1887

Whole Genome Sequencing in the Undergraduate Classroom: Outcomes and Lessons from a Pilot Course

    Authors: Jennifer C. Drew1,*, Eric W. Triplett1
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    Affiliations: 1: Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 17 May 2008
    • *Corresponding author. Mailing address: Space Life Sciences Laboratory, M6-1025/SLSL, Kennedy Space Center, FL 32899. Phone: (321) 861-3318. Fax: (321) 861-2925. E-mail: jdrew@ufl.edu.
    • Copyright © 2008, American Society for Microbiology. All Rights Reserved.
    Source: J. Microbiol. Biol. Educ. May 2008 vol. 9 no. 1 3-11. doi:10.1128/jmbe.v9.89
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    Abstract:

    The BIO2010 report challenged undergraduate institutions to prepare the next generation of researchers for the changing direction of biology that increasingly integrates advanced technologies, digital information, and large-scale analyses. In response, the Microbiology and Cell Science Department at the University of Florida developed a research-based course, “Bacterial Genome Sequencing.” The objectives were to teach undergraduates about genomics and original research by sequencing a bacterial genome, to develop scientific communication skills by writing and submitting the project results as a class effort, and to promote an interest in biological research, particularly genomics. The students worked together to sequence, assemble, and annotate the P101 genome. We assessed student learning, scientific communication skills, and student attitudes by a variety of methods including exams, writing assignments, oral presentations, pre- and postcourse surveys, and a final exit survey. Assessment results demonstrate student learning gains and positive attitudes regarding the course.

Key Concept Ranking

DNA Sequencing Methods
0.6450643
Enterobacter cloacae
0.61344165
16s rRNA Sequencing
0.50438535
Haemophilus influenzae
0.47712126
0.6450643

References & Citations

1. Boomer S, Dutton B2002Bacterial diversity studies using the 16s rRNA gene provide a powerful research-based curriculum for molecular biology laboratoryMicrobiol Educ316http://www.microbelibrary.org.
2. Brodl MR2005Tapping recent alumni for the development of cutting-edge, investigative teaching lab experimentsBioscene: J. Coll. Biol. Teach.311320
3. Campbell AM2002Meeting report: genomics in the undergraduate curriculum—rocket science or basic scienceCBE Life Sci Educ1707210.1187/cbe.02-06-0014 http://dx.doi.org/10.1187/cbe.02-06-0014
4. Campbell AM2003Public access for teaching genomics, proteomics, and bioinformaticsCBE Life Sci Educ29811110.1187/cbe.03-02-0007 http://dx.doi.org/10.1187/cbe.03-02-0007
5. Chan EY2005Advances in sequencing technologyMutat Res573134010.1016/j.mrfmmm.2005.01.00415829235 http://dx.doi.org/10.1016/j.mrfmmm.2005.01.004
6. Chen J, Call GB, Beyer E, Bui C, Cespedes A, Chan A, Chan J, Chan S, Chhabra A, Dang P, Deravanesian A, Hermogeno B, Jen J, Kim E, Lee E, Lewis G, Marshall J, Regalia K, Shadpour F, Shemmassian A, Spivey K, Wells M, Wu J, Yamauchi Y, Yavari A, Abrams A, Abramson A, Amado L, Arson J, Bashour K, Bibikova E, Bookatz A, Brewer S, Buu N, Calvillo S, Cao J, Chang A, Chang D, Chang Y, Chen Y, Choi J, Chou J, Datta S, Davarifar A, Desai P, Fabrikant J, Farnad S, Fu K, Garcia E, Garrone N, Gasparyan S, Gayda P, Goffstein C, Gonzalez C, Guirguis M, Hassid R, Hong A, Hong J, Hovestreydt L, Hu C, Jamshidian F, Kahen K, Kao L, Kelley M, Kho T, Kim S, Kim Y, Kirkpatrick B, Kohan E, Kwak R, Langenbacher A, Laxamana S, Lee C, Lee J, Lee S, Lee T, Lee T, Lezcano S, Lin H, Lin P, Luu J, Luu T, Marrs W, Marsh E, Min S, Minasian T, Misra A, Morimoto M, Moshfegh Y, Murray J, Nguyen C, Nguyen K, Nodado E, O’Donahue A, Onugha N, Orjiakor N, Padhiar B, Pavel-Dinu M, Pavlenko A, Paz E, Phaklides S, Pham L, Poulose P, Powell R, Pusic A, Ramola D, Ribbens M, Rifai B, Rosselli D, Saakyan M, Saarikoski P, Segura M, Singh R, Singh V, Skinner E, Solomin D, Soneji K, Stageberg E, Stavchanskiy M, Tekchandani L, Thai L, Thiyanaratnam J, Tong M, Toor A, Tovar S, Trangsrud K, Tsang W, Uemura M, Unkovic M, Vollmer E, Weiss E, Wood D, Wu S, Wu W, Xu Q, Yackle K, Yarosh W, Yee L, Yen G, Alkin G, Go S, Huff D, Minye H, Paul E, Villarasa N, Milchanowski A, Banerjee U2005Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchersPLoS Biol32e59http://biology.plosjournals.org.10.1371/journal.pbio.003005915719063548953 http://dx.doi.org/10.1371/journal.pbio.0030059
7. Committee on Undergraduate Biology Education to Prepare Research Scientists for the 21st Century2003BIO2010: transforming undergraduate education for future research biologistsNational Research CouncilWashington, DC
8. Committee on Undergraduate Science Education1997Science teaching reconsidered: a handbookNational Research CouncilWashington, DC
9. Dyer BD, LeBlanc MD2002Meeting report: incorporating genomics research into undergraduate curriculaCBE Life Sci Educ110110410.1187/cbe.02-07-0016 http://dx.doi.org/10.1187/cbe.02-07-0016
10. Elwess NL, Latourelle SL2004Inducing mutations in paramecium: an inquiry-based approachBioscene: J. Coll. Biol. Teach.302535
11. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, McKenney K, Sutton GW, FitzHugh W, Fields C, Gocyne JD, Scott J, Shirley R, Liu L, Glodek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback TR, Hanna MC, Nguyen David T, Saudek DM, Brandon RC, Fine LD, Fritchman JL, Fuhrmann JL, Geoghagen NSM, Gnehm CL, McDonald LA, Small KV, Fraser CM, Smith HO, Venter JC1995Whole-genome random sequencing and assembly of Haemophilus influenzae RdScience26949651210.1126/science.75428007542800 http://dx.doi.org/10.1126/science.7542800
12. Flowers SK, Easter C, Holmes A, Cohen B, Bednarski AE, Mardis ER, Wilson RK, Elgin SCR2005Genome science: a video tour of the Washington University Genome Sequencing Center for high school and undergraduate studentsCBE Life Sci Educ429129610.1187/cbe.05-07-0088 http://dx.doi.org/10.1187/cbe.05-07-0088
13. Forst S, Goodner B2006Comparative bacterial genomics and its use in undergraduate educationBiol Control38475310.1016/j.biocontrol.2005.11.006 http://dx.doi.org/10.1016/j.biocontrol.2005.11.006
14. Gibson G, Muse SV2005A prime of genome scienceSinauer Associates IncSunderland, MA
15. Goodner B, Wheeler C2006Functional genomics: using reverse genetics to test bioinformatics predictionsASM MicrobeLibrary Curriculum Collection. http://www.microbelibrary.org.
16. Handelsman J, Ebert-May D, Beichner R, Bruns P, Chang A, DeHaan R, Gentile J, Lauffer S, Stewart J, Tilghman SM, Wood WB2004Scientific teachingScience30452152210.1126/science.109602215105480 http://dx.doi.org/10.1126/science.1096022
17. Harwood WS2003Course enhancement: a road map for devising active-learning and inquiry-based science coursesInt J Dev Biol4721322112705672
18. Holtzclaw JD, Eisen A, Whitney EM, Penumetcha M, Hoey JJ, Kimbro KS2006Incorporating a new bioinformatics component into genetics at a historically black college: outcomes and lessonsCBE Life Sci Educ5526410.1187/cbe.05-04-0071170121911635137 http://dx.doi.org/10.1187/cbe.05-04-0071
19. Honts JE2003Evolving strategies for the incorporation of bioinformatics within the undergraduate cell biology curriculumCBE Life Sci Educ223324510.1187/cbe.03-06-0026 http://dx.doi.org/10.1187/cbe.03-06-0026
20. Howard DR, Miskowski JA2005Using a module-based laboratory to incorporate inquiry into a large cell biology courseCBE Life Sci Educ424926010.1187/cbe.04-09-0052 http://dx.doi.org/10.1187/cbe.04-09-0052
21. Kenny RWBoyer Commission on Educating Undergraduates in the Research University1998Reinventing undergraduate education: a blueprint for America’s research universitiesState University of New York—StonybrookStonybrook, NY
22. Klionsky DJ2002Constructing knowledge in the lecture hall: a quiz-based group-learning approach to introductory biologyJ Coll Sci Teach31246251
23. Malacinski GM2003Student-oriented learning: an inquiry-based developmental biology lecture courseInt J Dev Biol4713514012705660
24. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XY, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM2005Genome sequencing in microfabricated high-density picoliter reactorsNature43737638116056220
25. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V2005The subsystems approach to genome annotation and its use in the project to annotate 1,000 genomesNucleic Acids Res335691570210.1093/nar/gki866162148031251668 http://dx.doi.org/10.1093/nar/gki866
26. Riggs PJ, Moritz RL, Chelius MK, Dong Y, Iniguez AL, Kaeppler SM, Casler MD, Triplett EW2002Isolation and characterization of diazotrophic endophytes from grasses and their effects on plant growth263267 Finan TR, O’Brian MR, Layzell DB, Vessey JK, Newton WENitrogen fixation: global perspectives Proceedings of the 13th International Congress on Nitrogen FixationCABINew York, NY
27. Riggs PJ, Chelius MK, Iniguez AL, Kaeppler SM, Triplett EW2001Enhanced maize productivity by inoculation with diazotrophic bacteriaAust J Plant Physiol28829836
28. Rothman FG, Narum JL1999Then, now, and in the next decade: a commentary on strengthening undergraduate science, mathematics, engineering and technology educationProject KaleidoscopeWashington DC
29. Smith AC, Stewart R, Shields P, Hayes-Klosteridis J, Robinson P, Yuan R2005Introductory biology courses: a framework to support active learning in large enrollment introductory science coursesCBE Life Sci Educ414315610.1187/cbe.04-08-0048 http://dx.doi.org/10.1187/cbe.04-08-0048
30. Strong M, Cascio D, Eisenberg D2004A web-based comparative genomics tutorial for investigating microbial genomesMicrobiol Educ518http://www.microbelibrary.org.
31. Suchman E, Timpson W, Linch K, Ahermae S, Smith R2001Student responses to active learning strategies in a large lecture introductory microbiology courseBioscene: J. Coll. Bio. Teach.272126
32. Takayama K2004Three-dimensional visualizations in teaching genomics and bioinformatics: mutations in HIV envelope proteins and their consequences for vaccine designMicrobiol Educ5111http://www.microbelibrary.org.
33. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo AC, Dong XL, Lu P, Szafron D, Greiner R, Wishart DS2005BASys a web server for automated bacterial genome annotationNucleic Acids Res.33Suppl. 2W455W459http://nar.oxfordjournals.org/archive/.10.1093/nar/gki593159805111160269 http://dx.doi.org/10.1093/nar/gki593
34. Ward N, Fraser CM2005How genomics has affected the concept of microbiologyCurr Opin Microbiol856457110.1016/j.mib.2005.08.01116125442 http://dx.doi.org/10.1016/j.mib.2005.08.011
35. Wyckoff S2001Changing the culture of undergraduate science teachingJ Coll Sci Teach29409414
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/content/journal/jmbe/10.1128/jmbe.v9.89
2008-05-17
2017-09-24

Abstract:

The BIO2010 report challenged undergraduate institutions to prepare the next generation of researchers for the changing direction of biology that increasingly integrates advanced technologies, digital information, and large-scale analyses. In response, the Microbiology and Cell Science Department at the University of Florida developed a research-based course, “Bacterial Genome Sequencing.” The objectives were to teach undergraduates about genomics and original research by sequencing a bacterial genome, to develop scientific communication skills by writing and submitting the project results as a class effort, and to promote an interest in biological research, particularly genomics. The students worked together to sequence, assemble, and annotate the P101 genome. We assessed student learning, scientific communication skills, and student attitudes by a variety of methods including exams, writing assignments, oral presentations, pre- and postcourse surveys, and a final exit survey. Assessment results demonstrate student learning gains and positive attitudes regarding the course.

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FIG. 1

Course syllabus for “Bacterial Genome Sequencing.”

Source: J. Microbiol. Biol. Educ. May 2008 vol. 9 no. 1 3-11. doi:10.1128/jmbe.v9.89
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FIG. 2

For all four statements, students demonstrated a significant increase in genomics knowledge and skills in the postcourse survey results versus the precourse survey. The precourse survey mean scores were significantly lower than the postcourse survey mean scores in all four categories ( <0.005) according to Student’s t test, two-sided analysis. The postcourse survey bar denoting the percentage of students who indicated that they “strongly agreed” with the above statements is significantly higher than the precourse results. In all four graphs, the value is less than 0.003 according to Fisher’s exact test, two-sided analysis (denoted with an asterisk).

Source: J. Microbiol. Biol. Educ. May 2008 vol. 9 no. 1 3-11. doi:10.1128/jmbe.v9.89
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FIG. 3

Sample questions and answers from course exams. For the first question shown, the average score earned was 5.8 out of 6 points total, with 76% of students earning full credit for their answer. For the second question, the average score was 4.8 out of 6 points with 60% of the students earning full credit for their answer.

Source: J. Microbiol. Biol. Educ. May 2008 vol. 9 no. 1 3-11. doi:10.1128/jmbe.v9.89
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FIG. 4

Assessment of student scientific reading and writing skills from course surveys. The postcourse survey results demonstrated a significant increase in the students’ ability to understand the sections of a primary research paper and to read and interpret genomic literature ( = 0.003 and 0.006, respectively). Based on the postcourse survey results, students experienced only modest gains in their science writing skills that were not statistically significant.

Source: J. Microbiol. Biol. Educ. May 2008 vol. 9 no. 1 3-11. doi:10.1128/jmbe.v9.89
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FIG. 5

Assessment of student interest in biological research and genomics research from course surveys. There were no significant differences in the mean responses in the pre and post-course surveys to both of the questions about student interest in research. However, when asked to agree with a statement about their interest in pursuing a career in biological research, there was a marked increase in the percentage of students who responded “Strongly agree” on the post-course survey versus the pre-course survey results (77% vs. 41%; value = 0.06). In response to the statement regarding the student interest level in participating in future genomics research, there was also an increased level in the proportion of students who “strongly agreed” with the statement in the post-course survey as compared to the pre-course results (59% vs. 17%; value = 0.05), denoted by an asterisk.

Source: J. Microbiol. Biol. Educ. May 2008 vol. 9 no. 1 3-11. doi:10.1128/jmbe.v9.89
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