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Lopatto D, Rosenwald AG, Burgess RC, Silver Key C, Van Stry M, Wawersik M, DiAngelo JR, Hark AT, Skerritt M, Allen AK, Alvarez C, Anderson S, Arrigo C, Arsham A, Barnard D, Bedard JEJ, Bose I, Braverman JM, Burg MG, Croonquist P, Du C, Dubowsky S, Eisler H, Escobar MA, Foulk M, Giarla T, Glaser RL, Goodman AL, Gosser Y, Haberman A, Hauser C, Hays S, Howell CE, Jemc J, Jones CJ, Kadlec L, Kagey JD, Keller KL, Kennell J, Kleinschmit AJ, Kleinschmit M, Kokan NP, Kopp OR, Laakso MM, Leatherman J, Long LJ, Manier M, Martinez-Cruzado JC, Matos LF, McClellan AJ, McNeil G, Merkhofer E, Mingo V, Mistry H, Mitchell E, Mortimer NT, Myka JL, Nagengast A, Overvoorde P, Paetkau D, Paliulis L, Parrish S, Toering Peters S, Preuss ML, Price JV, Pullen NA, Reinke C, Revie D, Robic S, Roecklein-Canfield JA, Rubin MR, Sadikot T, Sanford JS, Santisteban M, Saville K, Schroeder S, Shaffer CD, Sharif KA, Sklensky DE, Small C, Smith S, Spokony R, Sreenivasan A, Stamm J, Sterne-Marr R, Teeter KC, Thackeray J, Thompson JS, Velazquez-Ulloa N, Wolfe C, Youngblom J, Yowler B, Zhou L, Brennan J, Buhler J, Leung W, Elgin SCR, Reed LK. Student Attitudes Contribute to the Effectiveness of a Genomics CURE. J Microbiol Biol Educ 2022; 23:e00208-21. [PMID: 36061313 PMCID: PMC9429879 DOI: 10.1128/jmbe.00208-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.
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Affiliation(s)
- David Lopatto
- Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, Iowa, USA
| | | | - Rebecca C. Burgess
- Department of Biological Sciences, Stevenson University, Owings Mills, Maryland, USA
| | - Catherine Silver Key
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina, USA
| | | | - Matthew Wawersik
- Department of Biology, College of William and Mary, Williamsburg, Virginia, USA
| | | | - Amy T. Hark
- Department of Biology, Muhlenberg College, Allentown, Pennsylvania, USA
| | - Matthew Skerritt
- Department of Science, SUNY Corning Community College, Corning, New York, USA
| | - Anna K. Allen
- Department of Biology, Howard University, Washington, DC, USA
| | - Consuelo Alvarez
- Department of Biology, Longwood University, Farmville, Virginia, USA
| | - Sara Anderson
- Department of Biosciences, Minnesota State University Moorhead, Moorhead, Minnesota, USA
| | - Cindy Arrigo
- Department of Biology, New Jersey City University, Jersey City, New Jersey, USA
| | - Andrew Arsham
- Department of Biology, Bemidji State University, Bemidji, Minnesota, USA
| | - Daron Barnard
- Department of Biology, Worcester State University, Worcester, Massachusetts, USA
| | - James E. J. Bedard
- Department of Biology, University of the Fraser Valley, Abbotsford, British Columbia, Canada
| | - Indrani Bose
- Department of Biology, Western Carolina University, Cullowhee, North Carolina, USA
| | - John M. Braverman
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Martin G. Burg
- Department of Biomedical Sciences, Grand Valley State University, Allendale, Michigan, USA
- Department of Cell & Molecular Biology, Grand Valley State University, Allendale, Michigan, USA
| | - Paula Croonquist
- Department of Biology, Anoka-Ramsey Community College, Coon Rapids, Minnesota, USA
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, New Jersey, USA
| | - Sondra Dubowsky
- Department of Biology, McLennan Community College, Waco, Texas, USA
| | - Heather Eisler
- Department of Biology, University of the Cumberlands, Williamsburg, Kentucky, USA
| | - Matthew A. Escobar
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Michael Foulk
- Department of Biology, Mercyhurst University, Erie, Pennsylvania, USA
| | - Thomas Giarla
- Department of Biology, Siena College, Loudonville, New York, USA
| | - Rivka L. Glaser
- Department of Biological Sciences, Stevenson University, Owings Mills, Maryland, USA
| | - Anya L. Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California, USA
| | - Yuying Gosser
- Student Research and Scholarship, City College CUNY, New York, New York, USA
| | - Adam Haberman
- Department of Biology, University of San Diego, San Diego, California, USA
| | - Charles Hauser
- Department of Biology, St. Edward’s University, Austin, Texas, USA
| | - Shan Hays
- Department of Biology, Western Colorado University, Gunnison, Colorado, USA
| | - Carina E. Howell
- Department of Biological Sciences, Lock Haven University, Lock Haven, Pennsylvania, USA
| | - Jennifer Jemc
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Christopher J. Jones
- Department of Biological Sciences, Moravian University, Bethlehem, Pennsylvania, USA
| | - Lisa Kadlec
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - Jacob D. Kagey
- Department of Biology, University of Detroit Mercy, Detroit, Michigan, USA
| | | | - Jennifer Kennell
- Department of Biology, Vassar College, Poughkeepsie, New York, USA
| | | | - Melissa Kleinschmit
- Department of Liberal Arts, Science, and Business, Northeast Iowa Community College, Peosta, Iowa, USA
| | - Nighat P. Kokan
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, Wisconsin, USA
| | - Olga Ruiz Kopp
- Department of Biology, Utah Valley University, Orem, Utah, USA
| | - Meg M. Laakso
- Department of Biology, Eastern University, St. Davids, Pennsylvania, USA
| | - Judith Leatherman
- Department of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Lindsey J. Long
- Department of Biology, Oklahoma Christian University, Oklahoma City, Oklahoma, USA
| | - Mollie Manier
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | | | - Luis F. Matos
- Department of Biology, Eastern Washington University, Cheney, Washington, USA
| | - Amie Jo McClellan
- Science and Mathematics, Bennington College, Bennington, Vermont, USA
| | - Gerard McNeil
- Department of Biology, York College/CUNY, Jamaica, New York, USA
| | - Evan Merkhofer
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, USA
| | - Vida Mingo
- Department of Biology, Columbia College, Columbia, South Carolina, USA
| | - Hemlata Mistry
- Department of Biology, Widener University, Chester, Pennsylvania, USA
- Department of Biochemistry, Widener University, Chester, Pennsylvania, USA
| | | | - Nathan T. Mortimer
- Department of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Jennifer Leigh Myka
- Department of Biology, Gateway Community and Technical College, Covington, Kentucky, USA
| | - Alexis Nagengast
- Department of Biochemistry, Widener University, Chester, Pennsylvania, USA
- Department of Chemistry, Widener University, Chester, Pennsylvania, USA
| | - Paul Overvoorde
- Department of Biology, Macalester College, St. Paul, Minnesota, USA
| | - Don Paetkau
- Department of Biology, Saint Mary’s College, Notre Dame, Indiana, USA
| | - Leocadia Paliulis
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Susan Parrish
- Department of Biology, McDaniel College, Westminster, Maryland, USA
| | | | - Mary Lai Preuss
- Department of Biological Sciences, Webster University, St. Louis, Missouri, USA
| | - James V. Price
- Department of Biology, Utah Valley University, Orem, Utah, USA
| | - Nicholas A. Pullen
- Department of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Catherine Reinke
- Department of Biology, Linfield University, McMinnville, Oregon, USA
| | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, California, USA
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, Georgia, USA
| | | | - Michael R. Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, Puerto Rico, USA
| | - Takrima Sadikot
- Department of Biology, Washburn University, Topeka, Kansas, USA
| | | | - Maria Santisteban
- Department of Biology, University of North Carolina at Pembroke, Pembroke, North Carolina, USA
| | - Kenneth Saville
- Department of Biology, Albion College, Albion, Michigan, USA
| | - Stephanie Schroeder
- Department of Biological Sciences, Webster University, St. Louis, Missouri, USA
| | | | - Karim A. Sharif
- Department of Biology, Massasoit Community College, Brockton, Massachusetts, USA
| | | | - Chiyedza Small
- Department of Biology, Medgar Evers College, CUNY, Brooklyn, New York, USA
| | - Sheryl Smith
- Department of Biology, Arcadia University, Glenside, Pennsylvania, USA
| | - Rebecca Spokony
- Department of Natural Sciences, Baruch College, CUNY, New York, New York, USA
| | - Aparna Sreenivasan
- Department of Biology, School of Natural Sciences, California State University, Monterey Bay, Seaside, California, USA
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | | | - Katherine C. Teeter
- Department of Biology, Northern Michigan University, Marquette, Michigan, USA
| | - Justin Thackeray
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | | | | | - Cindy Wolfe
- Department of Biology, Kentucky Wesleyan College, Owensboro, Kentucky, USA
| | - James Youngblom
- Department of Biological Sciences, California State University Stanislaus, Turlock, California, USA
| | - Brian Yowler
- Department of Biology, Geneva College, Beaver Falls, Pennsylvania, USA
| | - Leming Zhou
- Health Information Management, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Janie Brennan
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jeremy Buhler
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
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2
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Hanauer DI, Graham MJ, Arnold RJ, Ayuk MA, Balish MF, Beyer AR, Butela KA, Byrum CA, Chia CP, Chung HM, Clase KL, Conant S, Coomans RJ, D’Elia T, Diaz J, Diaz A, Doty JA, Edgington NP, Edwards DC, Eivazova E, Emmons CB, Fast KM, Fisher EJ, Fleischacker CL, Frederick GD, Freise AC, Gainey MD, Gissendanner CR, Golebiewska UP, Guild NA, Hendrickson HL, Herren CD, Hopson-Fernandes MS, Hughes LE, Jacobs-Sera D, Johnson AA, Kirkpatrick BL, Klyczek KK, Koga AP, Kotturi H, LeBlanc-Straceski J, Lee-Soety JY, Leonard JE, Mastropaolo MD, Merkhofer EC, Michael SF, Mitchell JC, Mohan S, Monti DL, Noutsos C, Nsa IY, Peters NT, Plymale R, Pollenz RS, Porter ML, Rinehart CA, Rosas-Acosta G, Ross JF, Rubin MR, Scherer AE, Schroeder SC, Shaffer CD, Sprenkle AB, Sunnen CN, Swerdlow SJ, Tobiason D, Tolsma SS, Tsourkas PK, Ward RE, Ware VC, Warner MH, Washington JM, Westover KM, White SJ, Whitefleet-Smith JL, Williams DC, Wolyniak MJ, Zeilstra-Ryalls JH, Asai DJ, Hatfull GF, Sivanathan V. Instructional Models for Course-Based Research Experience (CRE) Teaching. CBE Life Sci Educ 2022; 21:ar8. [PMID: 34978921 PMCID: PMC9250372 DOI: 10.1187/cbe.21-03-0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
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.
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Affiliation(s)
- David I. Hanauer
- Department of English, Indiana University of Pennsylvania, Indiana, PA 15705
| | - Mark J. Graham
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511
| | - Rachel J. Arnold
- Salish Sea Research Center, Northwest Indian College, Bellingham, WA 98229
| | - Mary A. Ayuk
- Biology, Howard University, Washington, DC 20059
| | | | - Andrea R. Beyer
- Department of Biology, Virginia State University, Petersburg, VA 23806
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Catherine P. Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Hui-Min Chung
- Biology, University of West Florida, Pensacola, FL 32514
| | - Kari L. Clase
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Stephanie Conant
- Department of Biology, University of Detroit Mercy, Detroit, MI 48221
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411
| | - Tom D’Elia
- Department of Biology, Indian River State College, Fort Pierce, FL 34981
| | - Jason Diaz
- Integrated Science, Business, and Technology, La Salle University, Philadelphia, PA 19141
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, CA 92505
| | - Jean A. Doty
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938
| | | | - Dustin C. Edwards
- Biological Sciences, Tarleton State University, Stephenville, TX 76402
| | - Elvira Eivazova
- Biology Department, Columbia State Community College, Columbia, Tennessee 38401
| | | | - Kayla M. Fast
- Biological and Environmental Sciences, University of West Alabama, Livingston, AL 35470
| | - Emily J. Fisher
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | | | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, TX 75602
| | - Amanda C. Freise
- Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90025
| | - Maria D. Gainey
- Chemistry and Physics, Western Carolina University, Cullowhee, NC 28723
| | | | | | - Nancy A. Guild
- Molecular Cellular and Developmental Biology (MCDB), University of Colorado, Boulder, CO 80309
| | - Heather L. Hendrickson
- School of Natural and Computational Science, Massey University, Auckland 0632, New Zealand
| | | | | | - Lee E. Hughes
- Biological Sciences, University of North Texas, Denton, TX 76203
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Allison A. Johnson
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284
| | | | - Karen K. Klyczek
- Biology Department, University of Wisconsin-River Falls, River Falls, WI 54022
| | - Ann P. Koga
- Department of Biology, College of Idaho, Caldwell, ID 83605
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034
| | | | - Julia Y. Lee-Soety
- Department of Biology, Saint Joseph’s University, Philadelphia, PA 19131
| | | | - Matthew D. Mastropaolo
- Mathematics and Sciences, School of Arts and Sciences, Neumann University, Aston, PA 19014
| | | | - Scott F. Michael
- Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965
| | - Jon C. Mitchell
- Department of Science and Mathematics, Northern State University, Aberdeen, SD 57401
| | - Swarna Mohan
- College of Computer, Mathematical, and Natural Sciences, University of Maryland College Park, College Park, MD 20742
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35223
| | | | - Imade Y. Nsa
- Microbiology, University of Lagos, Lagos 101017, Nigeria
| | - Nick T. Peters
- Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| | - Ruth Plymale
- Department of Biology, Ouachita Baptist University, Arkadelphia, AR 71998
| | - Richard S. Pollenz
- Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620
| | - Megan L. Porter
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI 96822
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101
| | - German Rosas-Acosta
- Department of Biological Sciences, University of Texas at El Paso (UTEP), El Paso, TX 79968
| | - Joseph F. Ross
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125
| | - Michael R. Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | | | | | - C. Nicole Sunnen
- Biological Sciences, University of the Sciences, Philadelphia, PA 19104
| | | | | | - Sara S. Tolsma
- Department of Biology, Northwestern College, Orange City, IA 51041
| | | | - Robert E. Ward
- Biology, Case Western Reserve University, Cleveland, OH 44106
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | | | - Simon J. White
- Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | | | | | | | | | - David J. Asai
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Viknesh Sivanathan
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
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3
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Jacobs-Sera D, Abad LA, Alvey RM, Anders KR, Aull HG, Bhalla SS, Blumer LS, Bollivar DW, Bonilla JA, Butela KA, Coomans RJ, Cresawn SG, D'Elia T, Diaz A, Divens AM, Edgington NP, Frederick GD, Gainey MD, Garlena RA, Grant KW, Gurney SMR, Hendrickson HL, Hughes LE, Kenna MA, Klyczek KK, Kotturi H, Mavrich TN, McKinney AL, Merkhofer EC, Moberg Parker J, Molloy SD, Monti DL, Pape-Zambito DA, Pollenz RS, Pope WH, Reyna NS, Rinehart CA, Russell DA, Shaffer CD, Sivanathan V, Stoner TH, Stukey J, Sunnen CN, Tolsma SS, Tsourkas PK, Wallen JR, Ware VC, Warner MH, Washington JM, Westover KM, Whitefleet-Smith JL, Wiersma-Koch HI, Williams DC, Zack KM, Hatfull GF. Genomic diversity of bacteriophages infecting Microbacterium spp. PLoS One 2020; 15:e0234636. [PMID: 32555720 PMCID: PMC7302621 DOI: 10.1371/journal.pone.0234636] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/29/2020] [Indexed: 11/19/2022] Open
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.
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Affiliation(s)
- Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lawrence A. Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Richard M. Alvey
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - Kirk R. Anders
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Haley G. Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Suparna S. Bhalla
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Lawrence S. Blumer
- Department of Biology, Morehouse College, Atlanta, Georgia, United States of America
| | - David W. Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - J. Alfred Bonilla
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Tom D'Elia
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, California, United States of America
| | - Ashley M. Divens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicholas P. Edgington
- Department of Biology, Southern Connecticut State University, New Haven, Connecticut, United States of America
| | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, Texas, United States of America
| | - Maria D. Gainey
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kenneth W. Grant
- Department of Pathology, Wake Forest Baptist Health, Winston-Salem, North Carolina, United States of America
| | - Susan M. R. Gurney
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | | | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Margaret A. Kenna
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Karen K. Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, Oklahoma, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Angela L. McKinney
- Department of Biology, Nebraska Wesleyan University, Lincoln, Nebraska, United States of America
| | - Evan C. Merkhofer
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Sally D. Molloy
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, United States of America
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Dana A. Pape-Zambito
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard S. Pollenz
- Department Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan S. Reyna
- Department of Biology, Ouachita Baptist University, Arkadelphia, Arkansas, United States of America
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher D. Shaffer
- Department of Biology, University of Washington in St. Louis, St. Louis, Missouri, United States of America
| | - Viknesh Sivanathan
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Ty H. Stoner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph Stukey
- Biology Department, Hope College, Holland, Michigan, United States of America
| | - C. Nicole Sunnen
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Sara S. Tolsma
- Biology Department, Northwestern College, Orange City, Iowa, United States of America
| | - Philippos K. Tsourkas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, United States of America
| | - Jamie R. Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Kristi M. Westover
- Department of Biology, Winthrop University, Rock Hill, South Carolina, United States of America
| | - JoAnn L. Whitefleet-Smith
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Helen I. Wiersma-Koch
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Daniel C. Williams
- Department of Biology, Coastal Carolina University, Conway, South Carolina, United States of America
| | - Kira M. Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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4
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Lopatto D, Rosenwald AG, DiAngelo JR, Hark AT, Skerritt M, Wawersik M, Allen AK, Alvarez C, Anderson S, Arrigo C, Arsham A, Barnard D, Bazinet C, Bedard JEJ, Bose I, Braverman JM, Burg MG, Burgess RC, Croonquist P, Du C, Dubowsky S, Eisler H, Escobar MA, Foulk M, Furbee E, Giarla T, Glaser RL, Goodman AL, Gosser Y, Haberman A, Hauser C, Hays S, Howell CE, Jemc J, Johnson ML, Jones CJ, Kadlec L, Kagey JD, Keller KL, Kennell J, Key SCS, Kleinschmit AJ, Kleinschmit M, Kokan NP, Kopp OR, Laakso MM, Leatherman J, Long LJ, Manier M, Martinez-Cruzado JC, Matos LF, McClellan AJ, McNeil G, Merkhofer E, Mingo V, Mistry H, Mitchell E, Mortimer NT, Mukhopadhyay D, Myka JL, Nagengast A, Overvoorde P, Paetkau D, Paliulis L, Parrish S, Preuss ML, Price JV, Pullen NA, Reinke C, Revie D, Robic S, Roecklein-Canfield JA, Rubin MR, Sadikot T, Sanford JS, Santisteban M, Saville K, Schroeder S, Shaffer CD, Sharif KA, Sklensky DE, Small C, Smith M, Smith S, Spokony R, Sreenivasan A, Stamm J, Sterne-Marr R, Teeter KC, Thackeray J, Thompson JS, Peters ST, Van Stry M, Velazquez-Ulloa N, Wolfe C, Youngblom J, Yowler B, Zhou L, Brennan J, Buhler J, Leung W, Reed LK, Elgin SCR. Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience. J Microbiol Biol Educ 2020; 21:jmbe-21-6. [PMID: 32148609 PMCID: PMC7048401 DOI: 10.1128/jmbe.v21i1.2005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students' learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our "formative frustration" hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of "formative frustration" is an important aspect for a successful CURE.
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Affiliation(s)
- David Lopatto
- Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, IA 50112, USA
| | | | | | - Amy T. Hark
- Biology, Muhlenberg College, Allentown, PA 18104, USA
| | | | - Matthew Wawersik
- Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Anna K. Allen
- Biology, Howard University, Washington, DC 20059, USA
| | | | - Sara Anderson
- Biosciences, Minnesota State University Moorhead, Moorhead, MN 56563, USA
| | - Cindy Arrigo
- Biology, New Jersey City University, Jersey City, NJ 07305, USA
| | - Andrew Arsham
- Biology, Bemidji State University, Bemidji, MN 56601, USA
| | - Daron Barnard
- Biology, Worcester State University, Worcester, MA 01602, USA
| | | | - James E. J. Bedard
- Biology, University of the Fraser Valley, Abbotsford, BC, V2S 7M8, Canada
| | - Indrani Bose
- Biology, Western Carolina University, Cullowhee, NC 28723, USA
| | | | - Martin G. Burg
- Biomedical Sciences and Cell & Molecular Biology, Grand Valley State University, Allendale, MI 49401, USA
| | | | - Paula Croonquist
- Biology, Anoka-Ramsey Community College, Coon Rapids, MN 55433, USA
| | - Chunguang Du
- Biology, Montclair State University, Montclair, NJ 07043, USA
| | | | - Heather Eisler
- Biology, University of the Cumberlands, Williamsburg, KY 40769, USA
| | - Matthew A. Escobar
- Biological Sciences, California State University San Marcos, CA 92096, USA
| | | | - Emily Furbee
- Biology, Washington and Jefferson College, Washington, PA 15301, USA
| | | | - Rivka L. Glaser
- Biological Sciences, Stevenson University, Owings Mills, MD 21117, USA
| | - Anya L. Goodman
- Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Yuying Gosser
- Student Research and Scholarship, City College CUNY, New York, NY 10031, USA
| | - Adam Haberman
- Biology, University of San Diego, San Diego, CA 92110, USA
| | | | - Shan Hays
- Biology, Western Colorado University, Gunnison, CO 81231, USA
| | - Carina E. Howell
- Biological Sciences, Lock Haven University, Lock Haven, PA 17745, USA
| | - Jennifer Jemc
- Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | | | | | - Lisa Kadlec
- Biology, Wilkes University, Wilkes-Barre, PA 18766, USA
| | - Jacob D. Kagey
- Biology, University of Detroit Mercy, Detroit, MI 48221, USA
| | | | | | - S. Catherine Silver Key
- Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
| | | | | | - Nighat P. Kokan
- Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217, USA
| | | | - Meg M. Laakso
- Biology, Eastern University, St. Davids, PA 19087, USA
| | - Judith Leatherman
- Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Lindsey J. Long
- Biology, Oklahoma Christian University, Oklahoma City, OK 73136, USA
| | - Mollie Manier
- Biological Sciences, George Washington University, Washington, DC 20052, USA
| | | | - Luis F. Matos
- Biology, Eastern Washington University, Cheney, WA 99004, USA
| | - Amie Jo McClellan
- Science and Mathematics, Bennington College, Bennington, VT 05201, USA
| | - Gerard McNeil
- Biology, York College / CUNY, Jamaica, NY 11451, USA
| | - Evan Merkhofer
- Natural Sciences, Mount Saint Mary College, Newbergh, NY 12550, USA
| | - Vida Mingo
- Biology, Columbia College, Columbia, SC 29203, USA
| | - Hemlata Mistry
- Biology and Biochemistry, Widener University, Chester, PA 19013, USA
| | | | | | - Debaditya Mukhopadhyay
- Molecular Biology, Biochemistry, and Bioinformatics, Towson University, Towson, MD 21252, USA
| | | | - Alexis Nagengast
- Chemistry and Biochemistry, Widener University, Chester, PA 19013, USA
| | | | - Don Paetkau
- Biology, Saint Mary’s College, Notre Dame, IN 46556, USA
| | | | - Susan Parrish
- Biology, McDaniel College, Westminster, MD 21157, USA
| | - Mary Lai Preuss
- Biological Sciences, Webster University, St. Louis, MO 63119, USA
| | | | - Nicholas A. Pullen
- Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | | | - Dennis Revie
- Biology, California Lutheran University, Thousand Oaks, CA 91360, USA
| | | | | | - Michael R. Rubin
- Biology, University of Puerto Rico at Cayey, Cayey, PR 00736, USA
| | | | | | - Maria Santisteban
- Biology, University of North Carolina at Pembroke, Pembroke, NC 28372, USA
| | | | | | | | - Karim A. Sharif
- Biology, Massasoit Community College, Brockton, MA 02302, USA
| | | | - Chiyedza Small
- Biology, Medgar Evers College, CUNY, Brooklyn, NY 11225, USA
| | - Mary Smith
- Biology, North Carolina A & T State University, Greensboro, NC 27411, USA
| | - Sheryl Smith
- Biology, Arcadia, University, Glenside, PA 19038, USA
| | - Rebecca Spokony
- Natural Sciences, Baruch College, CUNY, New York, NY 10010, USA
| | - Aparna Sreenivasan
- Biology, School of Natural Sciences, California State University, Monterey Bay, Seaside, CA 93950, USA
| | - Joyce Stamm
- Biology, University of Evansville, Evansville, IN 47722, USA
| | | | | | | | | | | | | | | | - Cindy Wolfe
- Biology, Kentucky Wesleyan College, Owensboro, KY 42301, USA
| | - James Youngblom
- Biological Sciences, California State University Stanislaus, Turlock, CA 95382, USA
| | - Brian Yowler
- Biology, Grove City College, Grove City, PA 16127, USA
| | - Leming Zhou
- Health Information Management, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janie Brennan
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jeremy Buhler
- Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wilson Leung
- Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Laura K. Reed
- Biological Sciences, University of Alabama Tuscaloosa, AL 35487, USA
| | - Sarah C. R. Elgin
- Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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5
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Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy JJ, Denver DR, Dunbar D, Elgin SCR, 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. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. mBio 2014; 5:e01051-13. [PMID: 24496795 DOI: 10.1128/mbio.01051-13.editor] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
UNLABELLED 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.
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6
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Lopatto D, Hauser C, Jones CJ, Paetkau D, Chandrasekaran V, Dunbar D, MacKinnon C, Stamm J, Alvarez C, Barnard D, Bedard JEJ, Bednarski AE, Bhalla S, Braverman JM, Burg M, Chung HM, DeJong RJ, DiAngelo JR, Du C, Eckdahl TT, Emerson J, Frary A, Frohlich D, Goodman AL, Gosser Y, Govind S, Haberman A, Hark AT, Hoogewerf A, Johnson D, Kadlec L, Kaehler M, Key SCS, Kokan NP, Kopp OR, Kuleck GA, Lopilato J, Martinez-Cruzado JC, McNeil G, Mel S, Nagengast A, Overvoorde PJ, Parrish S, Preuss ML, Reed LD, Regisford EG, Revie D, Robic S, Roecklien-Canfield JA, Rosenwald AG, Rubin MR, Saville K, Schroeder S, Sharif KA, Shaw M, Skuse G, Smith CD, Smith M, Smith ST, Spana EP, Spratt M, Sreenivasan A, Thompson JS, Wawersik M, Wolyniak MJ, Youngblom J, Zhou L, Buhler J, Mardis E, Leung W, Shaffer CD, Threlfall J, Elgin SCR. A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics. CBE Life Sci Educ 2014; 13:711-23. [PMID: 25452493 PMCID: PMC4255357 DOI: 10.1187/cbe.13-10-0200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.
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Affiliation(s)
- David Lopatto
- Department of Psychology, Grinnell College, Grinnell, IA 50112
| | - Charles Hauser
- Bioinformatics, St. Edward's University, Austin, TX 78704
| | | | - Don Paetkau
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - David Dunbar
- Science Department, Cabrini College, Radnor, PA 19087
| | - Christy MacKinnon
- Biology Department, University of Incarnate Word, San Antonio, TX 78209
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Consuelo Alvarez
- Biological & Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Daron Barnard
- Biology Department, Worcester State University, Worcester, MA 01602
| | - James E J Bedard
- Department of Biology, Adams State University, Alamosa, CO 81101
| | | | - Satish Bhalla
- Department of Computer Science & Engineering, Johnson C. Smith University, Charlotte, NC 28216
| | - John M Braverman
- Department of Biology, Saint Joseph's University, Philadelphia, PA 19131
| | - Martin Burg
- Departments of Biomedical Sciences & Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Hui-Min Chung
- Department of Biology, University of West Florida, Pensacola, FL 32514
| | | | | | - Chunguang Du
- Department of Biology & Molecular Biology, Montclair State University, Montclair, NJ 07043
| | - Todd T Eckdahl
- Department of Biology, Missouri Western State University, St. Joseph, MO 64507
| | - Julia Emerson
- Department of Biology, Amherst College, Amherst, MA 01002
| | - Amy Frary
- Department of Biological Sciences, Mount Holyoke, South Hadley, MA 01075
| | - Donald Frohlich
- Biology Department, University of St. Thomas, Houston, TX 77006
| | - Anya L Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Yuying Gosser
- Grove School of Engineering, City College of New York, New York, NY 10031
| | - Shubha Govind
- Biology Department, City College of New York, New York, NY 10031
| | - Adam Haberman
- Biology Department, Oberlin College, Oberlin, OH 44074
| | - Amy T Hark
- Biology Department, Muhlenberg College, Allentown, PA 18104
| | | | - Diana Johnson
- Department of Biological Sciences, George Washington University, Washington, DC 20052
| | - Lisa Kadlec
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18766
| | | | | | - Nighat P Kokan
- Department of Biology, Cardinal Stritch University, Milwaukee, WI 53217
| | | | - Gary A Kuleck
- College of Engineering and Science, University of Detroit Mercy, Detroit, MI 48221
| | - Jane Lopilato
- Department of Biology, Simmons College, Boston, MA 02115
| | | | - Gerard McNeil
- Department of Biology, York College, City University of New York, Jamaica, NY 11451
| | - Stephanie Mel
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Alexis Nagengast
- Departments of Chemistry and Biochemistry, Widener University, Chester, PA 19013
| | | | - Susan Parrish
- Biology Department, McDaniel College, Westminster, MD 21157
| | - Mary L Preuss
- Department of Biological Sciences, Webster University, Webster Groves, MO 63119
| | - Laura D Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401
| | - E Gloria Regisford
- Department of Biology, Prairie View A&M University, Prairie View, TX 77446
| | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, GA 30030
| | | | - Anne G Rosenwald
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Michael R Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | - Stephanie Schroeder
- Department of Biological Sciences, Webster University, Webster Groves, MO 63119
| | - Karim A Sharif
- Department of Natural Sciences, LaGuardia Community College, Long Island City, NY 11101
| | - Mary Shaw
- Department of Biology and Chemistry, New Mexico Highlands University, Las Vegas, NM 87701
| | - Gary Skuse
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623
| | - Christopher D Smith
- Department of Biology, San Francisco State University, San Francisco, CA 94132
| | - Mary Smith
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411
| | - Sheryl T Smith
- Biology Department, Arcadia University, Glenside, PA 19038
| | - Eric P Spana
- Department of Biology, Duke University, Durham, NC 27708
| | - Mary Spratt
- Biology Department, William Woods University, Fulton, MO 65251
| | - Aparna Sreenivasan
- Science and Environmental Policy, California State University-Monterey Bay, Seaside, CA 93955
| | | | - Matthew Wawersik
- Biology Department, College of William and Mary, Williamsburg, VA 23185
| | | | - James Youngblom
- Department of Biology, California State University-Stanislaus, Turlock, CA 95382
| | - Leming Zhou
- Department of Health Information Management, University of Pittsburgh, Pittsburgh, PA 15213
| | - Jeremy Buhler
- Department of Computer Science and Engineering and Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130
| | - Elaine Mardis
- Genome Institute, Washington University in St. Louis, St. Louis, MO 63130
| | - Wilson Leung
- Biology Department, Washington University in St. Louis, St. Louis, MO 63130
| | | | - Jennifer Threlfall
- George Warren Brown School of Social Work, Washington University in St. Louis, St. Louis, MO 63130
| | - Sarah C R Elgin
- Biology Department, Washington University in St. Louis, St. Louis, MO 63130
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7
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Shaffer CD, Alvarez CJ, Bednarski AE, Dunbar D, Goodman AL, Reinke C, Rosenwald AG, Wolyniak MJ, Bailey C, Barnard D, Bazinet C, Beach DL, Bedard JEJ, Bhalla S, Braverman J, Burg M, Chandrasekaran V, Chung HM, Clase K, DeJong RJ, DiAngelo JR, Du C, Eckdahl TT, Eisler H, Emerson JA, Frary A, Frohlich D, Gosser Y, Govind S, Haberman A, Hark AT, Hauser C, Hoogewerf A, Hoopes LLM, Howell CE, Johnson D, Jones CJ, Kadlec L, Kaehler M, Silver Key SC, Kleinschmit A, Kokan NP, Kopp O, Kuleck G, Leatherman J, Lopilato J, MacKinnon C, Martinez-Cruzado JC, McNeil G, Mel S, Mistry H, Nagengast A, Overvoorde P, Paetkau DW, Parrish S, Peterson CN, Preuss M, Reed LK, Revie D, Robic S, Roecklein-Canfield J, Rubin MR, Saville K, Schroeder S, Sharif K, Shaw M, Skuse G, Smith CD, Smith MA, Smith ST, Spana E, Spratt M, Sreenivasan A, Stamm J, Szauter P, Thompson JS, Wawersik M, Youngblom J, Zhou L, Mardis ER, Buhler J, Leung W, Lopatto D, Elgin SCR. A course-based research experience: how benefits change with increased investment in instructional time. CBE Life Sci Educ 2014; 13:111-30. [PMID: 24591510 PMCID: PMC3940452 DOI: 10.1187/cbe-13-08-0152] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.
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Affiliation(s)
- Christopher D. Shaffer
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
- Address correspondence to: Christopher D. Shaffer ()
| | - Consuelo J. Alvarez
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | | | - David Dunbar
- Science Department, Cabrini College, Radnor, PA 19087
| | - Anya L. Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93405
| | | | | | | | - Cheryl Bailey
- Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE 68588
| | - Daron Barnard
- Biology Department, Worcester State University, Worcester, MA 01602
| | | | - Dale L. Beach
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | | | - Satish Bhalla
- Department of Computer Science & Engineering, Johnson C. Smith University, Charlotte, NC 28216
| | - John Braverman
- Department of Biology, Saint Joseph's University, Philadelphia, PA 19131
| | - Martin Burg
- Departments of Biomedical Sciences & Cell and Molecular Biology, Grand Valley State, Allendale, MI 49401
| | | | - Hui-Min Chung
- Department of Biology, University of West Florida, Pensacola, FL 32514
| | - Kari Clase
- Technology Leadership & Innovation Department, Purdue University, West Lafayette, IN 47907
| | | | | | - Chunguang Du
- Department of Biology & Molecular Biology, Montclair State University, Montclair, NJ 07043
| | - Todd T. Eckdahl
- Department of Biology, Missouri Western State University, St. Joseph, MO 64507
| | - Heather Eisler
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | | | - Amy Frary
- Department of Biological Sciences, Mount Holyoke, South Hadley, MA 01075
| | - Donald Frohlich
- Biology Department, University of St. Thomas, Houston, TX 77006
| | | | - Shubha Govind
- Biology Department, City College of New York, New York, NY 10031
| | - Adam Haberman
- Biology Department, Oberlin College, Oberlin, OH 44074
| | - Amy T. Hark
- Biology Department, Muhlenberg College, Allentown, PA 18104
| | - Charles Hauser
- Department of Bioinformatics, St. Edwards University, Austin, TX 78704
| | | | | | - Carina E. Howell
- Department of Biological Sciences, Lock Haven University of Pennsylvania, Lock Haven, PA 17745
| | - Diana Johnson
- Department of Biological Sciences, George Washington University, Washington, DC 20052
| | | | - Lisa Kadlec
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18701
| | | | | | - Adam Kleinschmit
- Department of Biology, Adams State University, Alamosa, CO 81101
| | - Nighat P. Kokan
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Olga Kopp
- Department of Biology, Utah Valley University, Orem, UT 84058
| | - Gary Kuleck
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045
| | - Judith Leatherman
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639
| | - Jane Lopilato
- Biology Department, Simmons College, Boston, MA 02115
| | - Christy MacKinnon
- Biology Department, University of the Incarnate Word, San Antonio, TX 78209
| | | | - Gerard McNeil
- Department of Biology, York College–City University of New York, Jamaica, NY 11451
| | - Stephanie Mel
- Division of Biological Sciences, University of California–San Diego, La Jolla, CA 92093
| | | | - Alexis Nagengast
- Departments of Chemistry and Biochemistry, Widener University, Chester, PA 19013
| | | | - Don W. Paetkau
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Susan Parrish
- Biology Department, McDaniel College, Westminster, MD 21157
| | | | - Mary Preuss
- Department of Biological Sciences, Webster University, Webster Groves, MO 63119
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401
| | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, GA 30030
| | | | - Michael R. Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | - Karim Sharif
- Department of Natural Sciences, LaGuardia Community College, Long Island City, NY 11101
| | - Mary Shaw
- Department of Biology, New Mexico Highlands University, Las Vegas, NM 87701
| | - Gary Skuse
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623
| | | | - Mary A. Smith
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411
| | - Sheryl T. Smith
- Department of Biology, Arcadia University, Glenside, PA 19038
| | - Eric Spana
- Department of Biology, Duke University, Durham, NC 27708
| | - Mary Spratt
- Department of Biology, William Woods University, Fulton, MO 65251
| | - Aparna Sreenivasan
- Science and Environmental Policy, California State University–Monterey Bay, Seaside, CA 93955
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Paul Szauter
- Biology Department, University of New Mexico, Albuquerque, NM 87106
| | | | - Matthew Wawersik
- Department of Biology, College of William & Mary, Williamsburg, VA 23187
| | - James Youngblom
- Department of Biology, California State University–Stanislaus, Turlock, CA 95382
| | - Leming Zhou
- Department of Health Information Management, University of Pittsburgh, Pittsburgh, PA 15213
| | - Elaine R. Mardis
- Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108
| | - Jeremy Buhler
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - David Lopatto
- Department of Psychology, Grinnell College, Grinnell, IA 50112
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
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8
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Pope WH, Ferreira CM, Jacobs-Sera D, Benjamin RC, Davis AJ, DeJong RJ, Elgin SCR, 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, Hendrix RW, Hatfull GF. Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4. PLoS One 2011; 6:e26750. [PMID: 22053209 PMCID: PMC3203893 DOI: 10.1371/journal.pone.0026750] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 10/03/2011] [Indexed: 01/21/2023] Open
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.
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Affiliation(s)
- Welkin H. Pope
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christina M. Ferreira
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert C. Benjamin
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Ariangela J. Davis
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Randall J. DeJong
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Sarah C. R. Elgin
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Forrest R. Guilfoile
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mark H. Forsyth
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Alexander D. Harris
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Samuel E. Harvey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Peter M. Hynes
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Arrykka S. Jackson
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Marilyn D. Jalal
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Elizabeth A. MacMurray
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Coreen M. Manley
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Molly J. McDonough
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Jordan L. Mosier
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Larissa J. Osterbann
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | - Hannah S. Rabinowitz
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Corwin N. Rhyan
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Daniel A. Russell
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Margaret S. Saha
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Christopher D. Shaffer
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Stephanie E. Simon
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Erika F. Sims
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Isabel G. Tovar
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Emilie G. Weisser
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - John T. Wertz
- Department of Biology, Calvin College, Grand Rapids , Michigan, United States of America
| | | | - Kurt E. Williamson
- Department of Biology, College of William and Mary, Williamsburg, Virginia, United States of America
| | - Bo Zhang
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg , Virginia, United States of America
| | - Paras Jain
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Mariana Piuri
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Roger W. Hendrix
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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9
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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 AAS, Ares M, Barber AJ, Barker LP, Barrett JM, Barshop WD, Bauerle CM, Bayles IM, Belfield KL, Best AA, Borjon A, 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 SCR, Engelsen AE, English BEV, 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 YJ, Yee BC, Zaidins DA, Zhang B, Zúniga MY, Hendrix RW, Hatfull GF. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PLoS One 2011; 6:e16329. [PMID: 21298013 PMCID: PMC3029335 DOI: 10.1371/journal.pone.0016329] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 12/09/2010] [Indexed: 11/25/2022] Open
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.
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Affiliation(s)
- Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Craig L. Peebles
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Zein Al-Atrache
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Turi A. Alcoser
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lisa M. Alexander
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Matthew B. Alfano
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Samantha T. Alford
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Nichols E. Amy
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Marie D. Anderson
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Alexander G. Anderson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Andrew A. S. Ang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Manuel Ares
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Amanda J. Barber
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Lucia P. Barker
- Howard Hughes Medical Institute, Science Education Alliance, Chevy Chase, Maryland United States of America
| | - Jonathan M. Barrett
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - William D. Barshop
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Cynthia M. Bauerle
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Ian M. Bayles
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Katherine L. Belfield
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Aaron A. Best
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Agustin Borjon
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Charles A. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christine A. Boyer
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kevin W. Bradley
- Howard Hughes Medical Institute, Science Education Alliance, Chevy Chase, Maryland United States of America
| | - Victoria A. Bradley
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Lauren N. Broadway
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Keshav Budwal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kayla N. Busby
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ian W. Campbell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Anne M. Campbell
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Alyssa Carey
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Rebekah D. Chew
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Chelsea L. Cockburn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Lianne B. Cohen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey M. Corajod
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Kimberly R. Davis
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Lisa Deng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Dee R. Denver
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Breyon R. Dixon
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Sahrish Ekram
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Angela E. Engelsen
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Belle E. V. English
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Marcella L. Erb
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Crystal Estrada
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Laura Z. Filliger
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ann M. Findley
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Lauren Forbes
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mark H. Forsyth
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Tyler M. Fox
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Melissa J. Fritz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roberto Garcia
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Zindzi D. George
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Anne E. Georges
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | | | - Shannon Goff
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Rebecca Goldstein
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Kobie C. Gordon
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Russell D. Green
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Stephanie L. Guerra
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Krysta R. Guiney-Olsen
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Bridget G. Guiza
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Leila Haghighat
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Garrett V. Hagopian
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Catherine J. Harmon
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jeremy S. Harmson
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Grant A. Hartzog
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Samuel E. Harvey
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Siping He
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kevin J. He
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kaitlin E. Healy
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ellen R. Higinbotham
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Erin N. Hildebrandt
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jason H. Ho
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Gina M. Hogan
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Victoria G. Hohenstein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan A. Holz
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Vincent J. Huang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Ericka L. Hufford
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Peter M. Hynes
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Arrykka S. Jackson
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Erica C. Jansen
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jonathan Jarvik
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Paul G. Jasinto
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Tuajuanda C. Jordan
- Howard Hughes Medical Institute, Science Education Alliance, Chevy Chase, Maryland United States of America
| | - Tomas Kasza
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Murray A. Katelyn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jessica S. Kelsey
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Larisa A. Kerrigan
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Daryl Khaw
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Junghee Kim
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Z. Knutter
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gail V. Larkin
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Jennifer R. Laroche
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Asma Latif
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kohana D. Leuba
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sequoia I. Leuba
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lynn O. Lewis
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kathryn E. Loesser-Casey
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Courtney A. Long
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - A. Javier Lopez
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Nicholas Lowery
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Tina Q. Lu
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Victor Mac
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Isaac R. Masters
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jazmyn J. McCloud
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Molly J. McDonough
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Andrew J. Medenbach
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Anjali Menon
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Rachel Miller
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Brandon K. Morgan
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Patrick C. Ng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Elvis Nguyen
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Katrina T. Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Emilie T. Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kaylee M. Nicholson
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Lindsay A. Parnell
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Caitlin E. Peirce
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Allison M. Perz
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Luke J. Peterson
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Rachel E. Pferdehirt
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Seegren V. Philip
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tamsen Polley
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Erica J. Puopolo
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Hannah S. Rabinowitz
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Michael J. Resiss
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Corwin N. Rhyan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Yetta M. Robinson
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Lauren L. Rodriguez
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Andrew C. Rose
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Jeffrey D. Rubin
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jessica A. Ruby
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Margaret S. Saha
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - James W. Sandoz
- Department of Biological Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Judith Savitskaya
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Dale J. Schipper
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | | | - Amanda R. Schott
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - J. Bradley Segal
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Christopher D. Shaffer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Kathryn E. Sheldon
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Erica M. Shepard
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan W. Shepardson
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Madav K. Shroff
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jessica M. Simmons
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Erika F. Simms
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brandy M. Simpson
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kathryn M. Sinclair
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Robert L. Sjoholm
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Ingrid J. Slette
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Blaire C. Spaulding
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Clark L. Straub
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Joseph Stukey
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Trevor Sughrue
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Tin-Yun Tang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Lyons M. Tatyana
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Stephen B. Taylor
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Barbara J. Taylor
- Department of Zoology, Oregon State University, Corvallis, Oregon, United States of America
| | - Louise M. Temple
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jasper V. Thompson
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Michael P. Tokarz
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Stephanie E. Trapani
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Alexander P. Troum
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Jonathan Tsay
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Anthony T. Tubbs
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jillian M. Walton
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Danielle H. Wang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Hannah Wang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - John R. Warner
- Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, United States of America
| | - Emilie G. Weisser
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Samantha C. Wendler
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, United States of America
| | - Kathleen A. Weston-Hafer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hilary M. Whelan
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Kurt E. Williamson
- Biology Department, College of William & Mary, Williamsburg, Virginia, United States of America
| | - Angelica N. Willis
- Biology Department, A. Paul Schaap Science Center, Hope College, Holland, Michigan, United States of America
| | - Hannah S. Wirtshafter
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Theresa W. Wong
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Phillip Wu
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Yun jeong Yang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Brandon C. Yee
- Biological Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - David A. Zaidins
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Bo Zhang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Melina Y. Zúniga
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Roger W. Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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10
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Shaffer CD, Alvarez C, Bailey C, Barnard D, Bhalla S, Chandrasekaran C, Chandrasekaran V, Chung HM, Dorer DR, Du C, Eckdahl TT, Poet JL, Frohlich D, Goodman AL, Gosser Y, Hauser C, Hoopes LL, Johnson D, Jones CJ, Kaehler M, Kokan N, Kopp OR, Kuleck GA, McNeil G, Moss R, Myka JL, Nagengast A, Morris R, Overvoorde PJ, Shoop E, Parrish S, Reed K, Regisford EG, Revie D, Rosenwald AG, Saville K, Schroeder S, Shaw M, Skuse G, Smith C, Smith M, Spana EP, Spratt M, Stamm J, Thompson JS, Wawersik M, Wilson BA, Youngblom J, Leung W, Buhler J, Mardis ER, Lopatto D, Elgin SC. The genomics education partnership: successful integration of research into laboratory classes at a diverse group of undergraduate institutions. CBE Life Sci Educ 2010; 9:55-69. [PMID: 20194808 PMCID: PMC2830162 DOI: 10.1187/09-11-0087] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.
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Affiliation(s)
| | - Consuelo Alvarez
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Cheryl Bailey
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664
| | - Daron Barnard
- Department of Biology, Worcester State College, Worcester, MA 01602
| | - Satish Bhalla
- Department of Computer Science and Engineering, Johnson C. Smith University, Charlotte, NC 28216
| | | | | | - Hui-Min Chung
- Department of Biology, University of West Florida, Pensacola, FL 32514
| | | | - Chunguang Du
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043
| | - Todd T. Eckdahl
- Department of Biology, Missouri Western State University, Saint Joseph, MO 64507
| | - Jeff L. Poet
- Department of Mathematics, Missouri Western State University, Saint Joseph, MO 64507
| | - Donald Frohlich
- Department of Biology, University of St. Thomas, Houston, TX 77006
| | - Anya L. Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407-0402
| | - Yuying Gosser
- Grove School of Engineering, The City College of New York, New York, NY 10031
| | - Charles Hauser
- Department of Bioinformatics, St. Edward's University, Austin, TX 78704
| | | | - Diana Johnson
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | | | - Marian Kaehler
- Department of Biology, Luther College, Decorah, IA 52101
| | - Nighat Kokan
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Olga R. Kopp
- Department of Biology, Utah Valley University, Orem, UT 84058
| | - Gary A. Kuleck
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045-2659
| | - Gerard McNeil
- Department of Biology, York College–The City University of New York, Jamaica, NY 11451
| | - Robert Moss
- Department of Biology, Wofford College, Spartanburg, SC 29303-3663
| | - Jennifer L. Myka
- Science Department, Galen College of Nursing, Cincinnati, OH 45241
| | - Alexis Nagengast
- Department of Chemistry and Biochemistry, Widener University, Chester, PA 19013
| | - Robert Morris
- Department of Biology and Biochemistry, Widener University, Chester, PA 19013
| | | | - Elizabeth Shoop
- Department of Mathematics and Computer Science, Macalester College, St. Paul, MN 55105
| | - Susan Parrish
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Kelynne Reed
- Department of Biology, Austin College, Sherman, TX 75090-4400
| | | | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | | | - Ken Saville
- Department of Biology, Albion College, Albion, MI 49224
| | | | - Mary Shaw
- Department of Biology, New Mexico Highlands University, Las Vegas, NM 87701
| | - Gary Skuse
- Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623
| | - Christopher Smith
- Department of Biology, San Francisco State University, San Francisco, CA 94132
| | - Mary Smith
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411
| | - Eric P. Spana
- Department of Biology, Duke University, Durham, NC 27708-0001
| | - Mary Spratt
- Department of Biology, William Woods University, Fulton, MO 65251
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, IN 47722
| | | | - Matthew Wawersik
- Department of Biology, College of William and Mary, Williamsburg, VA 23187-8795
| | | | - Jim Youngblom
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jeremy Buhler
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Elaine R. Mardis
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108; and
| | - David Lopatto
- Department of Psychology, Grinnell College, Grinnell, IA 50112
| | - Sarah C.R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
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Riddle NC, Shaffer CD, Elgin SCR. A lot about a little dot - lessons learned from Drosophila melanogaster chromosome 4. Biochem Cell Biol 2009; 87:229-41. [PMID: 19234537 DOI: 10.1139/o08-119] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The fourth chromosome of Drosophila melanogaster has a number of unique properties that make it a convenient model for the study of chromatin structure. Only 4.2 Mb overall, the 1.2 Mb distal arm of chromosome 4 seen in polytene chromosomes combines characteristics of heterochromatin and euchromatin. This domain has a repeat density of ~35%, comparable to some pericentric chromosome regions, while maintaining a gene density similar to that of the other euchromatic chromosome arms. Studies of position-effect variegation have revealed that heterochromatic and euchromatic domains are interspersed on chromosome 4, and both cytological and biochemical studies have demonstrated that chromosome 4 is associated with heterochromatic marks, such as heterochromatin protein 1 and histone 3 lysine 9 methylation. Chromosome 4 is also marked by POF (painting-of-fourth), a chromosome 4-specific chromosomal protein, and utilizes a dedicated histone methyltransferase, EGG. Studies of chromosome 4 have helped to shape our understanding of heterochromatin domains and their establishment and maintenance. In this review, we provide a synthesis of the work to date and an outlook to the future.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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Lopatto D, Alvarez C, Barnard D, Chandrasekaran C, Chung HM, Du C, Eckdahl T, Goodman AL, Hauser C, Jones CJ, Kopp OR, Kuleck GA, McNeil G, Morris R, Myka JL, Nagengast A, Overvoorde PJ, Poet JL, Reed K, Regisford G, Revie D, Rosenwald A, Saville K, Shaw M, Skuse GR, Smith C, Smith M, Spratt M, Stamm J, Thompson JS, Wilson BA, Witkowski C, Youngblom J, Leung W, Shaffer CD, Buhler J, Mardis E, Elgin SCR. Undergraduate research. Genomics Education Partnership. Science 2008; 322:684-5. [PMID: 18974335 DOI: 10.1126/science.1165351] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- D Lopatto
- Grinnell College, Grinnell, Iowa, USA.
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Lopatto D, Alvarez C, Barnard D, Chandrasekaran C, Chung HM, Du C, Eckdahl T, Goodman AL, Hauser C, Jones CJ, Kopp OR, Kuleck GA, McNeil G, Morris R, Myka JL, Nagengast A, Overvoorde PJ, Poet JL, Reed K, Regisford G, Revie D, Rosenwald A, Saville K, Shaw M, Skuse GR, Smith C, Smith M, Spratt M, Stamm J, Thompson JS, Wilson BA, Witkowski C, Youngblom J, Leung W, Shaffer CD, Buhler J, Mardis E, Elgin SCR. Undergraduate research. Genomics Education Partnership. Science 2008. [PMID: 18974335 DOI: 10.1126/science.1165351.under] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.
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Affiliation(s)
- D Lopatto
- Grinnell College, Grinnell, Iowa, USA.
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Shaffer CD, Cenci G, Thompson B, Stephens GE, Slawson EE, Adu-Wusu K, Gatti M, Elgin SCR. The large isoform of Drosophila melanogaster heterochromatin protein 2 plays a critical role in gene silencing and chromosome structure. Genetics 2006; 174:1189-204. [PMID: 16980400 PMCID: PMC1667101 DOI: 10.1534/genetics.106.057604] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster heterochromatin protein 2 (HP2) interacts with heterochromatin protein 1 (HP1). In polytene chromosomes, HP2 and HP1 colocalize at the chromocenter, telomeres, and the small fourth chromosome. We show here that HP2 is present in the arms as well as the centromeric regions of mitotic chromosomes. We also demonstrate that Su(var)2-HP2 exhibits a dosage-dependent modification of variegation of a yellow reporter transgene, indicating a structural role in heterochromatin formation. We have isolated and characterized 14 new mutations in the Su(var)2-HP2 gene. Using wm4h, many (but not all) mutant alleles show dominant Su(var) activity. Su(var)2-HP2 mutant larvae show a wide variety of mitotic abnormalities, but not the telomere fusion seen in larvae deficient for HP1. The Su(var)2-HP2 gene codes for two isoforms: HP2-L (approximately 365 kDa) and HP2-S (approximately 175 kDa), lacking exons 5 and 6. In general, mutations that affect only the larger isoform result in more pronounced defects than do mutations common to both isoforms. This suggests that an imbalance between large and small isoforms is particularly deleterious. These results indicate a role for HP2 in the structural organization of chromosomes and in heterochromatin-induced gene silencing and show that the larger isoform plays a critical role in these processes.
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Slawson EE, Shaffer CD, Malone CD, Leung W, Kellmann E, Shevchek RB, Craig CA, Bloom SM, Bogenpohl J, Dee J, Morimoto ETA, Myoung J, Nett AS, Ozsolak F, Tittiger ME, Zeug A, Pardue ML, Buhler J, Mardis ER, Elgin SCR. Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biol 2006; 7:R15. [PMID: 16507169 PMCID: PMC1431729 DOI: 10.1186/gb-2006-7-2-r15] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 09/15/2005] [Accepted: 01/25/2006] [Indexed: 11/10/2022] Open
Abstract
Sequencing and analysis of fosmid hybridization to the dot chromosomes of Drosophila virilis and D. melanogaster suggest that repetitive elements and density are important in determining higher-order chromatin packaging. Background Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago. Results Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4 %). Conclusion Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.
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Affiliation(s)
| | | | - Colin D Malone
- Biology Department, Washington University, St Louis, MO 63130, USA
| | - Wilson Leung
- Biology Department, Washington University, St Louis, MO 63130, USA
| | - Elmer Kellmann
- Biology Department, Washington University, St Louis, MO 63130, USA
| | | | - Carolyn A Craig
- Biology Department, Washington University, St Louis, MO 63130, USA
| | - Seth M Bloom
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - James Bogenpohl
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - James Dee
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Emiko TA Morimoto
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Jenny Myoung
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Andrew S Nett
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Fatih Ozsolak
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Mindy E Tittiger
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Andrea Zeug
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Mary-Lou Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jeremy Buhler
- Computer Science and Engineering, Washington University, St Louis, MO 63130, USA
| | - Elaine R Mardis
- Genome Sequencing Center and Department of Genetics, Washington University, St Louis, MO 63108, USA
| | - Sarah CR Elgin
- Biology Department, Washington University, St Louis, MO 63130, USA
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16
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Shaffer CD, Stephens GE, Thompson BA, Funches L, Bernat JA, Craig CA, Elgin SCR. Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin. Proc Natl Acad Sci U S A 2002; 99:14332-7. [PMID: 12376620 PMCID: PMC137884 DOI: 10.1073/pnas.212458899] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Indexed: 11/18/2022] Open
Abstract
Heterochromatin protein 1 (HP1), first discovered in Drosophila melanogaster, is a highly conserved chromosomal protein implicated in both heterochromatin formation and gene silencing. We report here characterization of an HP1-interacting protein, heterochromatin protein 2 (HP2), which codistributes with HP1 in the pericentric heterochromatin. HP2 is a large protein with two major isoforms of approximately 356 and 176 kDa. The smaller isoform is produced from an alternative splicing pattern in which two exons are skipped. Both isoforms contain the domain that interacts with HP1; the larger isoform contains two AT-hook motifs. Mutations recovered in HP2 act as dominant suppressors of position effect variegation, confirming a role in heterochromatin spreading and gene silencing.
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17
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Shaffer CD, Tong XM, Pratt RH. Triply differential cross section and polarization correlations in electron bremsstrahlung emission. Phys Rev A 1996; 53:4158-4163. [PMID: 9913382 DOI: 10.1103/physreva.53.4158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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18
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Abstract
Recent results suggest that the Drosophila transcriptional activator known as GAGA factor functions by influencing chromatin structure.
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Affiliation(s)
- H Granok
- Department of Biology, Washington University, St Louis, Missouri 63130, USA
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19
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Affiliation(s)
- C D Shaffer
- Department of Biology, Washington University, St. Louis, Missouri 63130
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20
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Affiliation(s)
- C D Shaffer
- Department of Biology, Washington University, St. Louis, Missouri 63130
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21
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Affiliation(s)
- C D Shaffer
- Department of Biology, Washington University, St Louis, MO 63130
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22
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Ffrench-Constant RH, Mortlock DP, Shaffer CD, MacIntyre RJ, Roush RT. Molecular cloning and transformation of cyclodiene resistance in Drosophila: an invertebrate gamma-aminobutyric acid subtype A receptor locus. Proc Natl Acad Sci U S A 1991; 88:7209-13. [PMID: 1651498 PMCID: PMC52263 DOI: 10.1073/pnas.88.16.7209] [Citation(s) in RCA: 193] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cyclodiene resistance represents 60% of the reported cases of insecticide resistance and is also present in vertebrates. Resistance is due to insensitivity of the cyclodiene/picrotoxinin binding site on the gamma-aminobutyric acid subtype A (GABAA) receptor-chloride ionophore complex. Following isolation of cyclodiene-resistant Drosophila mutants, we report the cloning of the locus conferring resistance via a "chromosomal walk" and rescue of the susceptible phenotype by P-element-mediated germ-line transformation. Amino acid sequence analysis of a cDNA from the locus reveals homology with vertebrate GABAA subunits. To our knowledge, this represents the first cloning of an invertebrate GABA receptor and also allows us to manipulate the resistance status of an insect via germ-line transformation. This gene may be useful as a selectable marker in other insect systems.
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Affiliation(s)
- R H Ffrench-Constant
- Department of Entomology, Russell Laboratories, University of Wisconsin, Madison 53706
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23
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Shaffer CD, MacIntyre RJ. The isolation of the acid phosphatase-1 gene of Drosophila melanogaster and a chromosomal breakpoint inducing its position effect variegation. Mol Gen Genet 1990; 224:49-56. [PMID: 2177524 DOI: 10.1007/bf00259450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over 120 kb of contiguous genomic DNA sequence derived from the 99C-99D region of the Drosophila melanogaster third chromosome were isolated by molecular cloning. Sequences within this region required for the expression of the lysosomal gene-enzyme system acid phosphatase-1 (Acph-1) were identified by both P element-mediated germline transformation and transient expression and lie within a single 5 kb fragment. Acph-1 is encoded by a 2.1 kb poly(A)+ RNA transcript, which is expressed throughout development. Enzyme activity peaks also correlate with increases in RNA abundance. The ca-74 deletion, which exhibits position effect variegation at the Acph-1 gene (Frisardi and MacIntyre 1984), was also partially characterized. The variegating ca-74 breakpoint is located approximately 20 kb proximal to the Acph-1 gene. Results suggest that the heterochromatin at this breakpoint comprises highly repetitive or satellite DNA.
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Affiliation(s)
- C D Shaffer
- Section of Genetics and Development, Cornell University, Ithaca, NY 14853
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Yamamoto AH, Komma DJ, Shaffer CD, Pirrotta V, Endow SA. The claret locus in Drosophila encodes products required for eyecolor and for meiotic chromosome segregation. EMBO J 1989; 8:3543-52. [PMID: 2479546 PMCID: PMC402033 DOI: 10.1002/j.1460-2075.1989.tb08526.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The claret (ca) locus in Drosophila encodes products that are needed both for wild-type eyecolor and for correct meiotic chromosome segregation. Mutants described previously provide evidence that two mutationally independent coding regions are present at ca. We have recovered six new P element-induced and one spontaneous ca mutant. Four of these new mutants affect both eyecolor and chromosome segregation. The high frequency of co-mutation of these two functions suggests that the corresponding genes are closely adjacent to one another. We recovered genomic DNA sequences corresponding to the ca locus by chromosome walking, and showed using revertant analysis that the cloned region encodes ca+. Transformation experiments demonstrate that the mutant effect resulting in meiotic chromosome non-disjunction (nd) and loss is fully rescued by DNA from the cloned region. Two RNAs of 7.4 and 2.2 kb have been identified by Northern blot analysis as the putative eyecolor and segregational products. Expression of the RNAs with respect to males and females, and their presence or absence in ca and nd mutants indicate that the 7.4 kb RNA corresponds to the product needed for wild-type eyecolor and the 2.2 kb RNA is the product required for normal chromosome segregation. These RNAs are transcribed in opposite directions to one another. Alleles that affect both eyecolor and chromosome segregation are deletion mutants that affect both transcripts. Thus, the putative eyecolor and segregational products are encoded by separate genes. Mutants that affect both eyecolor and chromosome segregation apparently do so because they delete essential regions of both genes.
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Affiliation(s)
- A H Yamamoto
- Department of Microbiology and Immunology, Duke University Medical Center, Durham, NC 27710
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