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Lopatto D, Silver Key SC, Van Stry M, Siders J, Leung W, Sandlin KM, Rele CP, Reed LK. Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy. J Microbiol Biol Educ 2023; 24:e00039-23. [PMID: 38230306 PMCID: PMC10790580 DOI: 10.1128/jmbe.00039-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 01/18/2024]
Abstract
The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https://www.thegep.org). However, our web-based research adapted well to the remote learning environment. As usual, students who engaged in the GEP's Course-based Undergraduate Research Experience (CURE) received digital projects based on genetic information within assembled Drosophila genomes. Adaptations for remote implementation included moving new member faculty training and peer Teaching Assistant office hours from in-person to online. Surprisingly, our faculty membership significantly increased and, hence, the number of supported students. Furthermore, despite the mostly virtual instruction of the 2020-2021 academic year, there was no significant decline in student learning nor attitudes. Based on successfully expanding the GEP CURE within a virtual learning environment, we provide four strategic lessons we infer toward democratizing science education. First, it appears that increasing access to scientific research and professional development opportunities by supporting virtual, cost-free attendance at national conferences attracts more faculty members to educational initiatives. Second, we observed that transitioning new member training to an online platform removed geographical barriers, reducing time and travel demands, and increased access for diverse faculty to join. Third, developing a Virtual Teaching Assistant program increased the availability of peer support, thereby improving the opportunities for student success. Finally, increasing access to web-based technology is critical for providing equitable opportunities for marginalized students to fully participate in research courses. Online CUREs have great potential for democratizing science education.
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Affiliation(s)
- David Lopatto
- Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, Iowa, USA
| | - S. Catherine Silver Key
- Biological and Biomedical Sciences Department, North Carolina Central University, Durham, North Carolina, USA
| | | | - Jamie Siders
- Department of Biological & Allied Health Sciences, Ohio Northern University, Ada, Ohio, USA
| | - Wilson Leung
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Katie M. Sandlin
- Department of Biological Sciences, University of Alabama at Tuscaloosa, Tuscaloosa, Alabama, USA
| | - Chinmay P. Rele
- Department of Biological Sciences, University of Alabama at Tuscaloosa, Tuscaloosa, Alabama, USA
| | - The Genomics Education PartnershipHare-HarrisAbby E.HabermanAdamKleinschmitAdam J.YuAlderSawaAlexaNagengastAlexisHowardAlishaAlmaEEstradaRodriguezHarkAmy T.AlmeidaAnaArshamAndrew M.CorsiAnn K.AllenAnna K.AragonAnthony D.SreenivasanAparnaYowlerBrianHowellCarina E.ReinkeCatherineMcKennaChelsey C.FleetChristine M.JonesChristopher J.ArrigoCindyWolfeCindyUhde-StoneClaudiaBarnardDaronDon PaetkauEnrique Rodriguez-BorreroMerkhoferEvanMellgrenEve M.Safadi-ChamberlainFaridaFindlayGeoffrey D.McNeilGerardBretscherHeidi S.UllahHemayetMistryHemlataHoward XuH.BoseIndraniVincentJackKageyJacob D.Wittke-ThompsonJacqueline K.BedardJames E. J.GoddeJames S.PriceJames V.DyerJamie O.Roecklein-CanfieldJennifer A.JemcJenniferKennellJenniferGillardJeroenBravermanJohn M.StangaJohn P.StammJoyceMartínez-CruzadoJuan C.LeathermanJudithDiAngeloJustin R.ThackerayJustinSchmeichelKaren L.TeeterKatherine C.BieserKaylaAgrimsonKellie S.SavilleKennethPaliulisLeocadiaLongLindsey J.KadlecLisaLogan JohnsonM.SustacekMaire K.SantistebanMariaMontes-MatiasMarieBurgMartin G.SmithMary Ann V.SkerrittMatthewWawersikMatthewYangMelinda A.RubinMichael R.EllerMicheleHall-WoodsMonica L.MinkovskyNatalieVelmeshevNicole SalazarKokanNighat P.TsotakosNikolaosVelazquez-UlloaNormaCroonquistPaulaGlaserRivka L.DrewellRobert A.ElginSarah C. R.JusticeSarahTannerScottPageShallee T.FungSiaumin
- Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, Iowa, USA
- Biological and Biomedical Sciences Department, North Carolina Central University, Durham, North Carolina, USA
- Department of Biology, Lane College, Jackson, Tennessee, USA
- Department of Biological & Allied Health Sciences, Ohio Northern University, Ada, Ohio, USA
- Department of Biology, Washington University, St. Louis, Missouri, USA
- Department of Biological Sciences, University of Alabama at Tuscaloosa, Tuscaloosa, Alabama, USA
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama at Tuscaloosa, Tuscaloosa, Alabama, USA
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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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3
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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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4
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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
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- Department of Biology, Wilkes University, Wilkes-Barre, PA 18701
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- 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
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- 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
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- 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
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- 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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5
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Sloan RS, Swanson CI, Gavilano L, Smith KN, Malek PY, Snow-Smith M, Duronio RJ, Key SCS. Characterization of null and hypomorphic alleles of the Drosophila l(2)dtl/cdt2 gene: Larval lethality and male fertility. Fly (Austin) 2012; 6:173-83. [PMID: 22722696 DOI: 10.4161/fly.20247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Drosophila lethal(2)denticleless (l(2)dtl) gene was originally reported as essential for embryogenesis and formation of the rows of tiny hairs on the larval ventral cuticle known as denticle belts. It is now well-established that l(2)dtl (also called cdt2) encodes a subunit of a Cullin 4-based E3 ubiquitin ligase complex that targets a number of key cell cycle regulatory proteins, including p21, Cdt1, E2F1 and Set8, to prevent replication defects and maintain cell cycle control. To investigate the role of l(2)dtl/cdt2 during development, we characterized existing l(2)dtl/cdt2 mutants and generated new deletion alleles, using P-element excision mutagenesis. Surprisingly, homozygous l(2)dtl/cdt2 mutant embryos developed beyond embryogenesis, had intact denticle belts, and lacked an observable embryonic replication defect. These mutants died during larval stages, affirming that loss of l(2)dtl/cdt2 function is lethal. Our data show that L(2)dtl/Cdt2 is maternally deposited, remains nuclear throughout the cell cycle, and has a previously unreported, elevated expression in the developing gonads. We also find that E2f1 regulates l(2)dtl/cdt2 expression during embryogenesis, possibly via several highly conserved putative E2f1 binding sites near the l(2)dtl/cdt2 promoter. Finally, hypomorphic allele combinations of the l(2)dtl/cdt2 gene result in a novel phenotype: viable, low-fertility males. We conclude that "denticleless" is a misnomer, but that l(2)dtl/cdt2 is an essential gene for Drosophila development.
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Affiliation(s)
- Roketa S Sloan
- Department of Biology, North Carolina Central University, Durham, NC USA
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Silver Key SC, Reaves D, Turner F, Bang JJ. Impacts of Silver Nanoparticle Ingestion on Pigmentation and Developmental Progression in Drosophila. ACTA ACUST UNITED AC 2011. [DOI: 10.5147/ajb.v1i3.10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Cayirlioglu P, Ward WO, Silver Key SC, Duronio RJ. Transcriptional repressor functions of Drosophila E2F1 and E2F2 cooperate to inhibit genomic DNA synthesis in ovarian follicle cells. Mol Cell Biol 2003; 23:2123-34. [PMID: 12612083 PMCID: PMC149482 DOI: 10.1128/mcb.23.6.2123-2134.2003] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [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: 10/21/2002] [Revised: 11/14/2002] [Accepted: 12/23/2002] [Indexed: 11/20/2022] Open
Abstract
Individual members of the E2F/DP protein family control cell cycle progression by acting predominantly as an activator or repressor of transcription. In Drosophila melanogaster the E2f1, E2f2, Dp, and Rbf1 genes all contribute to replication control in ovarian follicle cells, which become 16C polyploid and subsequently undergo chorion gene amplification late in oogenesis. Mutation of E2f2, Dp, or Rbf1 causes ectopic DNA replication throughout the follicle cell genome during gene amplification cycles. Here we show by both reverse transcription-PCR and DNA microarray analysis that the transcripts of prereplication complex (pre-RC) genes are elevated compared to the wild type in E2f2, Dp, and Rbf1 mutant follicle cells. For some genes the magnitude of this transcriptional derepression is greater in Rbf1 than in E2f2 mutants. These differences correlate with differences in the magnitude of the replication defects in follicle cells, which attain an inappropriate 32C DNA content in both Rbf1 and Dp mutants but not in E2f2 mutants. The ectopic genomic replication of E2f2 mutant follicle cells can be suppressed by reducing the Orc2, Orc5, or Mcm2 gene dose by half, indicating that small changes in pre-RC gene expression can affect DNA synthesis in these cells. We conclude that RBF1 forms complexes with both E2F1/DP and E2F2/DP that cooperate to repress the expression of pre-RC genes, which helps confine DNA synthesis to sites of gene amplification. In contrast, E2F1 and E2F2 repressors function redundantly for some genes in the embryo. Thus, the relative functional contributions of E2F1 and E2F2 to gene expression and cell cycle control depends on the developmental context.
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Affiliation(s)
- Pelin Cayirlioglu
- Department of Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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