, Z I Kostina",
"short_author_list": "Koz'min-Sokolov BN, Kostina ZI",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5159694",
"journal": "Problemy tuberkuleza",
"journal_volume": "49",
"journal_issue": "12",
"journal_pages": "74-5",
"pub_year": "1971",
"pubmed_id": "5159694"
},
{
"title": "Diagnostic procedures in sarcoidosis.",
"abstract": "One hundred consecutive patients suspected of having sarcoidosis were examined by means of available diagnostic procedures and the results of the examinations were compared. While Kveim tests and/or lymphocyte transformation tests gave the most significant results in cases of less than two years' standing, a combination of these and organ biopsies is required for the diagnosis of cases of more than two years' duration.An interpretation of the immunological deviations observed in sarcoidosis is attempted on the basis of observations made on leukocyte cultures and on isolations of mycobacteriophages from patients with sarcoidosis.",
"full_author_list": "E Mankiewicz, V Kurti, J Béland",
"short_author_list": "Mankiewicz E, Kurti V, Béland J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5550375",
"journal": "Canadian Medical Association journal",
"journal_volume": "104",
"journal_issue": "8",
"journal_pages": "684-90",
"pub_year": "1971",
"pubmed_id": "5550375"
},
{
"title": "Preparation of high-titer mycobacteriophage lysates and phage deoxyribonucleic acid.",
"abstract": "",
"full_author_list": "E Mankiewicz, M G Tamari",
"short_author_list": "Mankiewicz E, Tamari MG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4932945",
"journal": "The American review of respiratory disease",
"journal_volume": "103",
"journal_issue": "6",
"journal_pages": "850-2",
"pub_year": "1971",
"pubmed_id": "4932945"
},
{
"title": "The fluorescent staining of a mycobacteriophage (C2) nucleic acid.",
"abstract": "",
"full_author_list": "J Menezes",
"short_author_list": "Menezes J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4100955",
"journal": "Canadian journal of microbiology",
"journal_volume": "17",
"journal_issue": "2",
"journal_pages": "171-4",
"pub_year": "1971",
"pubmed_id": "4100955"
},
{
"title": "Mycobacteriophage in Crohn's disease.",
"abstract": "Numerous similarities between Crohn's disease and sarcoidosis are being reported. Because of previous findings of culturable mycobacteriophage in the serum of many patients with sarcoidosis, mycobacteriophages were sought in serum of patients with Crohn's disease. No difference was found in the frequency of positive cultures between patients with Crohn's disease and normal control subjects.",
"full_author_list": "K Parent, I D Wilson",
"short_author_list": "Parent K, Wilson ID",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5157132",
"journal": "Gut",
"journal_volume": "12",
"journal_issue": "12",
"journal_pages": "1019-20",
"pub_year": "1971",
"pubmed_id": "5157132"
},
{
"title": "Specific immunosuppression, polyinosinic--polycytidylic acid, and viruses in New Zealand mice.",
"abstract": "",
"full_author_list": "N Talal, A D Steinberg, A F Gazdar",
"short_author_list": "Talal N, Steinberg AD, Gazdar AF",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4330992",
"journal": "Federation proceedings",
"journal_volume": "30",
"journal_issue": "6",
"journal_pages": "1842-5",
"pub_year": "1971",
"pubmed_id": "4330992"
},
{
"title": "Phage typing of Mycobacterium tuberculosis strains isolated in Hungary.",
"abstract": "",
"full_author_list": "E Vandra, T Fodor",
"short_author_list": "Vandra E, Fodor T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5005045",
"journal": "Acta microbiologica Academiae Scientiarum Hungaricae",
"journal_volume": "18",
"journal_issue": "3",
"journal_pages": "155-8",
"pub_year": "1971",
"pubmed_id": "5005045"
},
{
"title": "Further exploratory studies in sarcoidosis. An epidemiologic investigation to compare the prevalence of tuberculosis infection and-or disease among contacts of matched sarcoidosis and asthmatic patients.",
"abstract": "",
"full_author_list": "M H Zaki, J R Addrizzo, J M Patton, J J Murphy",
"short_author_list": "Zaki MH et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4994460",
"journal": "The American review of respiratory disease",
"journal_volume": "103",
"journal_issue": "4",
"journal_pages": "539-45",
"pub_year": "1971",
"pubmed_id": "4994460"
},
{
"title": "[Influence of lysogenization on the enzyme-formation of mycobacteria]",
"abstract": "",
"full_author_list": "R Bönicke, S E Juhasz",
"short_author_list": "Bönicke R, Juhasz SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5497309",
"journal": "Pneumonologie. Pneumonology",
"journal_volume": "142",
"journal_issue": "2",
"journal_pages": "273-8",
"pub_year": "1970",
"pubmed_id": "5497309"
},
{
"title": "Phage conversion of biochemical properties in the genus Mycobacterium.",
"abstract": "",
"full_author_list": "R Bönicke, H Saito",
"short_author_list": "Bönicke R, Saito H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5425546",
"journal": "Bulletin of the International Union against Tuberculosis",
"journal_volume": "43",
"journal_issue": "",
"journal_pages": "217-25",
"pub_year": "1970",
"pubmed_id": "5425546"
},
{
"title": "[Mycobacteriophages and the possibility of their use in the diagnosis of tuberculosis]",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5420814",
"journal": "Polski tygodnik lekarski (Warsaw, Poland : 1960)",
"journal_volume": "25",
"journal_issue": "10",
"journal_pages": "366-8",
"pub_year": "1970",
"pubmed_id": "5420814"
},
{
"title": "[Studies on mycobacteriophages. Lytic properties of mycobacteriophages 33-D isolated from lysogenic bacilli]",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4913879",
"journal": "Gru?lica i choroby p?uc; tuberculosis et pneumonologia",
"journal_volume": "38",
"journal_issue": "6",
"journal_pages": "493-6",
"pub_year": "1970",
"pubmed_id": "4913879"
},
{
"title": "[Antigens of a mycobacteriophage: Phlei phage]",
"abstract": "",
"full_author_list": "G Castelnuovo, G Bellezza, F Borrelli",
"short_author_list": "Castelnuovo G, Bellezza G, Borrelli F",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4984612",
"journal": "Annales de l'Institut Pasteur",
"journal_volume": "118",
"journal_issue": "2",
"journal_pages": "214-9",
"pub_year": "1970",
"pubmed_id": "4984612"
},
{
"title": "Phage inhibiting substances of mycobacteria. I. The nature of phage inhibiting substances of Mycobacterium phlei.",
"abstract": "",
"full_author_list": "G Castelnuovo, G Bellezza, S Yamanaka",
"short_author_list": "Castelnuovo G, Bellezza G, Yamanaka S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5478543",
"journal": "Annales de l'Institut Pasteur",
"journal_volume": "119",
"journal_issue": "3",
"journal_pages": "302-11",
"pub_year": "1970",
"pubmed_id": "5478543"
},
{
"title": "[Bacteriophagic conversion in rapid growing mycobacteria after \"curing\" and lysogenization]",
"abstract": "",
"full_author_list": "B Damsker, S Sonea",
"short_author_list": "Damsker B, Sonea S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5513575",
"journal": "Revue canadienne de biologie / éditée par l'Université de Montréal",
"journal_volume": "29",
"journal_issue": "4",
"journal_pages": "331-8",
"pub_year": "1970",
"pubmed_id": "5513575"
},
{
"title": "Biosynthesis of a lipase by Mycobacterium smegmatis ATCC 607 infected by Mycobacteriophage D29.",
"abstract": "",
"full_author_list": "H L David, W D Jones",
"short_author_list": "David HL, Jones WD",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5475680",
"journal": "The American review of respiratory disease",
"journal_volume": "102",
"journal_issue": "5",
"journal_pages": "818-20",
"pub_year": "1970",
"pubmed_id": "5475680"
},
{
"title": "Critical studies of phage typing as an aid for the identification of mycobacteria.",
"abstract": "",
"full_author_list": "S Dernuet",
"short_author_list": "Dernuet S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5480712",
"journal": "Canadian journal of medical technology",
"journal_volume": "32",
"journal_issue": "5",
"journal_pages": "165-87",
"pub_year": "1970",
"pubmed_id": "5480712"
},
{
"title": "Genetic transfer in Mycobacterium phlei.",
"abstract": "",
"full_author_list": "S M Gelbart, S E Juhasz",
"short_author_list": "Gelbart SM, Juhasz SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5516453",
"journal": "Journal of general microbiology",
"journal_volume": "64",
"journal_issue": "2",
"journal_pages": "253-4",
"pub_year": "1970",
"pubmed_id": "5516453"
},
{
"title": "A special case of lysogeny in Mycobacterium avium.",
"abstract": "",
"full_author_list": "J Hubácek, H Kupková, H Mohelská",
"short_author_list": "Hubácek J, Kupková H, Mohelská H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5480309",
"journal": "Folia microbiologica",
"journal_volume": "15",
"journal_issue": "5",
"journal_pages": "341-6",
"pub_year": "1970",
"pubmed_id": "5480309"
},
{
"title": "The occurrence of lipids in Mycobacteriophage D29 propagated in Mycobacterium smegmatis ATCC 607.",
"abstract": "",
"full_author_list": "W D Jones, H L David, R E Beam",
"short_author_list": "Jones WD, David HL, Beam RE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5475679",
"journal": "The American review of respiratory disease",
"journal_volume": "102",
"journal_issue": "5",
"journal_pages": "814-7",
"pub_year": "1970",
"pubmed_id": "5475679"
},
{
"title": "Phage-associated mycobacterial variation.",
"abstract": "",
"full_author_list": "S E Juhasz",
"short_author_list": "Juhasz SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5278146",
"journal": "Annals of the New York Academy of Sciences",
"journal_volume": "174",
"journal_issue": "2",
"journal_pages": "847-51",
"pub_year": "1970",
"pubmed_id": "5278146"
},
{
"title": "The role of bacteriophage in mycobacterial variation.",
"abstract": "",
"full_author_list": "S E Juhasz",
"short_author_list": "Juhasz SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5425547",
"journal": "Bulletin of the International Union against Tuberculosis",
"journal_volume": "43",
"journal_issue": "",
"journal_pages": "226-8",
"pub_year": "1970",
"pubmed_id": "5425547"
},
{
"title": "Genetic interaction in mycobacterial host-phage system. The effect of lysogeny on the phage.",
"abstract": "",
"full_author_list": "S E Juhasz, R Bönicke",
"short_author_list": "Juhasz SE, Bönicke R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5497302",
"journal": "Pneumonologie. Pneumonology",
"journal_volume": "142",
"journal_issue": "2",
"journal_pages": "181-90",
"pub_year": "1970",
"pubmed_id": "5497302"
},
{
"title": "[The substrate of the variability of mycobacteria as seen in the electron microscope]",
"abstract": "",
"full_author_list": "H Kölbel",
"short_author_list": "Kölbel H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5497299",
"journal": "Pneumonologie. Pneumonology",
"journal_volume": "142",
"journal_issue": "2",
"journal_pages": "137-58",
"pub_year": "1970",
"pubmed_id": "5497299"
},
{
"title": "A specific type of organism cultivated from malignancy: bacteriology and proposed classification.",
"abstract": "",
"full_author_list": "V W Livingston, E Alexander-Jackson",
"short_author_list": "Livingston VW, Alexander-Jackson E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5278140",
"journal": "Annals of the New York Academy of Sciences",
"journal_volume": "174",
"journal_issue": "2",
"journal_pages": "636-54",
"pub_year": "1970",
"pubmed_id": "5278140"
},
{
"title": "Host-cell determined variations in mycobacteriophages.",
"abstract": "",
"full_author_list": "E Mankiewicz",
"short_author_list": "Mankiewicz E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5497304",
"journal": "Pneumonologie. Pneumonology",
"journal_volume": "142",
"journal_issue": "2",
"journal_pages": "198-9",
"pub_year": "1970",
"pubmed_id": "5497304"
},
{
"title": "Transduction in Mycobacterium smegmatis.",
"abstract": "",
"full_author_list": "C V Raj, T Ramakrishnan",
"short_author_list": "Raj CV, Ramakrishnan T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5479524",
"journal": "Nature",
"journal_volume": "228",
"journal_issue": "5268",
"journal_pages": "280-1",
"pub_year": "1970",
"pubmed_id": "5479524"
},
{
"title": "Mycobacterial variations as influenced by phage and other genomic factors.",
"abstract": "",
"full_author_list": "W B Redmond",
"short_author_list": "Redmond WB",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5497303",
"journal": "Pneumonologie. Pneumonology",
"journal_volume": "142",
"journal_issue": "2",
"journal_pages": "191-7",
"pub_year": "1970",
"pubmed_id": "5497303"
},
{
"title": "Infectious mycobacteriophage nucleic acids.",
"abstract": "",
"full_author_list": "M I Sellers",
"short_author_list": "Sellers MI",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5497305",
"journal": "Pneumonologie. Pneumonology",
"journal_volume": "142",
"journal_issue": "2",
"journal_pages": "200-9",
"pub_year": "1970",
"pubmed_id": "5497305"
},
{
"title": "The effects of ultraviolet irradiation on mycobacteriophages and their infectious DNAs.",
"abstract": "",
"full_author_list": "M I Sellers, R Nakamura, T Tokunaga",
"short_author_list": "Sellers MI, Nakamura R, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4953044",
"journal": "The Journal of general virology",
"journal_volume": "7",
"journal_issue": "3",
"journal_pages": "233-47",
"pub_year": "1970",
"pubmed_id": "4953044"
},
{
"title": "[Isolation of bacteriophage of tubercle bacilli (H37Rv) by addition of protamilase and buillon]",
"abstract": "",
"full_author_list": "K Sushida, N Hirano",
"short_author_list": "Sushida K, Hirano N",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4924837",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "81",
"journal_issue": "5",
"journal_pages": "221-5",
"pub_year": "1970",
"pubmed_id": "4924837"
},
{
"title": "Problems of genetic transformation of mycobacteria by deoxyribonucleic acid (DNA).",
"abstract": "",
"full_author_list": "I Tárnok, R Bönicke",
"short_author_list": "Tárnok I, Bönicke R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5425544",
"journal": "Bulletin of the International Union against Tuberculosis",
"journal_volume": "43",
"journal_issue": "",
"journal_pages": "210-3",
"pub_year": "1970",
"pubmed_id": "5425544"
},
{
"title": "Phage inactivation by an ethanol-ether extract of Mycobacterium smegmatis.",
"abstract": "",
"full_author_list": "T Tokunaga, T Kataoka, K Suga",
"short_author_list": "Tokunaga T, Kataoka T, Suga K",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5410970",
"journal": "The American review of respiratory disease",
"journal_volume": "101",
"journal_issue": "2",
"journal_pages": "309-13",
"pub_year": "1970",
"pubmed_id": "5410970"
},
{
"title": "[Phage adsorption of lysogenic strains of mycobacteria]",
"abstract": "",
"full_author_list": "E Vandra",
"short_author_list": "Vandra E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5497300",
"journal": "Pneumonologie. Pneumonology",
"journal_volume": "142",
"journal_issue": "2",
"journal_pages": "158-64",
"pub_year": "1970",
"pubmed_id": "5497300"
},
{
"title": "Subdivision of M. tuberculosis by means of bacteriophages. With special reference to epidemiological studies.",
"abstract": "",
"full_author_list": "I Baess",
"short_author_list": "Baess I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4980863",
"journal": "Acta pathologica et microbiologica Scandinavica",
"journal_volume": "76",
"journal_issue": "3",
"journal_pages": "464-74",
"pub_year": "1969",
"pubmed_id": "4980863"
},
{
"title": "Rapidly-growing mycobacteria. Susceptibility to bacteriophages, reactions in the amidase test, production of acid from carbohydrates, and growth at various temperatures.",
"abstract": "",
"full_author_list": "I Baess, M W Bentzon",
"short_author_list": "Baess I, Bentzon MW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4901732",
"journal": "Acta pathologica et microbiologica Scandinavica",
"journal_volume": "75",
"journal_issue": "2",
"journal_pages": "331-47",
"pub_year": "1969",
"pubmed_id": "4901732"
},
{
"title": "Lysogeny among mycobacteria.",
"abstract": "",
"full_author_list": "R Bönicke",
"short_author_list": "Bönicke R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4185978",
"journal": "Folia microbiologica",
"journal_volume": "14",
"journal_issue": "4",
"journal_pages": "297-304",
"pub_year": "1969",
"pubmed_id": "4185978"
},
{
"title": "Properties of mycobacteriophage DS6A. I. Immunogenicity in rabbits.",
"abstract": "",
"full_author_list": "B U Bowman",
"short_author_list": "Bowman BU",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5770099",
"journal": "Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology a",
"journal_volume": "131",
"journal_issue": "1",
"journal_pages": "196-200",
"pub_year": "1969",
"pubmed_id": "5770099"
},
{
"title": "[Studies on mycobacteriophages. 3. Adsorption of mycobacteriophages on bacillary cells]",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4977602",
"journal": "Gru?lica i choroby p?uc; tuberculosis et pneumonologia",
"journal_volume": "37",
"journal_issue": "3",
"journal_pages": "197-201",
"pub_year": "1969",
"pubmed_id": "4977602"
},
{
"title": "[Bacteriophages with special reference to mycobacteriophages (preliminary report)]",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4891545",
"journal": "Gru?lica i choroby p?uc; tuberculosis et pneumonologia",
"journal_volume": "37",
"journal_issue": "3",
"journal_pages": "261-7",
"pub_year": "1969",
"pubmed_id": "4891545"
},
{
"title": "Studies on mycobacteriophages. Adsorption of mycobacteriophages on bacillary cells.",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5370553",
"journal": "Polish medical journal",
"journal_volume": "8",
"journal_issue": "6",
"journal_pages": "1337-41",
"pub_year": "1969",
"pubmed_id": "5370553"
},
{
"title": "[Electron microscopic studies of some mycophages isolated in Rumania]",
"abstract": "",
"full_author_list": "S Cambir, P Stiube, A Petrovici, C Dimitriu",
"short_author_list": "Cambir S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5398939",
"journal": "Archives roumaines de pathologie expérimentales et de microbiologie",
"journal_volume": "28",
"journal_issue": "4",
"journal_pages": "801-8",
"pub_year": "1969",
"pubmed_id": "5398939"
},
{
"title": "Protein components of a mycobacteriophage.",
"abstract": "",
"full_author_list": "G Castelnuovo, H I Giuliani, E Luchini de Giuliani, G Arancia",
"short_author_list": "Castelnuovo G et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4977237",
"journal": "The Journal of general virology",
"journal_volume": "4",
"journal_issue": "2",
"journal_pages": "253-7",
"pub_year": "1969",
"pubmed_id": "4977237"
},
{
"title": "Effect of dibromomannitol and dibromodulcitol on immunological and microbiological systems.",
"abstract": "",
"full_author_list": "G Elek, I Földes, E Vandra",
"short_author_list": "Elek G, Földes I, Vandra E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4900391",
"journal": "Acta microbiologica Academiae Scientiarum Hungaricae",
"journal_volume": "16",
"journal_issue": "1",
"journal_pages": "63-8",
"pub_year": "1969",
"pubmed_id": "4900391"
},
{
"title": "Production of antibodies against Mycobacterium phlei phage.",
"abstract": "",
"full_author_list": "G Elek, E Vandra, I Földes",
"short_author_list": "Elek G, Vandra E, Földes I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4187018",
"journal": "Acta microbiologica Academiae Scientiarum Hungaricae",
"journal_volume": "16",
"journal_issue": "1",
"journal_pages": "69-75",
"pub_year": "1969",
"pubmed_id": "4187018"
},
{
"title": "Lysogeny in the mycobacteria. II. Alterations of bacterial antigens mediated by mycobacteriophage.",
"abstract": "",
"full_author_list": "W D Jones, R E Beam",
"short_author_list": "Jones WD, Beam RE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4906193",
"journal": "Canadian journal of microbiology",
"journal_volume": "15",
"journal_issue": "9",
"journal_pages": "1112-4",
"pub_year": "1969",
"pubmed_id": "4906193"
},
{
"title": "Phage-induced alteration of enzymic activity in lysogenic Mycobacterium smegmatis strains.",
"abstract": "",
"full_author_list": "S E Juhasz, S Gelbart, M Harize",
"short_author_list": "Juhasz SE, Gelbart S, Harize M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5792676",
"journal": "Journal of general microbiology",
"journal_volume": "56",
"journal_issue": "2",
"journal_pages": "251-5",
"pub_year": "1969",
"pubmed_id": "5792676"
},
{
"title": "Lysogenic mycobacteria: phage variations and changes in host cells.",
"abstract": "",
"full_author_list": "E Mankiewicz, M Liivak, S Dernuet",
"short_author_list": "Mankiewicz E, Liivak M, Dernuet S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4977448",
"journal": "Journal of general microbiology",
"journal_volume": "55",
"journal_issue": "3",
"journal_pages": "409-16",
"pub_year": "1969",
"pubmed_id": "4977448"
},
{
"title": "Properties of mycobacteriophage C2.",
"abstract": "",
"full_author_list": "J Menezes, V Pavilanis",
"short_author_list": "Menezes J, Pavilanis V",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5357127",
"journal": "Experientia",
"journal_volume": "25",
"journal_issue": "10",
"journal_pages": "1112-3",
"pub_year": "1969",
"pubmed_id": "5357127"
},
{
"title": "Anomalous induction of mycobacteriophages mediated by mitomycin C.",
"abstract": "Mitomycin C has been found to stimulate the production of long-tailed defective bacteriophages and poly tails in thick cell wall mycobacterial mutants.",
"full_author_list": "M Rieber, T Imaeda",
"short_author_list": "Rieber M, Imaeda T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4898586",
"journal": "Journal of virology",
"journal_volume": "4",
"journal_issue": "4",
"journal_pages": "542-4",
"pub_year": "1969",
"pubmed_id": "4898586"
},
{
"title": "Production of tubules and bacteriophage-like particles in mycobacteria after bacitracin treatment.",
"abstract": "Bacitracin-treated mycobacteria liberated tubules and phagelike particles which had no biological activity against selected species. These structures may reflect a state of defective lysogeny.",
"full_author_list": "M Rieber, T Imaeda",
"short_author_list": "Rieber M, Imaeda T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5784228",
"journal": "Journal of bacteriology",
"journal_volume": "98",
"journal_issue": "2",
"journal_pages": "821-3",
"pub_year": "1969",
"pubmed_id": "5784228"
},
{
"title": "[BCG spheroplasts induced by a specific bacteriophage]",
"abstract": "",
"full_author_list": "P Roos, B Gaudier, L Ballester",
"short_author_list": "Roos P, Gaudier B, Ballester L",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4926579",
"journal": "Annales de l'Institut Pasteur de Lille",
"journal_volume": "20",
"journal_issue": "",
"journal_pages": "75-83",
"pub_year": "1969",
"pubmed_id": "4926579"
},
{
"title": "A comparative study of special agar medium (Redmond) and simple agar medium for the phage-typing of mycobacteria.",
"abstract": "",
"full_author_list": "L Sula, J Sulová",
"short_author_list": "Sula L, Sulová J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5309082",
"journal": "Bulletin of the World Health Organization",
"journal_volume": "41",
"journal_issue": "1",
"journal_pages": "17-9",
"pub_year": "1969",
"pubmed_id": "5309082"
},
{
"title": "[Bacteriophage receptor of mycobacteria. 2. Inactivation of mycobacteriophages with the ethanol-ether extract from the cell wall fraction and electron microscopic studies]",
"abstract": "",
"full_author_list": "T Tokunaga, T Kataoka, K Suda, T Yasuda",
"short_author_list": "Tokunaga T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5817754",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "78",
"journal_issue": "4",
"journal_pages": "141-5",
"pub_year": "1969",
"pubmed_id": "5817754"
},
{
"title": "Neutralization of mycobacteriophages by sera of patients with and without sarcoidosis.",
"abstract": "",
"full_author_list": "B U Bowman",
"short_author_list": "Bowman BU",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5725077",
"journal": "Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology a",
"journal_volume": "129",
"journal_issue": "3",
"journal_pages": "696-9",
"pub_year": "1968",
"pubmed_id": "5725077"
},
{
"title": "Antigenicity of mycobacteriophages R1, D29, and Leo in rabbits .",
"abstract": "",
"full_author_list": "B U Bowman",
"short_author_list": "Bowman BU",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5663251",
"journal": "Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology a",
"journal_volume": "128",
"journal_issue": "2",
"journal_pages": "441-5",
"pub_year": "1968",
"pubmed_id": "5663251"
},
{
"title": "[Studies on mycobacteriophages. Biological properties of phage \"63\"]",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5699435",
"journal": "Gru?lica i choroby p?uc; tuberculosis et pneumonologia",
"journal_volume": "36",
"journal_issue": "7",
"journal_pages": "617-22",
"pub_year": "1968",
"pubmed_id": "5699435"
},
{
"title": "[Research on the isolation, ecology and identification of mycobacteriophages in the Socialist Republic of Rumania]",
"abstract": "",
"full_author_list": "S Cambir",
"short_author_list": "Cambir S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4974719",
"journal": "Studii ?i cercet?ri de inframicrobiologie",
"journal_volume": "19",
"journal_issue": "4",
"journal_pages": "259-65",
"pub_year": "1968",
"pubmed_id": "4974719"
},
{
"title": "Lytic phages produced by DNA-infected mycobacteria.",
"abstract": "",
"full_author_list": "F Capet-Antonini, E Mankiewicz",
"short_author_list": "Capet-Antonini F, Mankiewicz E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4969800",
"journal": "Canadian journal of microbiology",
"journal_volume": "14",
"journal_issue": "6",
"journal_pages": "647-52",
"pub_year": "1968",
"pubmed_id": "4969800"
},
{
"title": "In vitro synthesis of antibody to phages of Mycobacterium phlei.",
"abstract": "",
"full_author_list": "L Hetey, E Vandra, I Földes",
"short_author_list": "Hetey L, Vandra E, Földes I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5679787",
"journal": "Acta microbiologica Academiae Scientiarum Hungaricae",
"journal_volume": "15",
"journal_issue": "2",
"journal_pages": "125-7",
"pub_year": "1968",
"pubmed_id": "5679787"
},
{
"title": "Mitomycin C-induced phage-like particles in a mutant of Mycobacterium tuberculosis BCG.",
"abstract": "",
"full_author_list": "T Imaeda, M Rieber",
"short_author_list": "Imaeda T, Rieber M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4877130",
"journal": "Journal of bacteriology",
"journal_volume": "96",
"journal_issue": "2",
"journal_pages": "557-9",
"pub_year": "1968",
"pubmed_id": "4877130"
},
{
"title": "Lysogeny in mycobacteria. I. Conversion of colony morphology, nitrate reductase activity, and tween 80 hydrolysis of Mycobacterium sp. ATCC 607 associated with lysogeny.",
"abstract": "",
"full_author_list": "W Jones, A White",
"short_author_list": "Jones W, White A",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5665977",
"journal": "Canadian journal of microbiology",
"journal_volume": "14",
"journal_issue": "5",
"journal_pages": "551-5",
"pub_year": "1968",
"pubmed_id": "5665977"
},
{
"title": "Bacteriophage typing and chemical and biologic tests in the classification of mycobacteria. A comparative study.",
"abstract": "",
"full_author_list": "E Mankiewicz, S Dernuet",
"short_author_list": "Mankiewicz E, Dernuet S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5657151",
"journal": "The American review of respiratory disease",
"journal_volume": "98",
"journal_issue": "1",
"journal_pages": "35-40",
"pub_year": "1968",
"pubmed_id": "5657151"
},
{
"title": "Lytic phenomena of phage LEO isolated from a sarcoid lesion.",
"abstract": "",
"full_author_list": "E Mankiewicz, W B Redmond",
"short_author_list": "Mankiewicz E, Redmond WB",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5657152",
"journal": "The American review of respiratory disease",
"journal_volume": "98",
"journal_issue": "1",
"journal_pages": "41-6",
"pub_year": "1968",
"pubmed_id": "5657152"
},
{
"title": "[Spheroplasts of mycobacteria. 2. Infection of glycine treated mycobacteria and spheroplasts with the phage and its nucleic acid]",
"abstract": "",
"full_author_list": "Y Mizuguchi, T Tokunaga",
"short_author_list": "Mizuguchi Y, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5750576",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "77",
"journal_issue": "2",
"journal_pages": "57-60",
"pub_year": "1968",
"pubmed_id": "5750576"
},
{
"title": "Quantitative studies of a mycobacterial phage-host system. II. Electron microscopy.",
"abstract": "",
"full_author_list": "H Mohelská, A Makovcová",
"short_author_list": "Mohelská H, Makovcová A",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5736937",
"journal": "Zeitschrift für allgemeine Mikrobiologie",
"journal_volume": "8",
"journal_issue": "3",
"journal_pages": "187-94",
"pub_year": "1968",
"pubmed_id": "5736937"
},
{
"title": "Quantitative studies of a mycobacterial phage--host system. I. Characteristic properties of the phage MyF3P-59a.",
"abstract": "",
"full_author_list": "H Mohelská, A Makovcová",
"short_author_list": "Mohelská H, Makovcová A",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5700541",
"journal": "Zeitschrift für allgemeine Mikrobiologie",
"journal_volume": "8",
"journal_issue": "1",
"journal_pages": "29-37",
"pub_year": "1968",
"pubmed_id": "5700541"
},
{
"title": "Isolation and purification of the mycobacterial phages.",
"abstract": "",
"full_author_list": "J Pokorný, E Wisingerová, E Sassmanová, J Sulová",
"short_author_list": "Pokorný J et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4875586",
"journal": "The American review of respiratory disease",
"journal_volume": "98",
"journal_issue": "2",
"journal_pages": "292-4",
"pub_year": "1968",
"pubmed_id": "4875586"
},
{
"title": "[Studies on the possibility of new types of mycobacteriophage]",
"abstract": "",
"full_author_list": "J Segawa, Y Hagiwara, Y Hamada",
"short_author_list": "Segawa J, Hagiwara Y, Hamada Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5710121",
"journal": "Iryo",
"journal_volume": "22",
"journal_issue": "10",
"journal_pages": "1096-101",
"pub_year": "1968",
"pubmed_id": "5710121"
},
{
"title": "[Concentration and purification of mycobacteriophage D 29]",
"abstract": "",
"full_author_list": "E Sikorska",
"short_author_list": "Sikorska E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5670160",
"journal": "Medycyna do?wiadczalna i mikrobiologia",
"journal_volume": "20",
"journal_issue": "2",
"journal_pages": "183-90",
"pub_year": "1968",
"pubmed_id": "5670160"
},
{
"title": "[Bacteriophage receptor of Mycobacteria. 1. Preliminary experiments on the phage-receptor of Mycobacterium smegmatis]",
"abstract": "",
"full_author_list": "T Tokunaga, T Kataoka, K Suga",
"short_author_list": "Tokunaga T, Kataoka T, Suga K",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5752032",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "77",
"journal_issue": "6",
"journal_pages": "225-9",
"pub_year": "1968",
"pubmed_id": "5752032"
},
{
"title": "Classification of subtypes of human tubercle bacilli by phage susceptibility.",
"abstract": "",
"full_author_list": "T Tokunaga, Y Maruyama, T Murohashi",
"short_author_list": "Tokunaga T, Maruyama Y, Murohashi T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4966272",
"journal": "The American review of respiratory disease",
"journal_volume": "97",
"journal_issue": "3",
"journal_pages": "469-71",
"pub_year": "1968",
"pubmed_id": "4966272"
},
{
"title": "[Lysogeny and lysogenic conversion in mycobacteria]",
"abstract": "",
"full_author_list": "R Bönicke",
"short_author_list": "Bönicke R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6081482",
"journal": "Beiträge zur Klinik und Erforschung der Tuberkulose und der Lungenkrankheiten",
"journal_volume": "136",
"journal_issue": "1",
"journal_pages": "108-19",
"pub_year": "1967",
"pubmed_id": "6081482"
},
{
"title": "[Contribution to the phage typing of Mycobacterium tuberculosis var. hominis]",
"abstract": "",
"full_author_list": "G Caroli, S Matteucci, P Lauro, R Mazzarone",
"short_author_list": "Caroli G et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4976116",
"journal": "Lotta contro la tubercolosi",
"journal_volume": "37",
"journal_issue": "4",
"journal_pages": "265-71",
"pub_year": "1967",
"pubmed_id": "4976116"
},
{
"title": "Reciprocal in toto conversion of Mycobacterium phlei--Mycobacterium smegmatis by mediation of an intermediate hybrid genome: B2h.",
"abstract": "",
"full_author_list": "S E Juhasz",
"short_author_list": "Juhasz SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5340345",
"journal": "Nature",
"journal_volume": "214",
"journal_issue": "5087",
"journal_pages": "518-20",
"pub_year": "1967",
"pubmed_id": "5340345"
},
{
"title": "[On the mycobacteriophage theory (E. Mankiewicz) of the sarcoidosis]",
"abstract": "",
"full_author_list": "K W Kalkoff",
"short_author_list": "Kalkoff KW",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6081483",
"journal": "Beiträge zur Klinik und Erforschung der Tuberkulose und der Lungenkrankheiten",
"journal_volume": "136",
"journal_issue": "1",
"journal_pages": "119-28",
"pub_year": "1967",
"pubmed_id": "6081483"
},
{
"title": "[On the morphology of the mycobacteriophages]",
"abstract": "",
"full_author_list": "H Kölbel",
"short_author_list": "Kölbel H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6081481",
"journal": "Beiträge zur Klinik und Erforschung der Tuberkulose und der Lungenkrankheiten",
"journal_volume": "136",
"journal_issue": "1",
"journal_pages": "107",
"pub_year": "1967",
"pubmed_id": "6081481"
},
{
"title": "Mycobacteriophages isolated from human sources.",
"abstract": "",
"full_author_list": "E Mankiewicz, M Liivak",
"short_author_list": "Mankiewicz E, Liivak M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6057251",
"journal": "Nature",
"journal_volume": "216",
"journal_issue": "5114",
"journal_pages": "485-6",
"pub_year": "1967",
"pubmed_id": "6057251"
},
{
"title": "Premature lysis of bacteriophage-infected mycobacteria induced by kanamycin.",
"abstract": "",
"full_author_list": "R M Nakamura, T Tokunaga, T Murohashi",
"short_author_list": "Nakamura RM, Tokunaga T, Murohashi T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6039110",
"journal": "The American review of respiratory disease",
"journal_volume": "96",
"journal_issue": "3",
"journal_pages": "542-4",
"pub_year": "1967",
"pubmed_id": "6039110"
},
{
"title": "[Study of the antigenic structure of Mycobacterium phlei]",
"abstract": "",
"full_author_list": "P Roos, J Guillaume, A Tacquet",
"short_author_list": "Roos P, Guillaume J, Tacquet A",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5597340",
"journal": "Annales de l'Institut Pasteur de Lille",
"journal_volume": "18",
"journal_issue": "",
"journal_pages": "35-63",
"pub_year": "1967",
"pubmed_id": "5597340"
},
{
"title": "[Studies on susceptibility of K1 and S1 phage against Mycobacteria]",
"abstract": "",
"full_author_list": "M Shishido, K Sugita, T Tsuda, T Sakakibara",
"short_author_list": "Shishido M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4966673",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "42",
"journal_issue": "8",
"journal_pages": "273-7",
"pub_year": "1967",
"pubmed_id": "4966673"
},
{
"title": "[Isolation of bacteriophage of tubercle bacillus (H37Rv) by soil added with Protamylase. 1]",
"abstract": "",
"full_author_list": "K Sushida, N Hirano",
"short_author_list": "Sushida K, Hirano N",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4964777",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "74",
"journal_issue": "4",
"journal_pages": "187-91",
"pub_year": "1967",
"pubmed_id": "4964777"
},
{
"title": "Infection of Mycobacterium tuberculosis with deoxyribonucleic acid extracted from mycobacteriophage B1.",
"abstract": "",
"full_author_list": "T Tokunaga, R M Nakamura",
"short_author_list": "Tokunaga T, Nakamura RM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4990041",
"journal": "Journal of virology",
"journal_volume": "1",
"journal_issue": "2",
"journal_pages": "448-9",
"pub_year": "1967",
"pubmed_id": "4990041"
},
{
"title": "[Possibilities and limits of current phage typing of mycobacteria strains]",
"abstract": "",
"full_author_list": "E Vandra",
"short_author_list": "Vandra E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5632197",
"journal": "Zeitschrift für Tuberkulose und Erkrankungen der Thoraxorgane",
"journal_volume": "127",
"journal_issue": "1",
"journal_pages": "61-4",
"pub_year": "1967",
"pubmed_id": "5632197"
},
{
"title": "Non-tuberculosis mycobacteria in Africa. 2. Sensitivity to mycobacteriophages.",
"abstract": "",
"full_author_list": "M P Zykov, J I Donec, B A Godovannyi",
"short_author_list": "Zykov MP, Donec JI, Godovannyi BA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4872713",
"journal": "Bulletin of the World Health Organization",
"journal_volume": "37",
"journal_issue": "6",
"journal_pages": "939-46",
"pub_year": "1967",
"pubmed_id": "4872713"
},
{
"title": "[The significance of lysogenic bacteria in sarcoidosis]",
"abstract": "",
"full_author_list": "R Bönicke",
"short_author_list": "Bönicke R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5984823",
"journal": "Archiv für klinische und experimentelle Dermatologie",
"journal_volume": "227",
"journal_issue": "1",
"journal_pages": "77-85",
"pub_year": "1966",
"pubmed_id": "5984823"
},
{
"title": "[Studies on mycobacteriophages. I. Isolation of mycobacteriophages from various materials]",
"abstract": "",
"full_author_list": "M Buraczewska, W Manowska, H Rdultowska",
"short_author_list": "Buraczewska M, Manowska W, Rdultowska H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5913961",
"journal": "Medycyna do?wiadczalna i mikrobiologia",
"journal_volume": "18",
"journal_issue": "3",
"journal_pages": "255-61",
"pub_year": "1966",
"pubmed_id": "5913961"
},
{
"title": "[Some data concerning the distribution of mycobacteriophages in nature (soil, manure, excrements of birds and of bovines, etc.)]",
"abstract": "",
"full_author_list": "S Cambir",
"short_author_list": "Cambir S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6010739",
"journal": "Archives roumaines de pathologie expérimentales et de microbiologie",
"journal_volume": "25",
"journal_issue": "2",
"journal_pages": "396-401",
"pub_year": "1966",
"pubmed_id": "6010739"
},
{
"title": "Reciprocal genetic changes in mycobacterial host-virus systems: effect of lysogeny on the phage.",
"abstract": "",
"full_author_list": "S E Juhasz, R Bönicke",
"short_author_list": "Juhasz SE, Bönicke R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5964194",
"journal": "Nature",
"journal_volume": "210",
"journal_issue": "5041",
"journal_pages": "1185-6",
"pub_year": "1966",
"pubmed_id": "5964194"
},
{
"title": "Pulmonary and nonpulmonary disease in humans due to avian mycobacteria. II. Microbiologic analysis of strains isolated.",
"abstract": "",
"full_author_list": "M Kubin, K Dvorsky, R Eisnerova, L Mezensky, K Franc, M Matejka",
"short_author_list": "Kubin M et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5945338",
"journal": "The American review of respiratory disease",
"journal_volume": "94",
"journal_issue": "1",
"journal_pages": "31-9",
"pub_year": "1966",
"pubmed_id": "5945338"
},
{
"title": "[Comparative study of 6 mycobacteriophages]",
"abstract": "",
"full_author_list": "E Mankiewicz",
"short_author_list": "Mankiewicz E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5968087",
"journal": "Revue d'immunologie et de thérapie antimicrobienne",
"journal_volume": "30",
"journal_issue": "4",
"journal_pages": "231-41",
"pub_year": "1966",
"pubmed_id": "5968087"
},
{
"title": "[The significance of lysogenic mycobacteria in the etiology of sarcoidosis]",
"abstract": "",
"full_author_list": "E Mankiewicz",
"short_author_list": "Mankiewicz E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4964391",
"journal": "Archiv für klinische und experimentelle Dermatologie",
"journal_volume": "227",
"journal_issue": "1",
"journal_pages": "63-77",
"pub_year": "1966",
"pubmed_id": "4964391"
},
{
"title": "[Infectivity of Mycobacteriophage DNA. 4. Heat denaturation of DNA]",
"abstract": "",
"full_author_list": "R Nakamura, T Tokunaga",
"short_author_list": "Nakamura R, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5951565",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "72",
"journal_issue": "5",
"journal_pages": "296-9",
"pub_year": "1966",
"pubmed_id": "5951565"
},
{
"title": "[Infectivity of Mycobacteriophage DNA. 3. Velocity curve and one step growth curve of phage DNA infection]",
"abstract": "",
"full_author_list": "R Nakamura, T Tokunaga",
"short_author_list": "Nakamura R, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5951540",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "72",
"journal_issue": "2",
"journal_pages": "79-82",
"pub_year": "1966",
"pubmed_id": "5951540"
},
{
"title": "[Premature lysis of bacteriophage-infected mycobacteria by kanamycin]",
"abstract": "",
"full_author_list": "R Nakamura, T Tokunaga",
"short_author_list": "Nakamura R, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5951537",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "72",
"journal_issue": "2",
"journal_pages": "122-5",
"pub_year": "1966",
"pubmed_id": "5951537"
},
{
"title": "Synthesis of nucleic acids in normal cells of Mycobacterium sp. 607 and in cells infected with Mycophage D 29.",
"abstract": "",
"full_author_list": "A Odrzywolska",
"short_author_list": "Odrzywolska A",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5961915",
"journal": "Bulletin de l'Académie polonaise des sciences. Série des sciences biologiques",
"journal_volume": "14",
"journal_issue": "11",
"journal_pages": "741-5",
"pub_year": "1966",
"pubmed_id": "5961915"
},
{
"title": "[On electron microscopic aspects of mycobacteriophages]",
"abstract": "",
"full_author_list": "J F Pasquier, S Lindenmann, E Mankiewicz",
"short_author_list": "Pasquier JF, Lindenmann S, Mankiewicz E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5968088",
"journal": "Revue d'immunologie et de thérapie antimicrobienne",
"journal_volume": "30",
"journal_issue": "4",
"journal_pages": "242-6",
"pub_year": "1966",
"pubmed_id": "5968088"
},
{
"title": "[Bacteriophage of a culture of steroid dehydrating Mycobacterium globiforme 193]",
"abstract": "",
"full_author_list": "Ia I Rautenshte?n, E S Khavina, I S Zviagintseva, G K Skriabin",
"short_author_list": "Rautenshte?n IaI et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5979913",
"journal": "Izvestiia Akademii nauk SSSR. Seriia biologicheskaia",
"journal_volume": "1",
"journal_issue": "",
"journal_pages": "141-5",
"pub_year": "1966",
"pubmed_id": "5979913"
},
{
"title": "Media and methods for phage-typing mycobacteria.",
"abstract": "",
"full_author_list": "W B Redmond, D M Ward",
"short_author_list": "Redmond WB, Ward DM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5297555",
"journal": "Bulletin of the World Health Organization",
"journal_volume": "35",
"journal_issue": "4",
"journal_pages": "563-8",
"pub_year": "1966",
"pubmed_id": "5297555"
},
{
"title": "Further studies of infectious DNA extracted from mycobacteriophages.",
"abstract": "Results of the previous investigation in which it was found that DNA extracted from D29 mycobacteriophage was infectious for Mycobacterium smegmatis 607, have been extended. DNA extracted from mycobacteriophage D4 and D32 produced plaques when plated on their respective hosts; D28 DNA, extracted in the same manner and tested under similar conditions, failed to show infectivity. Species barriers were not crossed by mycobacteriophage DNA; bacteria resistant to intact phage were not infected with the phage DNA. The efficiency of plating of the DNA is very much lower than that of intact phage; infection of a given host was not accomplished by DNA when titration for plaque formation by the intact phage was less than 10(9) PFU. The base composition of DNA extracted from the four mycobacteriophages and the three propagating hosts was very similar. The bases were paired, adenine with thymine and guanine with cytosine. A relatively higher per cent of guanine-cytosine than of adenine-thymine, was found. The buoyant density of each DNA in CsCl was linearly related to its guanine-cytosine content whereas with the exception of D28 DNA, thermal denaturation temperatures failed to show this relationship. However, the thermal transition profiles were characteristic of double stranded DNA. Additional evidence that D29 DNA forms complexes with basic proteins was obtained. Binding between calf thymus histone and between RNAase and D29 DNA readily occurs with a resultant loss in DNA infectivity. Trypsin and D29 DNA are only weakly reactive.",
"full_author_list": "M I Sellers, T Tokunaga",
"short_author_list": "Sellers MI, Tokunaga T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5948324",
"journal": "The Journal of experimental medicine",
"journal_volume": "123",
"journal_issue": "2",
"journal_pages": "327-40",
"pub_year": "1966",
"pubmed_id": "5948324"
},
{
"title": "[Infectivity of mycobacteriophage DNA. 5. Host range of DNA]",
"abstract": "",
"full_author_list": "T Tokunaga, R Nakamura",
"short_author_list": "Tokunaga T, Nakamura R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6005891",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "72",
"journal_issue": "6",
"journal_pages": "321-4",
"pub_year": "1966",
"pubmed_id": "6005891"
},
{
"title": "[Infectiosity of Mycobacteriophage DNA. 2. Competence of Mycobacteria]",
"abstract": "",
"full_author_list": "T Tokunaga, R Nakamura",
"short_author_list": "Tokunaga T, Nakamura R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5951270",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "72",
"journal_issue": "1",
"journal_pages": "51-5",
"pub_year": "1966",
"pubmed_id": "5951270"
},
{
"title": "[A study of the phage lysability of mycobacteria isolated in Africa]",
"abstract": "",
"full_author_list": "M P Zykov, Iu I Donets, B A Godovanny?",
"short_author_list": "Zykov MP, Donets IuI, Godovanny? BA",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/6004856",
"journal": "Zhurnal mikrobiologii, epidemiologii, i immunobiologii",
"journal_volume": "43",
"journal_issue": "2",
"journal_pages": "74-80",
"pub_year": "1966",
"pubmed_id": "6004856"
},
{
"title": "[Structure of the D 29 mycophage]",
"abstract": "",
"full_author_list": "A Feltynowski, E Sikorska",
"short_author_list": "Feltynowski A, Sikorska E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4157795",
"journal": "Medycyna do?wiadczalna i mikrobiologia",
"journal_volume": "17",
"journal_issue": "2",
"journal_pages": "153-6",
"pub_year": "1965",
"pubmed_id": "4157795"
},
{
"title": "POSSIBLE CLASSIFICATION OF RAPIDLY GROWING MYCOBACTERIA ON THE BASIS OF THEIR PHAGE SUSCEPTIBILITY.",
"abstract": "",
"full_author_list": "S E JUHASZ, R BOENICKE",
"short_author_list": "JUHASZ SE, BOENICKE R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14323035",
"journal": "Canadian journal of microbiology",
"journal_volume": "11",
"journal_issue": "",
"journal_pages": "235-41",
"pub_year": "1965",
"pubmed_id": "14323035"
},
{
"title": "[Electron microscopical observations on the structure and propagation of a mycobacteriophage]",
"abstract": "",
"full_author_list": "H Kölbel",
"short_author_list": "Kölbel H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5885182",
"journal": "Beiträge zur Klinik und Erforschung der Tuberkulose und der Lungenkrankheiten",
"journal_volume": "132",
"journal_issue": "",
"journal_pages": "331-2",
"pub_year": "1965",
"pubmed_id": "5885182"
},
{
"title": "ANTIGENIC COMPONENTS SHARED BY BACTERIOPHAGES AND PHAGE-HOSTS: MYCOBACTERIA, CORYNEBACTERIA AND HELA CELLS.",
"abstract": "",
"full_author_list": "E MANKIEWICZ",
"short_author_list": "MANKIEWICZ E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14330398",
"journal": "Growth",
"journal_volume": "29",
"journal_issue": "",
"journal_pages": "125-39",
"pub_year": "1965",
"pubmed_id": "14330398"
},
{
"title": "BACTERIOPHAGES THAT LYSE MYCOBACTERIA AND CORYNEBACTERIA, AND SHOW CYTOPATHOGENIC EFFECT ON TISSUE CULTURES OF RENAL CELLS OF CERCOPITHECUS AETHIOPS: A PRELIMINARY COMMUNICATION.",
"abstract": "Bacteriophages isolated from sputum and resection specimens of patients suffering from carcinoma of the lung were found to lyse corynebacteria and mycobacteria, and to produce a cytopathogenic effect on certain cells in tissue cultures. From the same and other patients with neoplastic disease, bacteria were isolated and described as coryne-mycobacteria because of bacteriological features they shared with both species. These bacteria, which either were sensitive to mycobacteriophages and corynebacteriophages or were phage-immune lysogenic bacteria, could be induced to produce lytic particles with phagolytic activity on corynebacteria and mycobacteria and a cytopathogenic effect on HeLa cells and on the renal cells of Cercopithecus.",
"full_author_list": "E MANKIEWICZ",
"short_author_list": "MANKIEWICZ E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14218217",
"journal": "Canadian Medical Association journal",
"journal_volume": "92",
"journal_issue": "",
"journal_pages": "31-3",
"pub_year": "1965",
"pubmed_id": "14218217"
},
{
"title": "[Lysogenization of Mycobacteria. 3. Phage induction of lysogenized Mycobacteria by mitomycin C and other inducing agents]",
"abstract": "",
"full_author_list": "Y Mizuguchi",
"short_author_list": "Mizuguchi Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5889815",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "20",
"journal_issue": "6",
"journal_pages": "290-4",
"pub_year": "1965",
"pubmed_id": "5889815"
},
{
"title": "[BIOLOGICAL CHARACTERS OF MYCOBACTERIOPHAGE Y 13.]",
"abstract": "",
"full_author_list": "Y MIZUGUCHI, T TOKUNAGA, T MUROHASHI",
"short_author_list": "MIZUGUCHI Y, TOKUNAGA T, MUROHASHI T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14289828",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "40",
"journal_issue": "",
"journal_pages": "25-9",
"pub_year": "1965",
"pubmed_id": "14289828"
},
{
"title": "Studies on the bacteriophage susceptibility against Mycobacterium tuberculosis. 1. The difference in lysis range of mycobacteriophage propagated on various host strains.",
"abstract": "",
"full_author_list": "K Sugita, T Tsuda, T Sakakibara, R Ushiku, T Takahashi",
"short_author_list": "Sugita K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4956472",
"journal": "Yokohama medical bulletin",
"journal_volume": "16",
"journal_issue": "6",
"journal_pages": "229-35",
"pub_year": "1965",
"pubmed_id": "4956472"
},
{
"title": "The phage tellurite zonal phenomenon as a criterion for the differentiation of slowly growing Mycobacteria.",
"abstract": "",
"full_author_list": "L Sula, J Sulová",
"short_author_list": "Sula L, Sulová J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5294925",
"journal": "Bulletin of the World Health Organization",
"journal_volume": "33",
"journal_issue": "3",
"journal_pages": "413-7",
"pub_year": "1965",
"pubmed_id": "5294925"
},
{
"title": "[Further studies on the phage typing of rapidly growing Mycobacteria]",
"abstract": "",
"full_author_list": "T Tokunaga, Y Maruyama, T Murohashi",
"short_author_list": "Tokunaga T, Maruyama Y, Murohashi T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5893618",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "20",
"journal_issue": "9",
"journal_pages": "554-9",
"pub_year": "1965",
"pubmed_id": "5893618"
},
{
"title": "[Infective nucleic acid of Mycobacteriophages. 1. Effect of DNAase, anti-phage serum and Tween 80]",
"abstract": "",
"full_author_list": "T Tokunaga, R Nakamura",
"short_author_list": "Tokunaga T, Nakamura R",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5895003",
"journal": "Igaku to seibutsugaku. Medicine and biology",
"journal_volume": "71",
"journal_issue": "6",
"journal_pages": "384-8",
"pub_year": "1965",
"pubmed_id": "5895003"
},
{
"title": "STREPTOMYCIN INDUCTION OF PREMATURE LYSIS OF BACTERIOPHAGE-INFECTED MYCOBACTERIA.",
"abstract": "",
"full_author_list": "T TOKUNAGA, M I SELLERS",
"short_author_list": "TOKUNAGA T, SELLERS MI",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14255725",
"journal": "Journal of bacteriology",
"journal_volume": "89",
"journal_issue": "",
"journal_pages": "537-8",
"pub_year": "1965",
"pubmed_id": "14255725"
},
{
"title": "INDUCED LYSOGENESIS OF MYCOBACTERIA.",
"abstract": "",
"full_author_list": "E VANDRA, A TAKATS",
"short_author_list": "VANDRA E, TAKATS A",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14345172",
"journal": "Acta microbiologica Academiae Scientiarum Hungaricae",
"journal_volume": "12",
"journal_issue": "",
"journal_pages": "29-37",
"pub_year": "1965",
"pubmed_id": "14345172"
},
{
"title": "EVALUATION OF THE GEL DOUBLE DIFFUSION TEST USING A PHAGE LYSATE ANTIGEN OF MYCOBACTERIUM SMEGMATIS TO DIAGNOSE TUBERCULOSIS OF CATTLE.",
"abstract": "",
"full_author_list": "E E WEDMAN, W D RICHARDS, B S POMEROY",
"short_author_list": "WEDMAN EE, RICHARDS WD, POMEROY BS",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14294806",
"journal": "Canadian journal of comparative medicine and veterinary science",
"journal_volume": "29",
"journal_issue": "",
"journal_pages": "129-33",
"pub_year": "1965",
"pubmed_id": "14294806"
},
{
"title": "THE ACTION OF ULTRASONIC VIBRATIONS ON ACTINOPHAGES.",
"abstract": "",
"full_author_list": "D L ANDERSON, S G BRADLEY",
"short_author_list": "ANDERSON DL, BRADLEY SG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14215443",
"journal": "Journal of general microbiology",
"journal_volume": "37",
"journal_issue": "",
"journal_pages": "67-72",
"pub_year": "1964",
"pubmed_id": "14215443"
},
{
"title": "[DESCRIPTION OF THE NEW SPECIES MYCOBACTERIUM VACCAE N. SP.]",
"abstract": "",
"full_author_list": "R BOENICKSE, E JUHASZ",
"short_author_list": "BOENICKSE R, JUHASZ E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14176844",
"journal": "Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene. 1. Abt. Medizinis",
"journal_volume": "192",
"journal_issue": "",
"journal_pages": "133-5",
"pub_year": "1964",
"pubmed_id": "14176844"
},
{
"title": "[Contribution to the study of the variability of pathogenic avian bacteria]",
"abstract": "",
"full_author_list": "G Eustatziou, S Eustatziou, E Meitert, C Bonciu, M Petrovici",
"short_author_list": "Eustatziou G et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/4961115",
"journal": "Archives roumaines de pathologie expérimentales et de microbiologie",
"journal_volume": "23",
"journal_issue": "1",
"journal_pages": "109-14",
"pub_year": "1964",
"pubmed_id": "4961115"
},
{
"title": "EFFECT OF TEMPERATURE ON THE BACTERIOPHAGE SUSCEPTIBILITY OF STRAINS OF MYCOBACTERIUM AVIUM ISOLATED FROM FOWL.",
"abstract": "",
"full_author_list": "S FROMAN, L SCAMMON",
"short_author_list": "FROMAN S, SCAMMON L",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14117685",
"journal": "The American review of respiratory disease",
"journal_volume": "89",
"journal_issue": "",
"journal_pages": "236-9",
"pub_year": "1964",
"pubmed_id": "14117685"
},
{
"title": "Interrelationships among Mycobacteria and Nocardiae.",
"abstract": "Manion, R. E. (Veterans Administration Hospital, Minneapolis, Minn.), S. G. Bradley, H. H. Zinneman, and W. H. Hall. Interrelationships among mycobacteria and nocardiae. J. Bacteriol. 87:1056-1859. 1964.-A total of 134 strains of mycobacteria and nocardiae were tested for susceptibility of 24 mycobacteriophages. On the basis of capability of diverse strains to serve as alternative propagating hosts for particular viruses, relationships among the actinomycetes were proposed. Cultures received as Mycobacterium smegmatis, M. ranae, M. butyricum, and M. chelonei were nearly identical, indicating that they are members of a single taxon. M. phlei and M. fortuitum strains constituted two distinct but related groups. Moreover, strains of M. smegmatis and Nocardia asteroides were susceptible to two variant actinophages originally isolated on N. brasiliensis.",
"full_author_list": "R E Manion, S G Bradley, H H Zinneman, W H Hall",
"short_author_list": "Manion RE et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5874532",
"journal": "Journal of bacteriology",
"journal_volume": "87",
"journal_issue": "5",
"journal_pages": "1056-9",
"pub_year": "1964",
"pubmed_id": "5874532"
},
{
"title": "DERIVATION OF NEW MYCOBACTERIOPHAGE TYPING REAGENTS BY PROPAGATION ON ALTERNATIVE HOSTS.",
"abstract": "",
"full_author_list": "R E MANION, S G BRADLEY",
"short_author_list": "MANION RE, BRADLEY SG",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14145230",
"journal": "The American review of respiratory disease",
"journal_volume": "89",
"journal_issue": "",
"journal_pages": "764-6",
"pub_year": "1964",
"pubmed_id": "14145230"
},
{
"title": "The relationship of sarcoidosis to anonymous bacteria.",
"abstract": "",
"full_author_list": "E Mankiewicz",
"short_author_list": "Mankiewicz E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/5884521",
"journal": "Acta medica Scandinavica. Supplementum",
"journal_volume": "425",
"journal_issue": "",
"journal_pages": "68-73",
"pub_year": "1964",
"pubmed_id": "5884521"
},
{
"title": "THE ROLE OF MYCOBACTERIOPHAGES AND OF CORTISONE IN EXPERIMENTAL TUBERCULOSIS AND SARCOIDOSIS.",
"abstract": "",
"full_author_list": "E MANKIEWICZ, J BELAND",
"short_author_list": "MANKIEWICZ E, BELAND J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14145223",
"journal": "The American review of respiratory disease",
"journal_volume": "89",
"journal_issue": "",
"journal_pages": "707-20",
"pub_year": "1964",
"pubmed_id": "14145223"
},
{
"title": "[PHAGE LYSOGENY OF MYCOBACTERIA. 2. THE \"AUTOPLAQUE\" AND \"DISMUNE\" PHENOMENA BY Y13L PHAGE LYSOGENY.]",
"abstract": "",
"full_author_list": "Y MIZUGUCHI",
"short_author_list": "MIZUGUCHI Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14285724",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "19",
"journal_issue": "",
"journal_pages": "489-93",
"pub_year": "1964",
"pubmed_id": "14285724"
},
{
"title": "[STUDIES ON THE LYSOGENIZATION OF MYCOBACTERIA. I. LYSOGENIZATION OF MYCOBACTERIUM JUCHO BY PHAGE Y13.]",
"abstract": "",
"full_author_list": "Y MIZUGUCHI",
"short_author_list": "MIZUGUCHI Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14206506",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "19",
"journal_issue": "",
"journal_pages": "169-74",
"pub_year": "1964",
"pubmed_id": "14206506"
},
{
"title": "PHAGE PATTERNS OF THE FAST-GROWING ACID-FAST BACTERIA.",
"abstract": "",
"full_author_list": "G M RODDA",
"short_author_list": "RODDA GM",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14202186",
"journal": "The Australian journal of experimental biology and medical science",
"journal_volume": "42",
"journal_issue": "",
"journal_pages": "457-64",
"pub_year": "1964",
"pubmed_id": "14202186"
},
{
"title": "ISOLATION OF A LYSOGENIC MYCOBACTERIUM FORTUITUM FROM SOIL.",
"abstract": "",
"full_author_list": "R L RUSSELL, W D RICHARDS, L A SCAMMON, S FROMAN",
"short_author_list": "RUSSELL RL et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14117692",
"journal": "The American review of respiratory disease",
"journal_volume": "89",
"journal_issue": "",
"journal_pages": "287-8",
"pub_year": "1964",
"pubmed_id": "14117692"
},
{
"title": "THE STRUCTURE OF MYCOBACTERIOPHAGES.",
"abstract": "",
"full_author_list": "K TAKEYA, K AMAKO",
"short_author_list": "TAKEYA K, AMAKO K",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14227049",
"journal": "Virology",
"journal_volume": "24",
"journal_issue": "",
"journal_pages": "461-6",
"pub_year": "1964",
"pubmed_id": "14227049"
},
{
"title": "ABORTIVE INFECTION AND HOST KILLING OF MYCOBACTERIOPHAGE.",
"abstract": "",
"full_author_list": "T TOKUNAGA, T MIZUGUCHI, T MUROHASHI",
"short_author_list": "TOKUNAGA T, MIZUGUCHI T, MUROHASHI T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14169422",
"journal": "The American review of respiratory disease",
"journal_volume": "89",
"journal_issue": "",
"journal_pages": "929-32",
"pub_year": "1964",
"pubmed_id": "14169422"
},
{
"title": "INFECTION OF MYCOBACTERIUM SMEGMATIS WITH D29 PHAGE DNA.",
"abstract": "DNA extracted from D29 mycobacteriophage produced plaques when plated on Mycobacterium smegmatis 607. The host bacterium did not require alternation such as conversion to protoplasts; cells susceptible to infection with intact phage were susceptible to DNA. The bases found in calf thymus DNA constituted the bases of D29 DNA, adenine being paired with thymine and guanine with cytosine. The dissymmetry ratio (A + T/G + C) was 0.56, and the buoyant density in CsCl was 1.722 with a GC content of 63.77 per cent. The efficiency of plating of the DNA is very much lower than that of intact D29, and it penetrates the host at a slower rate. As does intact phage, D29 DNA requires calcium ions for productive infection of 607. D29 DNA is significantly inactivated by incubation with RNAase, but the inactivation probably results from a complexing with the DNA rather than from enzyme hydrolysis.",
"full_author_list": "T TOKUNAGA, M SELLERS",
"short_author_list": "TOKUNAGA T, SELLERS M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14113109",
"journal": "The Journal of experimental medicine",
"journal_volume": "119",
"journal_issue": "",
"journal_pages": "139-49",
"pub_year": "1964",
"pubmed_id": "14113109"
},
{
"title": "DEOXYRIBONUCLEIC ACID, PROTEIN, AND INDUCIBLE ENZYME SYNTHESIS IN PHAGE-INFECTED MYCOBACTERIUM SMEGMATIS ATCC 607.",
"abstract": "",
"full_author_list": "D M CARLBERG, G J JANN",
"short_author_list": "CARLBERG DM, JANN GJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14045229",
"journal": "The American review of respiratory disease",
"journal_volume": "88",
"journal_issue": "",
"journal_pages": "235-9",
"pub_year": "1963",
"pubmed_id": "14045229"
},
{
"title": "Mycobacterial phages isolated from stool specimens of patients with pulmonary disease.",
"abstract": "",
"full_author_list": "J C CATER, W B REDMOND",
"short_author_list": "CATER JC, REDMOND WB",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14019331",
"journal": "The American review of respiratory disease",
"journal_volume": "87",
"journal_issue": "",
"journal_pages": "726-9",
"pub_year": "1963",
"pubmed_id": "14019331"
},
{
"title": "[Attempt at treatment of BCG-vaccinated hamsters with a bacteriophage.]",
"abstract": "",
"full_author_list": "P HAUDUROY, W ROSSET",
"short_author_list": "HAUDUROY P, ROSSET W",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13960983",
"journal": "Annales de l'Institut Pasteur",
"journal_volume": "104",
"journal_issue": "",
"journal_pages": "419-20",
"pub_year": "1963",
"pubmed_id": "13960983"
},
{
"title": "[Apropos of the isolation, from soil, of bacteriophages active against mycobacteria.]",
"abstract": "",
"full_author_list": "P HAUDUROY, F TANNER",
"short_author_list": "HAUDUROY P, TANNER F",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13960984",
"journal": "Annales de l'Institut Pasteur",
"journal_volume": "104",
"journal_issue": "",
"journal_pages": "826-9",
"pub_year": "1963",
"pubmed_id": "13960984"
},
{
"title": "BACTERIOPHAGES SPECIFIC FOR SOME MYCOBACTERIA.",
"abstract": "",
"full_author_list": "S E JUHASZ",
"short_author_list": "JUHASZ SE",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14087032",
"journal": "Nature",
"journal_volume": "200",
"journal_issue": "",
"journal_pages": "804-5",
"pub_year": "1963",
"pubmed_id": "14087032"
},
{
"title": "[THE TUBERCULOSIS BACTERIOPHAGE. (REVIEW)]",
"abstract": "",
"full_author_list": "B N KOZMIN SOKOLOV",
"short_author_list": "KOZMIN SOKOLOV BN",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14072288",
"journal": "Zhurnal mikrobiologii, epidemiologii, i immunobiologii",
"journal_volume": "40",
"journal_issue": "",
"journal_pages": "35-8",
"pub_year": "1963",
"pubmed_id": "14072288"
},
{
"title": "PHAGE TYPING OF SLOW-GROWING MYCOBACTERIA.",
"abstract": "",
"full_author_list": "T MUROHASHI, T TOKUNAGA, Y MIZUGUCHI, Y MARUYAMA",
"short_author_list": "MUROHASHI T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14082680",
"journal": "The American review of respiratory disease",
"journal_volume": "88",
"journal_issue": "",
"journal_pages": "664-9",
"pub_year": "1963",
"pubmed_id": "14082680"
},
{
"title": "[Phage-typing of slow-growing mycobacteria.]",
"abstract": "",
"full_author_list": "T MUROHASHI, T TOKUNAGA, Y MIZUGUCHI, Y MARUYAMA",
"short_author_list": "MUROHASHI T et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13936708",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "38",
"journal_issue": "",
"journal_pages": "187-91",
"pub_year": "1963",
"pubmed_id": "13936708"
},
{
"title": "LYSOGENY IN THE MYCOBACTERIA. II. SOME PHAGE-HOST RELATIONSHIPS OF LYSOGENIC MYCOBACTERIA.",
"abstract": "",
"full_author_list": "R L RUSSELL, G J JANN, S FROMAN",
"short_author_list": "RUSSELL RL, JANN GJ, FROMAN S",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14068438",
"journal": "The American review of respiratory disease",
"journal_volume": "88",
"journal_issue": "",
"journal_pages": "528-38",
"pub_year": "1963",
"pubmed_id": "14068438"
},
{
"title": "The tellurite zonal phenomenon of mycobacterial lysis observed in a BCG strain exposed to mycophage My F2P/59.",
"abstract": "",
"full_author_list": "L SULA, J SULOVA",
"short_author_list": "SULA L, SULOVA J",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13979181",
"journal": "The American review of respiratory disease",
"journal_volume": "88",
"journal_issue": "",
"journal_pages": "77-9",
"pub_year": "1963",
"pubmed_id": "13979181"
},
{
"title": "[THE POSSIBILITY OF DETECTING THE SOURCE OF INFECTION BY DETERMINATION OF PHAGE-SENSITIVITY IN TUBERCULOSIS.]",
"abstract": "",
"full_author_list": "I SZABO, E VANDRA",
"short_author_list": "SZABO I, VANDRA E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14054911",
"journal": "Tuberkulózis és tüdöbetegségek",
"journal_volume": "16",
"journal_issue": "",
"journal_pages": "123-4",
"pub_year": "1963",
"pubmed_id": "14054911"
},
{
"title": "[STUDIES ON MYCOBACTERIOPHAGE AND ITS APPLICATION.]",
"abstract": "",
"full_author_list": "K TAKEYA",
"short_author_list": "TAKEYA K",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14110270",
"journal": "Fukuoka igaku zasshi = Hukuoka acta medica",
"journal_volume": "54",
"journal_issue": "",
"journal_pages": "1061-71",
"pub_year": "1963",
"pubmed_id": "14110270"
},
{
"title": "DEOXYRIBONUCLEIC ACID BASE COMPOSITION OF A MYCOBACTERIOPHAGE.",
"abstract": "",
"full_author_list": "T TOKUNAGA, Y MIZUGUCHI, T MUROHASHI",
"short_author_list": "TOKUNAGA T, MIZUGUCHI Y, MUROHASHI T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14066450",
"journal": "Journal of bacteriology",
"journal_volume": "86",
"journal_issue": "",
"journal_pages": "608-9",
"pub_year": "1963",
"pubmed_id": "14066450"
},
{
"title": "A ROUTINE TEST PROCEDURE FOR PHAGE TYPING OF MYCOBACTERIA.",
"abstract": "",
"full_author_list": "T TOKUNAGA, T MUROHASHI",
"short_author_list": "TOKUNAGA T, MUROHASHI T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14044250",
"journal": "Japanese journal of medical science & biology",
"journal_volume": "16",
"journal_issue": "",
"journal_pages": "21-30",
"pub_year": "1963",
"pubmed_id": "14044250"
},
{
"title": "CLASSIFICATION OF MYCOBACTERIOPHAGE.",
"abstract": "",
"full_author_list": "T TOKUNAGA, T MUROHASHI",
"short_author_list": "TOKUNAGA T, MUROHASHI T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14044248",
"journal": "Japanese journal of medical science & biology",
"journal_volume": "16",
"journal_issue": "",
"journal_pages": "13-20",
"pub_year": "1963",
"pubmed_id": "14044248"
},
{
"title": "Effect of human serum and Tween 80 on several mycobacteriophages and susceptible mycobacteria.",
"abstract": "",
"full_author_list": "A WHITE, L LYON, F FOSTER",
"short_author_list": "WHITE A, LYON L, FOSTER F",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14000279",
"journal": "The American review of respiratory disease",
"journal_volume": "87",
"journal_issue": "",
"journal_pages": "730-3",
"pub_year": "1963",
"pubmed_id": "14000279"
},
{
"title": "[THE OBTAINING AND USE OF MYCOBACTERIOPHAGES FOR MYCOBACTERIA TYPING.]",
"abstract": "",
"full_author_list": "M P ZYKOV",
"short_author_list": "ZYKOV MP",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14151757",
"journal": "Zhurnal mikrobiologii, epidemiologii, i immunobiologii",
"journal_volume": "40",
"journal_issue": "",
"journal_pages": "33-9",
"pub_year": "1963",
"pubmed_id": "14151757"
},
{
"title": "[Studies on the biological characteristics of mycobacteriophages. 1. Effects of various surfaceactive agents on the adsorption and multiplication of mycobacteriophages.]",
"abstract": "",
"full_author_list": "H KAWAHARA",
"short_author_list": "KAWAHARA H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14031478",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "17",
"journal_issue": "",
"journal_pages": "839-43",
"pub_year": "1962",
"pubmed_id": "14031478"
},
{
"title": "[Studies on the biological characteristics of mycobacteriophages.]",
"abstract": "",
"full_author_list": "H KAWAHARA",
"short_author_list": "KAWAHARA H",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14031479",
"journal": "Nippon saikingaku zasshi. Japanese journal of bacteriology",
"journal_volume": "17",
"journal_issue": "",
"journal_pages": "448-52",
"pub_year": "1962",
"pubmed_id": "14031479"
},
{
"title": "Mycobacteriophages. Their role in tuberculosis and sarcoidosis.",
"abstract": "",
"full_author_list": "E MANKIEWICZ, M VAN WALBEEK",
"short_author_list": "MANKIEWICZ E, VAN WALBEEK M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14469306",
"journal": "Archives of environmental health",
"journal_volume": "5",
"journal_issue": "",
"journal_pages": "122-8",
"pub_year": "1962",
"pubmed_id": "14469306"
},
{
"title": "Growth characteristics of mycobacteriophages D28 and D29.",
"abstract": "",
"full_author_list": "M I SELLERS, W L BAXTER, H R RUNNALS",
"short_author_list": "SELLERS MI, BAXTER WL, RUNNALS HR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13910468",
"journal": "Canadian journal of microbiology",
"journal_volume": "8",
"journal_issue": "",
"journal_pages": "389-99",
"pub_year": "1962",
"pubmed_id": "13910468"
},
{
"title": "[Classification of mycobacteriophages.]",
"abstract": "",
"full_author_list": "T TOKUNAGA, Y MARUYAMA, T MUROHASHI",
"short_author_list": "TOKUNAGA T, MARUYAMA Y, MUROHASHI T",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13985330",
"journal": "Kekkaku : [Tuberculosis]",
"journal_volume": "37",
"journal_issue": "",
"journal_pages": "672-6",
"pub_year": "1962",
"pubmed_id": "13985330"
},
{
"title": "Alteration of colony morphology of mycobacteria associated with lysogeny.",
"abstract": "White, Arthur (University of Louisville, Louisville, Ky.), Frances Foster, and Linda Lyon. Alteration of colony morphology of mycobacteria associated with lysogeny. J. Bacteriol. 84:815-818. 1962.-Smooth colonies of mycobacteria were obtained from previously rough strains after exposure to phages R(1) and D-32 in a higher frequency than could be expected from selection of mutants alone. A high proportion of the smooth colonies were lysogenized. Smooth lysogenized strains maintained both lysogeny and smooth morphology after repeated subcultures on agar or in Tween media. The available evidence suggests that lysogeny with certain mycobacteriophages alters colony morphology by a means other than selection of mutants.",
"full_author_list": "A WHITE, F FOSTER, L LYON",
"short_author_list": "WHITE A, FOSTER F, LYON L",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14000277",
"journal": "Journal of bacteriology",
"journal_volume": "84",
"journal_issue": "",
"journal_pages": "815-8",
"pub_year": "1962",
"pubmed_id": "14000277"
},
{
"title": "General nature of the genetic code for proteins",
"abstract": "See article.",
"full_author_list": "CRICK FH, BARNETT L, BRENNER S, WATTS-TOBIN RJ",
"short_author_list": "CRICK FH, BARNETT L, BRENNER S, WATTS-TOBIN RJ",
"article_url": "",
"journal": "Nature",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "1961",
"pubmed_id": "13882203"
},
{
"title": "Mycobacteriophage lysates as serologic antigens.",
"abstract": "",
"full_author_list": "S FROMAN, M D LECHTMAN, L SCAMMON, D W WILL, B R ECKMANN",
"short_author_list": "FROMAN S et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13702221",
"journal": "The American review of respiratory disease",
"journal_volume": "83",
"journal_issue": "",
"journal_pages": "901-2",
"pub_year": "1961",
"pubmed_id": "13702221"
},
{
"title": "Mycobacteriophages isolated from persons with tuberculous and non-tuberculous conditions.",
"abstract": "",
"full_author_list": "E MANKIEWICZ",
"short_author_list": "MANKIEWICZ E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14469307",
"journal": "Nature",
"journal_volume": "191",
"journal_issue": "",
"journal_pages": "1416-7",
"pub_year": "1961",
"pubmed_id": "14469307"
},
{
"title": "Biological properties of Y-group mycobacteriophage.",
"abstract": "",
"full_author_list": "T MUROHASHI, T TOKUNAGA, M SEKI",
"short_author_list": "MUROHASHI T, TOKUNAGA T, SEKI M",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14477383",
"journal": "Acta tuberculosea et pneumologica Scandinavica",
"journal_volume": "41",
"journal_issue": "",
"journal_pages": "33-46",
"pub_year": "1961",
"pubmed_id": "14477383"
},
{
"title": "Mycobacteriophage. I. Physicochemical characterization.",
"abstract": "",
"full_author_list": "M I SELLES, H R RUNNALS",
"short_author_list": "SELLES MI, RUNNALS HR",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13749921",
"journal": "Journal of bacteriology",
"journal_volume": "81",
"journal_issue": "",
"journal_pages": "442-7",
"pub_year": "1961",
"pubmed_id": "13749921"
},
{
"title": "Light and electron microscope studies of mycobacterium--mycobacteriophage interactions. III. Further studies on the ultrathin sections.",
"abstract": "The process of multiplication of mycobacteriophage B-1 in its host cell was studied by means of an improved technic of ultrathin sectioning. The appearance of the nuclear apparatus was not altered throughout the latent period. Phage-shaped dense particles appeared about 30 minutes after infection in less dense areas neighboring the nuclear apparatus and occasionally at the margin of the nuclear apparatus. The less dense areas, which may correspond to the phage multiplication foci according to the authors' interpretation, were not filled with such arrays of fine-stranded fibrils as are seen in the nuclear apparatus. Empty phage heads could frequently be seen within and outside the lysed cells, along with the mature phage particles, at the end of the latent period. Moreover, it was indicated that empty head membranes may possibly exist within the cells during the latent period",
"full_author_list": "K TAKEYA, M KOIKE, R MORI, T TODA",
"short_author_list": "TAKEYA K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13919270",
"journal": "The Journal of biophysical and biochemical cytology",
"journal_volume": "11",
"journal_issue": "",
"journal_pages": "441-7",
"pub_year": "1961",
"pubmed_id": "13919270"
},
{
"title": "[2 strains of mycobacteriophages recently isolated and their action on microcolonies of a saprophytic mycobacterium.]",
"abstract": "",
"full_author_list": "S UYEDA, Y ITO",
"short_author_list": "UYEDA S, ITO Y",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13779453",
"journal": "Annales de l'Institut Pasteur",
"journal_volume": "100",
"journal_issue": "",
"journal_pages": "681-4",
"pub_year": "1961",
"pubmed_id": "13779453"
},
{
"title": "The preservation of acid-fast bacilli and mycobacteriophages by rapid vaccum drying.",
"abstract": "",
"full_author_list": "D W WILL, S FROMAN, Y AKIYAMA, L SCAMMON",
"short_author_list": "WILL DW et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14007067",
"journal": "The American review of respiratory disease",
"journal_volume": "84",
"journal_issue": "",
"journal_pages": "739-43",
"pub_year": "1961",
"pubmed_id": "14007067"
},
{
"title": "[On the current status of Mycobacteriophage research.]",
"abstract": "",
"full_author_list": "W KAEPPLER",
"short_author_list": "KAEPPLER W",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14408356",
"journal": "Zeitschrift für ärztliche Fortbildung",
"journal_volume": "54",
"journal_issue": "",
"journal_pages": "627-31",
"pub_year": "1960",
"pubmed_id": "14408356"
},
{
"title": "[Results and problems of Mycobacteriophage research.]",
"abstract": "",
"full_author_list": "F J BASSERMANN",
"short_author_list": "BASSERMANN FJ",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13797409",
"journal": "Beiträge zur Klinik der Tuberkulose und spezifischen Tuberkulose-Forschung",
"journal_volume": "121",
"journal_issue": "",
"journal_pages": "185-98",
"pub_year": "1959",
"pubmed_id": "13797409"
},
{
"title": "[Effect of mycobacteriophage \"P17\" on acid-fast bacilli isolated from lymph node pus during increased reactions following BCG vaccination.]",
"abstract": "",
"full_author_list": "W MACANDER-GOLEZ",
"short_author_list": "MACANDER-GOLEZ W",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/14419253",
"journal": "Gru?lica (Warsaw, Poland : 1926)",
"journal_volume": "27",
"journal_issue": "",
"journal_pages": "1197-202",
"pub_year": "1959",
"pubmed_id": "14419253"
},
{
"title": "Studies on the biologic properties of mycobacteriophage.",
"abstract": "",
"full_author_list": "K TAKEYA, T YOSHIMURA, K YAMAURA, T TODA",
"short_author_list": "TAKEYA K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13836689",
"journal": "The American review of respiratory disease",
"journal_volume": "80",
"journal_issue": "",
"journal_pages": "543-53",
"pub_year": "1959",
"pubmed_id": "13836689"
},
{
"title": "Light and electron microscope studies of Mycobacterium-mycobacteriophage interactions. I. Light microscope studies.",
"abstract": "",
"full_author_list": "K TAKEYA, R MORI, N NAKASHIMA, M KOIKE, T TODA",
"short_author_list": "TAKEYA K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13836686",
"journal": "Journal of bacteriology",
"journal_volume": "78",
"journal_issue": "",
"journal_pages": "307-12",
"pub_year": "1959",
"pubmed_id": "13836686"
},
{
"title": "Light and electron microscope studies of Mycobacterium-mycobacteriophage interactions. II. Electron microscope studies.",
"abstract": "",
"full_author_list": "K TAKEYA, M KOIKE, R MORI, Y YUDA, T TODA",
"short_author_list": "TAKEYA K et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13836685",
"journal": "Journal of bacteriology",
"journal_volume": "78",
"journal_issue": "",
"journal_pages": "313-9",
"pub_year": "1959",
"pubmed_id": "13836685"
},
{
"title": "A factor in serum which prevents propagation of D-29 mycobacteriophage with human tubercle bacilli.",
"abstract": "",
"full_author_list": "A WHITE, V KNIGHT",
"short_author_list": "WHITE A, KNIGHT V",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13670384",
"journal": "The American review of respiratory disease",
"journal_volume": "80",
"journal_issue": "1, Part 1",
"journal_pages": "12-8",
"pub_year": "1959",
"pubmed_id": "13670384"
},
{
"title": "A factor in serum albumin which prevents the inhibition of propagation of D-29 mycobacteriophage by tween.",
"abstract": "",
"full_author_list": "A C WHITE, V KNIGHT",
"short_author_list": "WHITE AC, KNIGHT V",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13844329",
"journal": "The American review of respiratory disease",
"journal_volume": "80",
"journal_issue": "",
"journal_pages": "443-4",
"pub_year": "1959",
"pubmed_id": "13844329"
},
{
"title": "Formation of protoplasts from mycobacteria by mycobacteriophage.",
"abstract": "",
"full_author_list": "I MILLMAN",
"short_author_list": "MILLMAN I",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13601820",
"journal": "Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology a",
"journal_volume": "99",
"journal_issue": "1",
"journal_pages": "216-9",
"pub_year": "1958",
"pubmed_id": "13601820"
},
{
"title": "Effect of tween 80 and serum on the interaction of mycobacteriophage D-29 with certain mycobacterial species.",
"abstract": "",
"full_author_list": "A WHITE, V KNIGHT",
"short_author_list": "WHITE A, KNIGHT V",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13498299",
"journal": "American review of tuberculosis",
"journal_volume": "77",
"journal_issue": "1",
"journal_pages": "134-45",
"pub_year": "1958",
"pubmed_id": "13498299"
},
{
"title": "Electron microscopic studies of mycobacteriophages.",
"abstract": "",
"full_author_list": "M I SELLERS, K TOKUYASU, Z PRICE, S FROMAN",
"short_author_list": "SELLERS MI et al",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13488006",
"journal": "American review of tuberculosis",
"journal_volume": "76",
"journal_issue": "6",
"journal_pages": "964-9",
"pub_year": "1957",
"pubmed_id": "13488006"
},
{
"title": "Mycobacteriophage.",
"abstract": "",
"full_author_list": "S FROMAN, E BOGEN",
"short_author_list": "FROMAN S, BOGEN E",
"article_url": "http://www.ncbi.nlm.nih.gov/pubmed/13136287",
"journal": "Transactions of the annual meeting. National Tuberculosis Association",
"journal_volume": "49",
"journal_issue": "",
"journal_pages": "76-8",
"pub_year": "1953",
"pubmed_id": "13136287"
},
{
"title": "The Etiology of Tuberculosis",
"abstract": "None Provided",
"full_author_list": "R Koch",
"short_author_list": "R Koch",
"article_url": "",
"journal": "Dtsch Gesundheitsw",
"journal_volume": "",
"journal_issue": "",
"journal_pages": "",
"pub_year": "1952",
"pubmed_id": ""
}
]