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Yang MA, Korsnack K. Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom. Biol Methods Protoc 2024; 9:bpae013. [PMID: 38463936 PMCID: PMC10924719 DOI: 10.1093/biomethods/bpae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/27/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Introducing bioinformatics-focused concepts and skills in a biology classroom is difficult, especially in introductory biology classrooms. Course-based Undergraduate Research Experiences (CUREs) facilitate this process, introducing genomics and bioinformatics through authentic research experiences, but the many learning objectives needed in scientific research and communication, foundational biology concepts, and bioinformatics-focused concepts and skills can make the process challenging. Here, the pairing of specifications grading with a bioinformatics-focused CURE developed by the Genomics Education Partnership is described. The study examines how the course structure with specifications grading facilitated scaffolding of writing assignments, group work, and metacognitive activities; and describes the synergies between CUREs and specifications grading. CUREs require mastery of related concepts and skills for working through the research process, utilize common research practices of revision and iteration, and encourage a growth mindset to learning-all of which are heavily incentivized in assessment practices focused on specifications grading.
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Affiliation(s)
- Melinda A Yang
- Department of Biology, University of Richmond, Richmond, VA 23173, United States
| | - Kylie Korsnack
- Teaching and Scholarship Hub, University of Richmond, Richmond, VA 23173, United States
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Taylor MB, Warwick AR, Skophammer R, Boyer JM, Geck RC, Gunkelman K, Walson M, Rowley PA, Dunham MJ. yEvo: A modular eukaryotic genetics and evolution research experience for high school students. Ecol Evol 2024; 14:e10811. [PMID: 38192907 PMCID: PMC10771926 DOI: 10.1002/ece3.10811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 11/26/2023] [Indexed: 01/10/2024] Open
Abstract
The resources for carrying out and analyzing microbial evolution experiments have become more accessible, making it possible to expand these studies beyond the research laboratory and into the classroom. We developed five connected, standards-aligned yeast evolution laboratory modules, called "yEvo," for high school students. The modules enable students to take agency in answering open-ended research questions. In Module 1, students evolve baker's yeast to tolerate an antifungal drug, and in subsequent modules, investigate how evolved yeasts adapted to this stressful condition at both the phenotype and genotype levels. We used pre- and post-surveys from 72 students at two different schools and post-interviews with students and teachers to assess our program goals and guide module improvement over 3 years. We measured changes in student conceptions, confidence in scientific practices, and interest in STEM careers. Students who participated in yEvo showed improvements in understanding of activity-specific concepts and reported increased confidence in designing a valid biology experiment. Student experimental data replicated literature findings and has led to new insights into antifungal resistance. The modules and provided materials, alongside "proof of concept" evaluation metrics, will serve as a model for other university researchers and K - 16 classrooms interested in engaging in open-ended research questions using yeast as a model system.
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Affiliation(s)
- M. Bryce Taylor
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
- Program in BiologyLoras CollegeDubuqueIowaUSA
| | - Alexa R. Warwick
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | | | | | - Renee C. Geck
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Kristin Gunkelman
- Department of Teacher EducationMichigan State UniversityEast LansingMichiganUSA
| | - Margaux Walson
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Paul A. Rowley
- Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Maitreya J. Dunham
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
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Undergraduate Disabled Students as Knowledge Producers Including Researchers: Perspectives of Disabled Students. EDUCATION SCIENCES 2022. [DOI: 10.3390/educsci12020077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Knowledge influences policy development and policies impact disabled people. Scientific and technological advancements, including neuro-advancements and their governance, have social implications for disabled people. However, knowledge is missing on this topic. Although efforts are underway to increase the number of disabled academics, the numbers remain low. Engaging undergraduate disabled students in knowledge production, especially research, could decrease the knowledge deficit and increase the pool of disabled students considering an academic career. We performed 10 semi-structured interviews of disabled students to understand the reality of undergraduate disabled students as knowledge producers, including researchers. Using a directed thematic content analysis, we found that participants felt that undergraduate disabled students were insufficiently exposed to and supported in the identity of being knowledge producers including researchers. Participants identified ethical, legal, and social implications of science and technology and argued that undergraduate disabled students and disabled people have a role to play in the discussions of these. Exposing disabled students at the undergraduate and high school level to knowledge production including researcher identity could increase the numbers of undergraduate disabled researchers, disabled academics, and disabled students doing research in the community after graduation and decrease the knowledge gaps around the social situation of disabled people.
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Undergraduate Disabled Students as Knowledge Producers including Researchers: A Missed Topic in Academic Literature. EDUCATION SCIENCES 2019. [DOI: 10.3390/educsci9040259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Research experience is beneficial for undergraduate students for many reasons. For example, it is argued in academic literature and in reports produced by various organizations that engage with science, technology, engineering and math (STEM) education and science education that undergraduate research experience increases the graduation rate in STEM disciplines as well as the amount of students thinking about STEM careers. As such, being researchers should also be of benefit to undergraduate disabled students in all disciplines including STEM education. However, given that undergraduate disabled students encounter many problems within post-secondary education, including STEM education, undergraduate disabled students might encounter problems in becoming researchers. Policies are to be guided by knowledge and evidence. However, knowledge and evidence deficits exist in relation to the lived experience of disabled people. Undergraduate disabled students could decrease the knowledge deficit as researchers and knowledge producers. The numbers of disabled academic faculty are judged as being too low and efforts are under way to increase the number of disabled academics. Increasing the number of undergraduate disabled researchers might increase the available pool of disabled students that pursue an academic career. Given the important role research performed by undergraduate disabled students can play and given that many studies highlight problems for disabled students in post-secondary education in general, we used a scoping review approach to investigate the coverage of undergraduate disabled students as knowledge producers, including as researchers, in the academic literature. Using various search strategies, we obtained 1299 initial hits. However, only 15 had relevant content. No study investigated how undergraduate disabled students select their research topics or how they are enticed to pursue research projects outside of a course-based framework. No study looked at the linkage between being an undergraduate disabled researcher and career choices or using the obtained research skills on the undergraduate level in one’s role as a community member after graduation. Our findings suggest an opportunity for many fields, ranging from disability studies to STEM education, to generate more empirical data and conceptual work on the role of undergraduate disabled students as knowledge producers including as researchers. Such studies could help to increase the numbers of undergraduate disabled students as knowledge producers, including researchers, which in turn could help to increase (a) the number of disabled academics, (b) the number of disabled students who perform research in the community after graduation, (c) the degree success of disabled students and (d) the knowledge available on the social situation of disabled people.
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Involving undergraduates in genomics research to narrow the education-research gap. Nat Biotechnol 2018; 36:369-371. [PMID: 29621227 DOI: 10.1038/nbt.4113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Moitra K. Releasing the "GENI": integrating authentic microbial genomics research into the classroom through GENI-ACT. FEMS Microbiol Lett 2018; 364:4443195. [PMID: 29040493 DOI: 10.1093/femsle/fnx215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 10/04/2017] [Indexed: 11/15/2022] Open
Abstract
The integration of genomics research into the undergraduate biology curriculum provides students with the opportunity to become familiar with bioinformatics tools and answer original research questions. Our purpose with this research project was to upscale the research experience through integration with classroom experience giving students access to authentic research projects. Students annotated 60 predicted ABC genes of Methanothermobacter thermautotrophicus and Methanobacterium sp. SWAN-1, and they were required to present a research poster to demonstrate their understanding of the project. During this research project a number of tests, assessments and surveys were conducted to assess familiarity with technical and conceptual understanding of genome annotation, satisfaction with annotation instruction, gain in bioinformatics research skills, scientific communications skills and increased student interest in research. We found that students gained significant skills in bioinformatics, specifically genome annotation skills and also gained confidence in their abilities to carry out scientific research. As a result of this authentic undergraduate research experience under-represented students were motivated to pursue future careers in STEM fields.
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Affiliation(s)
- Karobi Moitra
- Department of Biology, Trinity Washington University, College Of Arts and Sciences, 125 Michigan Avenue NE, Washington DC 20017, USA
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Reeves TD, Warner DM, Ludlow LH, O'Connor CM. Pathways over Time: Functional Genomics Research in an Introductory Laboratory Course. CBE LIFE SCIENCES EDUCATION 2018; 17:ar1. [PMID: 29326101 PMCID: PMC6007769 DOI: 10.1187/cbe.17-01-0012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 07/28/2017] [Accepted: 10/04/2017] [Indexed: 05/30/2023]
Abstract
National reports have called for the introduction of research experiences throughout the undergraduate curriculum, but practical implementation at many institutions faces challenges associated with sustainability, cost, and large student populations. We describe a novel course-based undergraduate research experience (CURE) that introduces introductory-level students to research in functional genomics in a 3-credit, multisection laboratory class. In the Pathways over Time class project, students study the functional conservation of the methionine biosynthetic pathway between divergent yeast species. Over the five semesters described in this study, students (N = 793) showed statistically significant and sizable growth in content knowledge (d = 1.85) and in self-reported research methods skills (d = 0.65), experimental design, oral and written communication, database use, and collaboration. Statistical analyses indicated that content knowledge growth was larger for underrepresented minority students and that growth in content knowledge, but not research skills, varied by course section. Our findings add to the growing body of evidence that CUREs can support the scientific development of large numbers of students with diverse characteristics. The Pathways over Time project is designed to be sustainable and readily adapted to other institutional settings.
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Affiliation(s)
- Todd D Reeves
- Department of Measurement, Evaluation, Statistics, and Assessment, Boston College, Chestnut Hill, MA 02467
| | | | - Larry H Ludlow
- Department of Measurement, Evaluation, Statistics, and Assessment, Boston College, Chestnut Hill, MA 02467
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Temple L, Lewis L. Phage on the stage. BACTERIOPHAGE 2015; 5:e1062589. [PMID: 26442195 DOI: 10.1080/21597081.2015.1062589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/05/2015] [Accepted: 06/09/2015] [Indexed: 01/05/2023]
Abstract
The resurgence of interest in bacteriophages for use in combating antibiotic resistant bacteria is coincident with an urgent call for more effective science education practices, including hands-on learning opportunities. To address this issue, a number of solutions have been proposed, including a large educational experiment, begun in 2007 by the Howard Hughes Medical Institute and currently involving over 85 colleges and universities, which has students discovering unique phages, obtaining images, and purifying phage DNA. A subset of these phage genomes is sequenced and analyzed using bioinformatics tools. Papers describing individual phage discoveries and comparative genomic studies are being published regularly. The vast majority of students in the program are in their first year of college, a critical time in capturing their interest and retaining them as science majors. This viral discovery model is being adopted and modified by a wide variety of educational institutions using a number of different bacterial hosts. In the opinion of the authors, this program and others like it represent a model accessible to virtually any undergraduate setting. And because of these programs, bacteriophage enthusiasts (academics, health professionals, biotechnology companies) can look forward to more well prepared students entering their ranks and should anticipate many more potentially useful phages discovered and characterized.
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Affiliation(s)
- Louise Temple
- Department of Integrated Science & Technology; James Madison University ; Harrisonburg, VA USA ; Department of Biological Sciences; University of Mary Washington ; Fredericksburg, VA USA
| | - Lynn Lewis
- Department of Integrated Science & Technology; James Madison University ; Harrisonburg, VA USA ; Department of Biological Sciences; University of Mary Washington ; Fredericksburg, VA USA
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Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Front Microbiol 2015; 6:101. [PMID: 25745418 PMCID: PMC4333871 DOI: 10.3389/fmicb.2015.00101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/26/2015] [Indexed: 12/25/2022] Open
Abstract
With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | - Sébastien Aeby
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
| | | | - James Clulow
- School of Biology, University of Lausanne Lausanne, Switzerland
| | | | - Samuel Rappo
- School of Biology, University of Lausanne Lausanne, Switzerland
| | | | | | | | - Paola Benaglio
- Department of Medical Genetics, University of Lausanne Lausanne, Switzerland
| | - Laurent Falquet
- Division of Biochemistry, Department of Biology, University of Fribourg Fribourg, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | | | - Walid H Gharib
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany
| | - Keith Harshman
- Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland
| | - Burkhard Linke
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany
| | - Ryo Miyazaki
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | | | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
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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 SCIENCES EDUCATION 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] [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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Edwards RA, Haggerty JM, Cassman N, Busch JC, Aguinaldo K, Chinta S, Vaughn MH, Morey R, Harkins TT, Teiling C, Fredrikson K, Dinsdale EA. Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genomics 2013; 14:600. [PMID: 24007365 PMCID: PMC3766688 DOI: 10.1186/1471-2164-14-600] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 08/28/2013] [Indexed: 01/20/2023] Open
Abstract
Background The revolution in DNA sequencing technology continues unabated, and is affecting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences. Results Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores. Conclusions Students learned important skills for their future education and career opportunities, and a perceived increase in students’ ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life.
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Affiliation(s)
- Robert Alan Edwards
- Computer Sciences Department, San Diego State University, 5500 Campanile Dr,, San Diego 92182, CA, USA.
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May BJ. Engaging students in a bioinformatics activity to introduce gene structure and function. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2013; 14:107-109. [PMID: 23858361 PMCID: PMC3706140 DOI: 10.1128/jmbe.v14i1.496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools. This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools. Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the putative function of this gene with the use of additional online databases.
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Affiliation(s)
- Barbara J. May
- Corresponding author. Mailing address: Biology Department, College of St. Benedict/St. John’s University, PO Box 3000, Collegeville, MN 56321. Phone: 320-363-3173. Fax: 320-363-3202. E-mail:
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Beagley CT. Genome annotation in a community college cell biology lab. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:44-49. [PMID: 23382125 DOI: 10.1002/bmb.20669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Indexed: 06/01/2023]
Abstract
The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success.
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Affiliation(s)
- C Timothy Beagley
- Department of Biology, Salt Lake Community College, Salt Lake City, UT, USA.
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Shapiro C, Ayon C, Moberg-Parker J, Levis-Fitzgerald M, Sanders ER. Strategies for using peer-assisted learning effectively in an undergraduate bioinformatics course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:24-33. [PMID: 23382123 DOI: 10.1002/bmb.20665] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Indexed: 05/14/2023]
Abstract
This study used a mixed methods approach to evaluate hybrid peer-assisted learning approaches incorporated into a bioinformatics tutorial for a genome annotation research project. Quantitative and qualitative data were collected from undergraduates who enrolled in a research-based laboratory course during two different academic terms at UCLA. Findings indicate that a critical feature of the peer-assisted learning approach is to have near-peer leaders with genome annotation experience, allowing them to communicate technical and conceptual aspects of the process in the context of a research project (a.k.a., the "big picture"). These characteristics are important for creating connections between the wet lab experiments and the computer lab activities, engendering excitement about the research project and fostering engagement in bioinformatics as a discipline. Likewise, it is essential to couple tutorial training in genome annotation with appropriate instructional materials, providing detailed, step-by-step instructions for database navigation. Finally, the assessment results support this hybrid peer-assisted learning approach as a model for undergraduates to successfully learn bioinformatics in a course setting.
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Affiliation(s)
- Casey Shapiro
- Center for Educational Assessment, Office of Instructional Development, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Karsai I, Knisley J, Knisley D, Yampolsky L, Godbole A. Mentoring interdisciplinary undergraduate students via a team effort. CBE LIFE SCIENCES EDUCATION 2011; 10:250-258. [PMID: 21885821 PMCID: PMC3164564 DOI: 10.1187/cbe.10-03-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 05/30/2011] [Accepted: 06/06/2011] [Indexed: 05/31/2023]
Abstract
We describe how a team approach that we developed as a mentoring strategy can be used to recruit, advance, and guide students to be more interested in the interdisciplinary field of mathematical biology, and lead to success in undergraduate research in this field. Students are introduced to research in their first semester via lab rotations. Their participation in the research of four faculty members-two from biology and two from mathematics-gives them a first-hand overview of research in quantitative biology and also some initial experience in research itself. However, one of the primary goals of the lab rotation experience is that of developing teams of students and faculty that combine mathematics and statistics with biology and the life sciences, teams that subsequently mentor undergraduate research in genuine interdisciplinary environments. Thus, the team concept serves not only as a means of establishing interdisciplinary research, but also as a means of incorporating new students into existing research efforts that will then track those students into meaningful research of their own. We report how the team concept is used to support undergraduate research in mathematical biology and what types of team-building strategies have worked for us.
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Affiliation(s)
- Istvan Karsai
- Department of Biological Sciences, East Tennessee State University, Johnson City, USA.
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Shee K, Strong M, Guido NJ, Lue RA, Church GM, Viel A. Research, collaboration, and open science using web 2.0. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2010; 11:130-134. [PMID: 23653712 PMCID: PMC3577171 DOI: 10.1128/jmbe.v11i2.219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
There is little doubt that the Internet has transformed the world in which we live. Information that was once archived in bricks and mortar libraries is now only a click away, and people across the globe have become connected in a manner inconceivable only 20 years ago. Although many scientists and educators have embraced the Internet as an invaluable tool for research, education and data sharing, some have been somewhat slower to take full advantage of emerging Web 2.0 technologies. Here we discuss the benefits and challenges of integrating Web 2.0 applications into undergraduate research and education programs, based on our experience utilizing these technologies in a summer undergraduate research program in synthetic biology at Harvard University. We discuss the use of applications including wiki-based documentation, digital brainstorming, and open data sharing via the Web, to facilitate the educational aspects and collaborative progress of undergraduate research projects. We hope to inspire others to integrate these technologies into their own coursework or research projects.
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Affiliation(s)
- Kevin Shee
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Michael Strong
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- National Jewish Health, Denver, CO 80206
| | | | - Robert A. Lue
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Alain Viel
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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Abstract
A French research institute raises the bar for public outreach with an educational laboratory that engages 1,000 high school students per year in mini research projects.
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Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, Britton RA, Gordon SG, Heinhorst S, Reed K, Xu Z, Sanders-Lorenz ER, Axen S, Kim E, Johns M, Scott K, Kerfeld CA. Incorporating genomics and bioinformatics across the life sciences curriculum. PLoS Biol 2010; 8:e1000448. [PMID: 20711478 PMCID: PMC2919421 DOI: 10.1371/journal.pbio.1000448] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jayna L. Ditty
- Department of Biology, University of St. Thomas, St. Paul, Minnesota, United States of America
| | - Christopher A. Kvaal
- Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota, United States of America
| | - Brad Goodner
- Department of Biology, Hiram College, Hiram, Ohio, United States of America
| | - Sharyn K. Freyermuth
- Biochemistry Department, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Cheryl Bailey
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Robert A. Britton
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Stuart G. Gordon
- Department of Biology, Presbyterian College, Clinton, South Carolina, United States of America
| | - Sabine Heinhorst
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Kelynne Reed
- Biology Department, Austin College, Sherman, Texas, United States of America
| | - Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Erin R. Sanders-Lorenz
- Department of Microbiology, Immunology and Molecular Genetics, University of California – Los Angeles, Los Angeles, California, United States of America
| | - Seth Axen
- Department of Energy-Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edwin Kim
- Department of Energy-Joint Genome Institute, Walnut Creek, California, United States of America
| | - Mitrick Johns
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Kathleen Scott
- Department of Integrative Biology, University of South Florida, Tampa, Florida, United States of America
| | - Cheryl A. Kerfeld
- Department of Energy-Joint Genome Institute, Walnut Creek, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkley, Berkeley, California, United States of America
- * E-mail:
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Boyle MD. "Shovel-ready" Sequences as a Stimulus for the Next Generation of Life Scientists. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2010; 11:38-41. [PMID: 23653696 PMCID: PMC3577241 DOI: 10.1128/jmbe.v11.i1.133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Genomics and bioinformatics are dynamic fields well-suited for capturing the imagination of undergraduates in both research laboratories and classrooms. Currently, raw nucleotide sequence is being provided, as part of several genomics research initiatives, for undergraduate research and teaching. These initiatives could be easily extended and much more effective if the source of the sequenced material and the subsequent focus of the data analysis were aligned with the research interests of individual faculty at undergraduate institutions. By judicious use of surplus capacity in existing nucleotide sequencing cores, raw sequence data could be generated to support ongoing research efforts involving undergraduates. This would allow these students to participate actively in discovery research, with a goal of making novel contributions to their field through original research while nurturing the next generation of talented research scientists.
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Affiliation(s)
- Michael D. Boyle
- Corresponding author. Mailing address: Department of Biology, Juniata College, Department of Biology, 1700 Moore Street Huntingdon, PA 16652. Phone: (814) 641-3553. Fax: (814) 641-3685. E-mail:
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20
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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 SCIENCES EDUCATION 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] [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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Temple L, Cresawn SG, Monroe JD. Genomics and bioinformatics in undergraduate curricula: Contexts for hybrid laboratory/lecture courses for entering and advanced science students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 38:23-28. [PMID: 21567786 DOI: 10.1002/bmb.20359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Emerging interest in genomics in the scientific community prompted biologists at James Madison University to create two courses at different levels to modernize the biology curriculum. The courses are hybrids of classroom and laboratory experiences. An upper level class uses raw sequence of a genome (plasmid or virus) as the subject on which to base the experience of genomic analysis. Students also learn bioinformatics and software programs needed to support a project linking structure and function in proteins and showing evolutionary relatedness of similar genes. An optional entry-level course taken in addition to the required first-year curriculum and sponsored in part by the Howard Hughes Medical Institute, engages first year students in a primary research project. In the first semester, they isolate and characterize novel bacteriophages that infect soil bacteria. In the second semester, these young scientists annotate the genes on one or more of the unique viruses they discovered. These courses are demanding but exciting for both faculty and students and should be accessible to any interested faculty member.
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Affiliation(s)
- Louise Temple
- Department of Integrated Science and Technology, James Madison University, Harrisonburg, VA 22807.
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Hingamp P, Brochier C, Talla E, Gautheret D, Thieffry D, Herrmann C. Metagenome annotation using a distributed grid of undergraduate students. PLoS Biol 2009; 6:e296. [PMID: 19067492 PMCID: PMC2586363 DOI: 10.1371/journal.pbio.0060296] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Annotathon is a novel bioinformatics teaching environment, where undergraduate students join in a community annotation effort. Besides being a rewarding educational tool, it holds the added promise of potentially useful scientific findings.
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Affiliation(s)
- Pascal Hingamp
- Département de Biologie, Faculté des Sciences de Luminy, Université de la Méditerranée, Information Génomiqueet Structurale, CNRS, UPR2589, Marseille, France.
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Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. Genetics 2008; 181:13-21. [PMID: 19015540 DOI: 10.1534/genetics.108.096784] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into approximately 750-bp fragments. Once trained in assembly of such DNA "building blocks" by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular "lab meeting" sessions help prepare them for future roles in laboratory science.
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