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1. An inclusive Research and Education Community (iREC) model to facilitate undergraduate science education reform

Author

Denise L. Monti, Julia C. Gill, Tamarah L. Adair, Sandra D. Adams, Yesmi Patricia Ahumada-Santos, Isabel Amaya, Kirk Anders, Justin R. Anderson, Mauricio S. Antunes, Mary Ayuk, Frederick Baliraine, Tonya C. Bates, Andrea R. Beyer, Suparna Bhalla, Tejas Bouklas, Sharon K. Bullock, Kristen A. Butela, Christine Byrum, Steven M. Caruso, Rebecca Chong, Hui-Min Chung, Stephanie B. Conant, Brett Condon, Katie E. Crump, Tom D'Elia, Megan K. Dennis, Linda C. DeVeaux, Lautaro Diacovich, Arturo Diaz, Iain Duffy, Dustin Edwards, Patricia C. Fallest-Strobl, Ann Findley, Matthew R. Fisher, Marie P. Fogarty, Victoria Jane Frost, Maria D. Gainey, Courtney S. Galle, Bryan Gibb, Urszula Golebiewska, Hugo Gramajo, Anna S. Grinath, Jennifer Guerrero, Nancy Guild, Kathryn E. Gunn, Susan Gurney, Lee E. Hughes, Pradeepa Jayachandran, Kristen Johnson, Allison Johnson, Alison E. Kanak, Michelle L. Kanther, Rodney A. King, Kathryn Kohl, Julia Lee-Soety, Lynn O. Lewis, Heather Lindberg, Jaclyn A. Madden, Breonna J. Martin, Matthew D. Mastropaolo, Sean McClory, Evan C. Merkhofer, Julie A. Merkle, Jon Mitchell, María Alejandra Mussi, Fernando Nieto, Jillian Nissen, Imade Yolanda Nsa, Mary G. O'Donnell, R. Deborah Overath, Shallee T. Page, Andrea Panagakis, Jesús Ricardo Parra Unda, Michelle B. Pass, Tiara Perez Morales, Nick T. Peters, Ruth Plymale, Richard Pollenz, Nathan S. Reyna, Claire A. Rinehart, Jessica Rocheleau, John S. Rombold, Ombeline Rossier, Adam D. Rudner, Elizabeth E. Rueschhoff, Christopher D. Shaffer, Mary Ann V. Smith, Amy B. Sprenkle, C. Nicole Sunnen, Michael A. Thomas, Michelle M. Tigges, Deborah Tobiason, Sara Sybesma Tolsma, Julie Torruellas Garcia, Peter Uetz, Edwin Vazquez, Catherine M. Ward, Vassie C. Ware, Jacqueline M. Washington, Matthew J. Waterman, Daniel E. Westholm, Keith A. Wheaton, Simon J. White, Elizabeth C. Williams, Daniel C. Williams, Ellen M. Wisner, William H. Biederman, Steven G. Cresawn, Danielle M. Heller, Deborah Jacobs-Sera, Daniel A. Russell, Graham F. Hatfull, David J. Asai, David I. Hanauer, Mark J. Graham, and Viknesh Sivanathan

Subjects
Science Education Alliance, inclusive Research and Education Community, pathway modeling, course-based research experience, STEM faculty development, Education (General), L7-991
Abstract

Over the last two decades, there have been numerous initiatives to improve undergraduate student outcomes in STEM. One model for scalable reform is the inclusive Research Education Community (iREC). In an iREC, STEM faculty from colleges and universities across the nation are supported to adopt and sustainably implement course-based research – a form of science pedagogy that enhances student learning and persistence in science. In this study, we used pathway modeling to develop a qualitative description that explicates the HHMI Science Education Alliance (SEA) iREC as a model for facilitating the successful adoption and continued advancement of new curricular content and pedagogy. In particular, outcomes that faculty realize through their participation in the SEA iREC were identified, organized by time, and functionally linked. The resulting pathway model was then revised and refined based on several rounds of feedback from over 100 faculty members in the SEA iREC who participated in the study. Our results show that in an iREC, STEM faculty organized as a long-standing community of practice leverage one another, outside expertise, and data to adopt, implement, and iteratively advance their pedagogy. The opportunity to collaborate in this manner and, additionally, to be recognized for pedagogical contributions sustainably engages STEM faculty in the advancement of their pedagogy. Here, we present a detailed pathway model of SEA that, together with underpinning features of an iREC identified in this study, offers a framework to facilitate transformations in undergraduate science education.

Published
2024
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2. Models of classroom assessment for course-based research experiences

Author

David I. Hanauer, Tong Zhang, Mark J. Graham, Sandra D. Adams, Yesmi Patricia Ahumada-Santos, Richard M. Alvey, Mauricio S. Antunes, Mary A. Ayuk, María Elena Báez-Flores, Christa T. Bancroft, Tonya C. Bates, Meghan J. Bechman, Elizabeth Behr, Andrea R. Beyer, Rebecca L. Bortz, Dane M. Bowder, Laura A. Briggs, Victoria Brown-Kennerly, Michael A. Buckholt, Sharon K. Bullock, Kristen A. Butela, Christine A. Byrum, Steven M. Caruso, Catherine P. Chia, Rebecca A. Chong, Hui-Min Chung, Kari L. Clase, Sean T. Coleman, D. Parks Collins, Stephanie B. Conant, Brett M. Condon, Pamela L. Connerly, Bernadette J. Connors, Jennifer E. Cook-Easterwood, Katie E. Crump, Tom D’Elia, Megan K. Dennis, Linda C. DeVeaux, Lautaro Diacovich, Iain Duffy, Nicholas P. Edgington, Dustin C. Edwards, Tenny O. G. Egwuatu, Elvira R. Eivazova, Patricia C. Fallest-Strobl, Christy L. Fillman, Ann M. Findley, Emily Fisher, Matthew R. Fisher, Marie P. Fogarty, Amanda C. Freise, Victoria J. Frost, Maria D. Gainey, Amaya M. Garcia Costas, Atenea A. Garza, Hannah E. Gavin, Raffaella Ghittoni, Bryan Gibb, Urszula P. Golebiewska, Anna S. Grinath, Susan M. R. Gurney, Rebekah F. Hare, Steven G. Heninger, John M. Hinz, Lee E. Hughes, Pradeepa Jayachandran, Kristen C. Johnson, Allison A. Johnson, Michelle Kanther, Margaret Kenna, Bridgette L. Kirkpatrick, Karen K. Klyczek, Kathryn P. Kohl, Michael Kuchka, Amber J. LaPeruta, Julia Y. Lee-Soety, Lynn O. Lewis, Heather M. Lindberg, Jaclyn A. Madden, Sergei A. Markov, Matthew D. Mastropaolo, Vinayak Mathur, Sean P. McClory, Evan C. Merkhofer, Julie A. Merkle, Scott F. Michael, Jon C. Mitchell, Sally D. Molloy, Denise L. Monti, María Alejandra Mussi, Holly Nance, Fernando E. Nieto-Fernandez, Jillian C. Nissen, Imade Y. Nsa, Mary G. O’Donnell, Shallee T. Page, Andrea Panagakis, Jesús Ricardo Parra-Unda, Tara A. Pelletier, Tiara G. Perez Morales, Nick T. Peters, Vipaporn Phuntumart, Richard S. Pollenz, Mary L. Preuss, David P. Puthoff, Muideen K. Raifu, Nathan S. Reyna, Claire A. Rinehart, Jessica M. Rocheleau, Ombeline Rossier, Adam D. Rudner, Elizabeth E. Rueschhoff, Amy Ryan, Sanghamitra Saha, Christopher D. Shaffer, Mary Ann V. Smith, Amy B. Sprenkle, Christy L. Strong, C. Nicole Sunnen, Brian P. Tarbox, Louise Temple, Kara R. Thoemke, Michael A. Thomas, Deborah M. Tobiason, Sara S. Tolsma, Julie Torruellas Garcia, Megan S. Valentine, Edwin Vazquez, Robert E. Ward, Catherine M. Ward, Vassie C. Ware, Marcie H. Warner, Jacqueline M. Washington, Daniel E. Westholm, Keith A. Wheaton, Beth M. Wilkes, Elizabeth C. Williams, William H. Biederman, Steven G. Cresawn, Danielle M. Heller, Deborah Jacobs-Sera, Graham F. Hatfull, David J. Asai, and Viknesh Sivanathan

Subjects
course-based research experience (CURE), science education, assessment, intergrated research and education community (iREC), grading, Education (General), L7-991
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.

Published
2023
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3. A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

Author

Tuajuanda C. Jordan, Sandra H. Burnett, Susan Carson, Steven M. Caruso, Kari Clase, Randall J. DeJong, John J. Dennehy, Dee R. Denver, David Dunbar, Sarah C. R. Elgin, Ann M. Findley, Chris R. Gissendanner, Urszula P. Golebiewska, Nancy Guild, Grant A. Hartzog, Wendy H. Grillo, Gail P. Hollowell, Lee E. Hughes, Allison Johnson, Rodney A. King, Lynn O. Lewis, Wei Li, Frank Rosenzweig, Michael R. Rubin, Margaret S. Saha, James Sandoz, Christopher D. Shaffer, Barbara Taylor, Louise Temple, Edwin Vazquez, Vassie C. Ware, Lucia P. Barker, Kevin W. Bradley, Deborah Jacobs-Sera, Welkin H. Pope, Daniel A. Russell, Steven G. Cresawn, David Lopatto, Cheryl P. Bailey, and Graham F. Hatfull

Subjects
Microbiology, QR1-502
Abstract

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. IMPORTANCE Engagement 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.

Published
2014
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4. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Author

Welkin H Pope, Deborah Jacobs-Sera, Daniel A Russell, Craig L Peebles, Zein Al-Atrache, Turi A Alcoser, Lisa M Alexander, Matthew B Alfano, Samantha T Alford, Nichols E Amy, Marie D Anderson, Alexander G Anderson, Andrew A S Ang, Manuel Ares, Amanda J Barber, Lucia P Barker, Jonathan M Barrett, William D Barshop, Cynthia M Bauerle, Ian M Bayles, Katherine L Belfield, Aaron A Best, Agustin Borjon, Charles A Bowman, Christine A Boyer, Kevin W Bradley, Victoria A Bradley, Lauren N Broadway, Keshav Budwal, Kayla N Busby, Ian W Campbell, Anne M Campbell, Alyssa Carey, Steven M Caruso, Rebekah D Chew, Chelsea L Cockburn, Lianne B Cohen, Jeffrey M Corajod, Steven G Cresawn, Kimberly R Davis, Lisa Deng, Dee R Denver, Breyon R Dixon, Sahrish Ekram, Sarah C R Elgin, Angela E Engelsen, Belle E V English, Marcella L Erb, Crystal Estrada, Laura Z Filliger, Ann M Findley, Lauren Forbes, Mark H Forsyth, Tyler M Fox, Melissa J Fritz, Roberto Garcia, Zindzi D George, Anne E Georges, Christopher R Gissendanner, Shannon Goff, Rebecca Goldstein, Kobie C Gordon, Russell D Green, Stephanie L Guerra, Krysta R Guiney-Olsen, Bridget G Guiza, Leila Haghighat, Garrett V Hagopian, Catherine J Harmon, Jeremy S Harmson, Grant A Hartzog, Samuel E Harvey, Siping He, Kevin J He, Kaitlin E Healy, Ellen R Higinbotham, Erin N Hildebrandt, Jason H Ho, Gina M Hogan, Victoria G Hohenstein, Nathan A Holz, Vincent J Huang, Ericka L Hufford, Peter M Hynes, Arrykka S Jackson, Erica C Jansen, Jonathan Jarvik, Paul G Jasinto, Tuajuanda C Jordan, Tomas Kasza, Murray A Katelyn, Jessica S Kelsey, Larisa A Kerrigan, Daryl Khaw, Junghee Kim, Justin Z Knutter, Ching-Chung Ko, Gail V Larkin, Jennifer R Laroche, Asma Latif, Kohana D Leuba, Sequoia I Leuba, Lynn O Lewis, Kathryn E Loesser-Casey, Courtney A Long, A Javier Lopez, Nicholas Lowery, Tina Q Lu, Victor Mac, Isaac R Masters, Jazmyn J McCloud, Molly J McDonough, Andrew J Medenbach, Anjali Menon, Rachel Miller, Brandon K Morgan, Patrick C Ng, Elvis Nguyen, Katrina T Nguyen, Emilie T Nguyen, Kaylee M Nicholson, Lindsay A Parnell, Caitlin E Peirce, Allison M Perz, Luke J Peterson, Rachel E Pferdehirt, Seegren V Philip, Kit Pogliano, Joe Pogliano, Tamsen Polley, Erica J Puopolo, Hannah S Rabinowitz, Michael J Resiss, Corwin N Rhyan, Yetta M Robinson, Lauren L Rodriguez, Andrew C Rose, Jeffrey D Rubin, Jessica A Ruby, Margaret S Saha, James W Sandoz, Judith Savitskaya, Dale J Schipper, Christine E Schnitzler, Amanda R Schott, J Bradley Segal, Christopher D Shaffer, Kathryn E Sheldon, Erica M Shepard, Jonathan W Shepardson, Madav K Shroff, Jessica M Simmons, Erika F Simms, Brandy M Simpson, Kathryn M Sinclair, Robert L Sjoholm, Ingrid J Slette, Blaire C Spaulding, Clark L Straub, Joseph Stukey, Trevor Sughrue, Tin-Yun Tang, Lyons M Tatyana, Stephen B Taylor, Barbara J Taylor, Louise M Temple, Jasper V Thompson, Michael P Tokarz, Stephanie E Trapani, Alexander P Troum, Jonathan Tsay, Anthony T Tubbs, Jillian M Walton, Danielle H Wang, Hannah Wang, John R Warner, Emilie G Weisser, Samantha C Wendler, Kathleen A Weston-Hafer, Hilary M Whelan, Kurt E Williamson, Angelica N Willis, Hannah S Wirtshafter, Theresa W Wong, Phillip Wu, Yun jeong Yang, Brandon C Yee, David A Zaidins, Bo Zhang, Melina Y Zúniga, Roger W Hendrix, and Graham F Hatfull

Subjects
Medicine, Science
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.

Published
2011
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5. Identification of Inhibitors of Fatty Acid Synthesis Enzymes in Mycobacterium Smegmatis

Author

David Toth, Lynn O. Lewis, E. Davis Oldham, and Alexander Priest

Subjects
chemistry.chemical_classification, Drug, Virtual screening, Tuberculosis, biology, media_common.quotation_subject, Mycobacterium smegmatis, medicine.disease, biology.organism_classification, Microbiology, Mycobacterium tuberculosis, chemistry.chemical_compound, Enzyme, chemistry, medicine, Fatty acid synthesis, media_common
Abstract

Antibiotic-resistant strains of Mycobacterium tuberculosis have rendered some of the current treatments for tuberculosis ineffective, creating a need for new treatments. Today, the most efficient way to find new drugs to treat tuberculosis and other diseases is to use virtual screening to quickly consider millions of potential drug candidates and filter out all but the ones most likely to inhibit the disease. These top hits can then be tested in a traditional wet lab to determine their potential effectiveness. Using supercomputers, we screened over 4 million potential drug molecules against each of two enzymes that are critical to the survival of Mycobacterium tuberculosis. During this process, we determined the top candidate molecules to test in the wet lab.

Published
2015
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6. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students

Author

Lucia P. Barker, Lee E. Hughes, David Dunbar, Rodney A. King, Daniel A. Russell, Edwin Vazquez, Vassie C. Ware, Chris R. Gissendanner, Wendy H. Grillo, Nancy Guild, Allison Johnson, John J. Dennehy, Randall J. DeJong, Kevin W. Bradley, Christopher D. Shaffer, Steven G. Cresawn, Wei Li, David Lopatto, Urszula Golebiewska, Graham F. Hatfull, Steven M. Caruso, Margaret S. Saha, Dee R. Denver, Ann M. Findley, Grant A. Hartzog, Sandra H. Burnett, Michael R. Rubin, Gail P. Hollowell, Deborah Jacobs-Sera, Sarah C. R. Elgin, Cheryl Bailey, Lynn O. Lewis, Frank Rosenzweig, Welkin H. Pope, Barbara J. Taylor, Larissa K. Temple, Kari Clase, Susan Carson, James Sandoz, Tuajuanda C. Jordan, and Losick, Richard

Subjects
Adult, Male, media_common.quotation_subject, Population, Context (language use), Academic achievement, Science education, Microbiology, Young Adult, Virology, Mathematics education, ComputingMilieux_COMPUTERSANDEDUCATION, Genetics, Humans, Bacteriophages, education, Students, Curriculum, Mathematics, media_common, education.field_of_study, Bacteria, Human Genome, Genomics, QR1-502, Quality Education, Transformative learning, Undergraduate research, Female, Research Article, Diversity (politics), Biotechnology
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., IMPORTANCE Engagement 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.

Published
2014

7. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution

Author

Chris R. Gissendanner, Jasper Van Kirk Thompson, Cynthia M. Bauerle, Kobie C. Gordon, Stephanie E. Trapani, Sarah C. R. Elgin, Ching-Chung Ko, Asma Latif, Caitlin E. Peirce, Jeremy S. Harmson, Elvis Nguyen, Jillian M. Walton, Siping He, Lauren L. Rodriguez, Jazmyn J. McCloud, Catherine J. Harmon, Angelica N. Willis, Melissa J. Fritz, Jessica A. Ruby, Michael P. Tokarz, Lisa Deng, Samantha T. Alford, Kathryn M. Sinclair, Victoria G. Hohenstein, Lauren Forbes, Erika F. Simms, Jessica M. Simmons, David A. Zaidins, Anthony T. Tubbs, Tyler M. Fox, Erica J. Puopolo, Garrett V. Hagopian, Hilary M. Whelan, Tina Q. Lu, Rachel Miller, Brandy M. Simpson, Emilie G. Weisser, Theresa W. Wong, Luke J. Peterson, Andrew C. Rose, Chelsea L. Cockburn, Tuajuanda C. Jordan, Daniel A. Russell, Yetta M. Robinson, Justin Z. Knutter, Tin-Yun Tang, Daryl Khaw, Ian Winsten Campbell, Stephen B. Taylor, Arrykka S. Jackson, Zein Al-Atrache, Amanda R. Schott, Samantha C. Wendler, John R. Warner, Sequoia I. Leuba, Steven G. Cresawn, J. Bradley Segal, Hannah S. Wirtshafter, Margaret S. Saha, Christine A. Boyer, Melina Y. Zúniga, Lucia P. Barker, Tamsen Polley, Marcella L. Erb, Anjali Menon, Victoria A. Bradley, Amanda J. Barber, Charles A. Bowman, Kaitlin E. Healy, Molly J. McDonough, Kaylee M. Nicholson, A. Javier Lopez, Andrew A. S. Ang, Erica M. Shepard, Leila Haghighat, Matthew B. Alfano, Manuel Ares, Kathryn Sheldon, Murray A. Katelyn, Alexander G. Anderson, Jeffrey D. Rubin, Larisa A. Kerrigan, Lisa Alexander, Krysta R. Guiney-Olsen, Deborah Jacobs-Sera, Junghee Kim, Rebecca Goldstein, Clark L. Straub, Lianne B. Cohen, Anne Georges, Erin N. Hildebrandt, Angela E. Engelsen, Bridget G. Guiza, Russell D. Green, Paul G. Jasinto, Allison M. Perz, Turi A. Alcoser, Laura Z. Filliger, H. S. Rabinowitz, Christopher D. Shaffer, Kathleen Weston-Hafer, William D. Barshop, Blaire C. Spaulding, Andrew J. Medenbach, Joseph Stukey, Michael J. Resiss, Samuel E. Harvey, Aaron A. Best, Nichols E. Amy, Kevin J. He, Erica C. Jansen, Danielle H. Wang, Katrina Nguyen, Katherine Belfield, Christine E. Schnitzler, Seegren V. Philip, Ian M. Bayles, Belle E. V. English, Graham F. Hatfull, Victor Mac, Barbara J. Taylor, Kathryn E. Loesser-Casey, Ingrid J. Slette, Nathan A. Holz, Rachel E. Pferdehirt, Emilie T. Nguyen, Nicholas Lowery, Agustin Borjon, Bo Zhang, Gail V. Larkin, Lynn O. Lewis, Ellen R. Higinbotham, Kevin W. Bradley, Patrick Ng, Brandon C. Yee, Kurt E. Williamson, Anne M. Campbell, Welkin H. Pope, Roger W. Hendrix, Craig L. Peebles, Jonathan M. Barrett, Brandon K. Morgan, Ericka L. Hufford, Ann M. Findley, Kayla N. Busby, Jonathan W. Shepardson, Breyon R. Dixon, Joe Pogliano, Stephanie Guerra, Robert Sjoholm, Dale J. Schipper, Phillip Wu, Steven M. Caruso, Larissa K. Temple, Yun jeong Yang, Jason H. Ho, Kohana D. Leuba, Judith Savitskaya, Alyssa Carey, Peter M. Hynes, Jonathan W. Jarvik, Jonathan Tsay, Corwin N. Rhyan, Marie D. Anderson, Lyons M. Tatyana, Rebekah D. Chew, Jennifer R. Laroche, Jessica S. Kelsey, Jeffrey Corajod, Keshav Budwal, James Sandoz, Tomas Kasza, Alexander P. Troum, Lindsay A. Parnell, Crystal Estrada, Sahrish Ekram, Shannon Goff, Hannah Wang, Mark H. Forsyth, Lauren N. Broadway, Madav K. Shroff, Zindzi D. George, Dee R. Denver, Grant A. Hartzog, Kimberly R. Davis, Kit Pogliano, Isaac R. Masters, Trevor Sughrue, Courtney A. Long, Vincent J. Huang, Gina M. Hogan, and Roberto Puertas Garcia

Subjects
Genome evolution, Science Policy, Mycobacteriophage, Population, lcsh:Medicine, Genome, Viral, Biology, Microbiology, Genome, 03 medical and health sciences, Virology, education, lcsh:Science, Genome Evolution, 030304 developmental biology, Genetics, Comparative genomics, 0303 health sciences, education.field_of_study, Multidisciplinary, Base Sequence, Geography, Mycobacteriophages, 030306 microbiology, lcsh:R, Genetic Variation, Sequence Analysis, DNA, Genomics, Comparative Genomics, Biological Evolution, United States, 3. Good health, Science Education, Evolutionary biology, Viral evolution, DNA, Viral, lcsh:Q, Mobile genetic elements, Research Article
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.

Published
2011

8. Bacteriophage attachment to the S-layer proteins of the mosquito-pathogenic strains ofBacillus sphaericus

Author

Lynn O. Lewis and Allan A. Yousten

Subjects
Bacillaceae, biology, Mutant, General Medicine, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Bacillus sphaericus, Bacteriophage, Lytic cycle, Phage group, Bacteria, Phage typing
Abstract

The linearly arrayed surface layer proteins found on the mosquito-pathogenic strains ofBacillus sphaericus function as the site of bacteriophage attachment for the ten lytic bacteriophages used in a bacteriophage typing scheme. Attachment to the surface layer proteins was demonstrated by the ability to block bacteriophage binding with antisera and the ability of the purified proteins to neutralize bacteriophage. Bacteriophage-resistant mutants have modified surface proteins that are less able to neutralize bacteriophages than is the protein of the parent strain. No evidence was obtained that sugar residues play a part in bacteriophage attachment. Phage neutralization by surface proteins from strains that do not serve as host to the phage indicates that, although strains in each phage group have a unique surface protein, the proteins do not determine the phage groups.

Published
1988
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9. Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis

Author

Morgan Pate, Steven M. Caruso, McKenzie Rea Quinn, Larissa K. Temple, Ivan Erill, Amber Brooke Sauder, Stephanie B. Stockwell, Lynn O. Lewis, Steven G. Cresawn, Crystal Scott, Alexis Brouillette, and Kathryn E. Loesser-Casey

Subjects
0301 basic medicine, Bioinformatics, Molecular Sequence Data, Bacillus cereus, Bacillus thuringiensis, Myoviridae, Bacillus Phages, Genome, Viral, Genome, Microbiology, Bacteriophage, Viral Proteins, 03 medical and health sciences, Genome Size, Virology, Sequencing, Bacteriophages, Phylogeny, Synteny, Genetics, biology, fungi, Genomics, biology.organism_classification, Bacillus Phage, 030104 developmental biology, Phages, GC-content
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.

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