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: [email protected].
    • 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 B 2002 Bacterial diversity studies using the 16s rRNA gene provide a powerful research-based curriculum for molecular biology laboratory Microbiol Educ 3 1 6 http://www.microbelibrary.org.
2. Brodl MR 2005 Tapping recent alumni for the development of cutting-edge, investigative teaching lab experiments Bioscene: J. Coll. Biol. Teach. 31 13 20
3. Campbell AM 2002 Meeting report: genomics in the undergraduate curriculum—rocket science or basic science CBE Life Sci Educ 1 70 72 10.1187/cbe.02-06-0014 http://dx.doi.org/10.1187/cbe.02-06-0014
4. Campbell AM 2003 Public access for teaching genomics, proteomics, and bioinformatics CBE Life Sci Educ 2 98 111 10.1187/cbe.03-02-0007 http://dx.doi.org/10.1187/cbe.03-02-0007
5. Chan EY 2005 Advances in sequencing technology Mutat Res 573 13 40 10.1016/j.mrfmmm.2005.01.004 15829235 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 U 2005 Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers PLoS Biol 3 2 e59 http://biology.plosjournals.org. 10.1371/journal.pbio.0030059 15719063 548953 http://dx.doi.org/10.1371/journal.pbio.0030059
7. Committee on Undergraduate Biology Education to Prepare Research Scientists for the 21st Century 2003 BIO2010: transforming undergraduate education for future research biologists National Research Council Washington, DC
8. Committee on Undergraduate Science Education 1997 Science teaching reconsidered: a handbook National Research Council Washington, DC
9. Dyer BD, LeBlanc MD 2002 Meeting report: incorporating genomics research into undergraduate curricula CBE Life Sci Educ 1 101 104 10.1187/cbe.02-07-0016 http://dx.doi.org/10.1187/cbe.02-07-0016
10. Elwess NL, Latourelle SL 2004 Inducing mutations in paramecium: an inquiry-based approach Bioscene: J. Coll. Biol. Teach. 30 25 35
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 JC 1995 Whole-genome random sequencing and assembly of Haemophilus influenzae Rd Science 269 496 512 10.1126/science.7542800 7542800 http://dx.doi.org/10.1126/science.7542800
12. Flowers SK, Easter C, Holmes A, Cohen B, Bednarski AE, Mardis ER, Wilson RK, Elgin SCR 2005 Genome science: a video tour of the Washington University Genome Sequencing Center for high school and undergraduate students CBE Life Sci Educ 4 291 296 10.1187/cbe.05-07-0088 http://dx.doi.org/10.1187/cbe.05-07-0088
13. Forst S, Goodner B 2006 Comparative bacterial genomics and its use in undergraduate education Biol Control 38 47 53 10.1016/j.biocontrol.2005.11.006 http://dx.doi.org/10.1016/j.biocontrol.2005.11.006
14. Gibson G, Muse SV 2005 A prime of genome science Sinauer Associates Inc Sunderland, MA
15. Goodner B, Wheeler C 2006 Functional genomics: using reverse genetics to test bioinformatics predictions ASM 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 WB 2004 Scientific teaching Science 304 521 522 10.1126/science.1096022 15105480 http://dx.doi.org/10.1126/science.1096022
17. Harwood WS 2003 Course enhancement: a road map for devising active-learning and inquiry-based science courses Int J Dev Biol 47 213 221 12705672
18. Holtzclaw JD, Eisen A, Whitney EM, Penumetcha M, Hoey JJ, Kimbro KS 2006 Incorporating a new bioinformatics component into genetics at a historically black college: outcomes and lessons CBE Life Sci Educ 5 52 64 10.1187/cbe.05-04-0071 17012191 1635137 http://dx.doi.org/10.1187/cbe.05-04-0071
19. Honts JE 2003 Evolving strategies for the incorporation of bioinformatics within the undergraduate cell biology curriculum CBE Life Sci Educ 2 233 245 10.1187/cbe.03-06-0026 http://dx.doi.org/10.1187/cbe.03-06-0026
20. Howard DR, Miskowski JA 2005 Using a module-based laboratory to incorporate inquiry into a large cell biology course CBE Life Sci Educ 4 249 260 10.1187/cbe.04-09-0052 http://dx.doi.org/10.1187/cbe.04-09-0052
21. Kenny RW Boyer Commission on Educating Undergraduates in the Research University 1998 Reinventing undergraduate education: a blueprint for America’s research universities State University of New York—Stonybrook Stonybrook, NY
22. Klionsky DJ 2002 Constructing knowledge in the lecture hall: a quiz-based group-learning approach to introductory biology J Coll Sci Teach 31 246 251
23. Malacinski GM 2003 Student-oriented learning: an inquiry-based developmental biology lecture course Int J Dev Biol 47 135 140 12705660
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 JM 2005 Genome sequencing in microfabricated high-density picoliter reactors Nature 437 376 381 16056220
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 V 2005 The subsystems approach to genome annotation and its use in the project to annotate 1,000 genomes Nucleic Acids Res 33 5691 5702 10.1093/nar/gki866 16214803 1251668 http://dx.doi.org/10.1093/nar/gki866
26. Riggs PJ, Moritz RL, Chelius MK, Dong Y, Iniguez AL, Kaeppler SM, Casler MD, Triplett EW 2002 Isolation and characterization of diazotrophic endophytes from grasses and their effects on plant growth 263 267 Finan TR, O’Brian MR, Layzell DB, Vessey JK, Newton WE Nitrogen fixation: global perspectives Proceedings of the 13th International Congress on Nitrogen Fixation CABI New York, NY
27. Riggs PJ, Chelius MK, Iniguez AL, Kaeppler SM, Triplett EW 2001 Enhanced maize productivity by inoculation with diazotrophic bacteria Aust J Plant Physiol 28 829 836
28. Rothman FG, Narum JL 1999 Then, now, and in the next decade: a commentary on strengthening undergraduate science, mathematics, engineering and technology education Project Kaleidoscope Washington DC
29. Smith AC, Stewart R, Shields P, Hayes-Klosteridis J, Robinson P, Yuan R 2005 Introductory biology courses: a framework to support active learning in large enrollment introductory science courses CBE Life Sci Educ 4 143 156 10.1187/cbe.04-08-0048 http://dx.doi.org/10.1187/cbe.04-08-0048
30. Strong M, Cascio D, Eisenberg D 2004 A web-based comparative genomics tutorial for investigating microbial genomes Microbiol Educ 5 1 8 http://www.microbelibrary.org.
31. Suchman E, Timpson W, Linch K, Ahermae S, Smith R 2001 Student responses to active learning strategies in a large lecture introductory microbiology course Bioscene: J. Coll. Bio. Teach. 27 21 26
32. Takayama K 2004 Three-dimensional visualizations in teaching genomics and bioinformatics: mutations in HIV envelope proteins and their consequences for vaccine design Microbiol Educ 5 1 11 http://www.microbelibrary.org.
33. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo AC, Dong XL, Lu P, Szafron D, Greiner R, Wishart DS 2005 BASys a web server for automated bacterial genome annotation Nucleic Acids Res. 33 Suppl. 2 W455 W459 http://nar.oxfordjournals.org/archive/. 10.1093/nar/gki593 15980511 1160269 http://dx.doi.org/10.1093/nar/gki593
34. Ward N, Fraser CM 2005 How genomics has affected the concept of microbiology Curr Opin Microbiol 8 564 571 10.1016/j.mib.2005.08.011 16125442 http://dx.doi.org/10.1016/j.mib.2005.08.011
35. Wyckoff S 2001 Changing the culture of undergraduate science teaching J Coll Sci Teach 29 409 414

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/content/journal/jmbe/10.1128/jmbe.v9.89
2008-05-17
2019-03-18

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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