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Integrating CRISPR-Cas9 Technology into Undergraduate Courses: Perspectives from a National Science Foundation (NSF) Workshop for Undergraduate Faculty, June 2018

    Authors: Michael J. Wolyniak1,*, Shane Austin2, Lucian F. Bloodworth III1, Dawn Carter3, Scott H. Harrison4, Tiffany Hoage5, Lisa Hollis-Brown6, Felicia Jefferson7, Alison Krufka8, Farida Safadi-Chamberlin9, Maria S. Santisteban10, Paula Soneral11, Beth VanWinkle3, Anil K. Challa12
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943; 2: Department of Biological and Chemical Sciences, The University of the West Indies at Cave Hill, Bridgetown, BB11000, Barbados; 3: Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623; 4: Department of Biology, North Carolina A&T State University, Greensboro, NC 27411; 5: Department of Biology, University of Wisconsin—Stout, Menomonie, WI 54751; 6: Department of Biology, Pikes Peak Community College, Colorado Springs, CO 80906; 7: Department of Biology, Fort Valley State University, Fort Valley, GA 31030; 8: Department of Biological Sciences, Rowan University, Glassboro, NJ 08028; 9: Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523; 10: Department of Biology, University of North Carolina at Pembroke, Pembroke, NC 28372; 11: Department of Biological Sciences, Bethel University, St. Paul, MN 55112; 12: Department of Biology, The University of Alabama Birmingham, Birmingham, AL 35294
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 22 October 2018 Accepted 23 February 2019 Published 26 April 2019
    • ©2019 Author(s). Published by the American Society for Microbiology

    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
    • *Corresponding author. Mailing address: Box 183, Hampden-Sydney, VA 23943. Phone: 434-223-6175. E-mail: [email protected].
    Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1702
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    Abstract:

    As CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 technology becomes more mainstream in life science research, it becomes critical for undergraduate instructors to devise engaging ways to bring the technology into their classrooms. To help meet this challenge, the National Science Foundation sponsored a workshop for undergraduate instructors in June 2018 at The Ohio State University in conjunction with the annual Association of Biology Laboratory Educators meeting based on a workflow developed by the workshop’s facilitators. Over the course of two and a half days, participants worked through a modular workflow for the use of CRISPR-Cas9 in a course-based (undergraduate) research experience (CURE) setting while discussing the barriers each of their institutions had to implementing such work, and how such barriers could be overcome. The result of the workshop was a team with newfound energy and confidence to implement CRISPR-Cas9 technology in their courses and the development of a community of undergraduate educators dedicated to supporting each other in the implementation of the workflow either in a CURE or modular format. In this article, we review the activities and discussions from the workshop that helped each participant devise their own tailored approaches of how best to bring this exciting new technology into their classes.

References & Citations

1. Vanesa A, Chapapas H, Cisneros M, Deaton C, Deichmann S, Gadek C, Lovato TL, Chechenova MB, Guerin P, Cripps RM 2016 An undergraduate laboratory class using CRISPR-Cas9 technology to mutate Drosophila genes Biochem Mol Biol Educ 44 263 275 10.1002/bmb.20950 http://dx.doi.org/10.1002/bmb.20950
2. Evans Anderson HJ 2017 Abstract: CRISPR in the undergraduate classroom: a CURE FASEB J 31 abstr 589.6
3. Thurtle-Schmidt DM, Lo TW 2018 Molecular biology at the cutting edge: a review of CRISPR-Cas9 gene editing for undergraduates Biochem Mol Biol Educ 46 195 205 10.1002/bmb.21108 29381252 5901406 http://dx.doi.org/10.1002/bmb.21108
4. Walsh S, Becker A, Sickler PS, Clarke DG, Jimenez E 2017 An undergraduate laboratory manual for analyzing a CRISPR mutant with a predicted role in regeneration Faculty Publications Rollins College 188
5. Zulak A 2018 Undergraduates get rare chance to work with groundbreaking genetic engineering technique CRISPR University of Toronto News Toronto, ON April 6
6. Bhatt JM, Challa AK 2018 First year course-based undergraduate research experience (CURE) using the CRISPR-Cas9 genome engineering technology in zebrafish J Microbiol Biol Educ 19 1 9 10.1128/jmbe.v19i1.1245 http://dx.doi.org/10.1128/jmbe.v19i1.1245
7. Turner AN, Andersen RS, Bookout IE, Brashear LN, Davis JC, Gahan DM, Gotham JP, Hijaz BA, Kaushik AS, McGill JB, Miller VL, Moseley ZP, Nowell CL, Patel RK, Rodgers MC, Patel RK, Shihab YA, Walker AP, Glover SR, Foster SD, Challa AK 2018 Analysis of novel domain-specific mutations in the zebrafish ndr2/cyclops gene generated using CRISPR-Cas9 RNPs J Genet 97 5 1315 1325 10.1007/s12041-018-1033-6 30555080 http://dx.doi.org/10.1007/s12041-018-1033-6
8. Innovative Genomics Institute 2017 Intensive Undergraduate Summer CRISPR Workshop https://innovativegenomics.org/events/undergrad-workshop-2017/
9. Dahlberg L, Groat Carmona AM 2018 CRISPR-Cas technology in and out of the classroom CRISPR J 1 107 114 10.1089/crispr.2018.0007 http://dx.doi.org/10.1089/crispr.2018.0007
10. Wiggins G, McTighe J 1998 Understanding by design Association for Supervision and Curriculum Development Alexandria, VA
11. Cooper K, Soneral P, Brownell S 2017 Define your goals before you design a CURE: a call to use backward design in planning course-based undergraduate research experiences J Microbiol Biol Educ 18 2 10.1128/jmbe.v18i2.1287 28861130 5576764 http://dx.doi.org/10.1128/jmbe.v18i2.1287
12. Lave J, Wenger E 1991 Situated learning: legitimate peripheral participation Cambridge University Press Cambridge, UK 10.1017/CBO9780511815355 http://dx.doi.org/10.1017/CBO9780511815355
13. Sharma A, Scott CT 2015 The ethics of publishing human germline research Nature Biotechnol 33 590 10.1038/nbt.3252 http://dx.doi.org/10.1038/nbt.3252
14. Kanchiswamy CN, Sargent DJ, Velasco R, Maffei ME, Malnoy M 2015 Looking forward to genetically edited fruit crops Trends Biotechnol 33 62 64 10.1016/j.tibtech.2014.07.003 http://dx.doi.org/10.1016/j.tibtech.2014.07.003
15. Courtier-Orgogozo V, Morizot B, Boëte C 2017 Using CRISPR-based gene drive for agriculture pest control EMBO Reports 18 1481 10.15252/embr.201744822 28784604 5579344 http://dx.doi.org/10.15252/embr.201744822
16. Esvelt KM, Gemmell NJ 2017 Conservation demands safe gene drive PLOS Biol 15 e2003850 10.1371/journal.pbio.2003850 29145398 5689824 http://dx.doi.org/10.1371/journal.pbio.2003850
17. Kloser MJ, Brownell SE, Shavelson RJ, Fukami T 2013 Research and teaching. Effects of a research-based ecology lab course: a study of nonvolunteer achievement, self-confidence, and perception of lab course purpose J Coll Sci Teach 42 72 81
18. Brownell SE, Kloser M, Shavelson R, Fukami T 2012 Undergraduate biology lab courses: comparing the impact of traditionally based “cookbook” and authentic research-based courses on student lab experiences J Coll Sci Teach 41 36 45
19. Shortlidge EE, Bangera G, Brownell SE 2016 Faculty perspectives on developing and teaching course-based undergraduate research experiences BioScience 66 54 62 10.1093/biosci/biv167 http://dx.doi.org/10.1093/biosci/biv167
20. Corwin LA, Graham MJ, Dolan EL 2015 Modeling course-based undergraduate research experiences: an agenda for future research and evaluation CBE Life Sci Educ 14 1 13 10.1187/cbe.14-10-0167 http://dx.doi.org/10.1187/cbe.14-10-0167
21. Hanauer D, Dolan EL 2014 The project ownership survey: measuring differences in scientific inquiry experiences CBE Life Sci Educ 13 149 158 10.1187/cbe.13-06-0123 24591513 3940455 http://dx.doi.org/10.1187/cbe.13-06-0123
22. Semsar K, Knight JK, Birol G, Smith MK 2011 The Colorado learning attitudes about science survey (CLASS) for use in biology CBE Life Sci Educ 10 268 278 10.1187/cbe.10-10-0133 21885823 3164566 http://dx.doi.org/10.1187/cbe.10-10-0133
23. Corwin LA, Runyon C, Robinson A, Dolan EL 2015 The laboratory course assessment survey: a tool to measure three dimensions of research-course design CBE Life Sci Educ 14 ar37 10.1187/cbe.15-03-0073 26466990 4710398 http://dx.doi.org/10.1187/cbe.15-03-0073
24. Sirum K, Humburg J 2011 The experimental design ability test (EDAT) Bioscene J Coll Biol Teach 37 8 16
25. Wilson KJ, Rigakos B 2016 Scientific process flowchart assessment (SPFA): a method for evaluating changes in understanding and visualization of the scientific process in a multidisciplinary student population CBE Life Sci Educ 15 ar63 10.1187/cbe.15-10-0212 27856551 5132360 http://dx.doi.org/10.1187/cbe.15-10-0212
26. Hoskins SG, Stevens LM, Nehm RH 2007 Selective use of primary literature transforms the classroom into a virtual laboratory Genetics 176 1381 1389 10.1534/genetics.107.071183 17483426 1931557 http://dx.doi.org/10.1534/genetics.107.071183

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2019-04-26
2019-08-21

Abstract:

As CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 technology becomes more mainstream in life science research, it becomes critical for undergraduate instructors to devise engaging ways to bring the technology into their classrooms. To help meet this challenge, the National Science Foundation sponsored a workshop for undergraduate instructors in June 2018 at The Ohio State University in conjunction with the annual Association of Biology Laboratory Educators meeting based on a workflow developed by the workshop’s facilitators. Over the course of two and a half days, participants worked through a modular workflow for the use of CRISPR-Cas9 in a course-based (undergraduate) research experience (CURE) setting while discussing the barriers each of their institutions had to implementing such work, and how such barriers could be overcome. The result of the workshop was a team with newfound energy and confidence to implement CRISPR-Cas9 technology in their courses and the development of a community of undergraduate educators dedicated to supporting each other in the implementation of the workflow either in a CURE or modular format. In this article, we review the activities and discussions from the workshop that helped each participant devise their own tailored approaches of how best to bring this exciting new technology into their classes.

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Author and Article Information

  • Received 22 October 2018 Accepted 23 February 2019 Published 26 April 2019
  • ©2019 Author(s). Published by the American Society for Microbiology

  • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
  • *Corresponding author. Mailing address: Box 183, Hampden-Sydney, VA 23943. Phone: 434-223-6175. E-mail: [email protected].

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Integrating CRISPR-Cas9 Technology into Undergraduate Courses: Perspectives from a National Science Foundation (NSF) Workshop for Undergraduate Faculty, June 2018
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Citation: Wolyniak M, Austin S, Bloodworth L, Carter D, Harrison S, Hoage T, Hollis-Brown L, Jefferson F, Krufka A, Safadi-Chamberlin F, Santisteban M, Soneral P, VanWinkle B, Challa A. 2019. Integrating crispr-cas9 technology into undergraduate courses: perspectives from a national science foundation (nsf) workshop for undergraduate faculty, june 2018. J. Microbiol. Biol. Educ. 20(1): doi:10.1128/jmbe.v20i1.1702
/content/jmbe/10.1128/jmbe.v20i1.1702.f1-jmbe-20-19
FIGURE 1
Overview of the CRISPR-Cas9 lab workflow and correspondence with the flow of genetic information (Central Dogma of Molecular Biology). The yellow box shows the flow of genetic information culminating in the effect of gene function. The cream-colored boxes indicate bioinformatics. Boxes in dark blue indicate laboratory exercises, and boxes in light blue indicate variations and potential extensions for those lab exercises. CRISPR = clustered regularly interspaced short palindromic repeats; sgRNA = single guide RNA.
jmbe/20/1/jmbe-20-19f1_thmb.gif
jmbe/20/1/jmbe-20-19f1.gif
Image of FIGURE 1

Click to view

FIGURE 1

Overview of the CRISPR-Cas9 lab workflow and correspondence with the flow of genetic information (Central Dogma of Molecular Biology). The yellow box shows the flow of genetic information culminating in the effect of gene function. The cream-colored boxes indicate bioinformatics. Boxes in dark blue indicate laboratory exercises, and boxes in light blue indicate variations and potential extensions for those lab exercises. CRISPR = clustered regularly interspaced short palindromic repeats; sgRNA = single guide RNA.

Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1702
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v20i1.1702.f2-jmbe-20-19
FIGURE 2
Steps of the CRISPR-Cas9 workshop workflow. Phase 1 of the workflow involves gene analysis using a genome browser (e.g., ENSEMBL) and CRISPR/sgRNA design using bioinformatics tools (e.g., Benchling, CRISPRScan, ChopChop). In Phase 2, a double-stranded DNA (dsDNA) that will be used as a template for sgRNA synthesis is prepared. Phase 3 involves the synthesis of sgRNA by T7 RNA polymerase-driven transcription followed by quantitative and qualitative analysis of the synthesized RNA. During Phase 4, the nuclease activity of the sgRNA-Cas9 ribonucleoprotein complex on the PCR-amplified genomic target region is tested . CRISPR = clustered regularly interspaced short palindromic repeats; sgRNA = single guide RNA.
jmbe/20/1/jmbe-20-19f2_thmb.gif
jmbe/20/1/jmbe-20-19f2.gif
Image of FIGURE 2

Click to view

FIGURE 2

Steps of the CRISPR-Cas9 workshop workflow. Phase 1 of the workflow involves gene analysis using a genome browser (e.g., ENSEMBL) and CRISPR/sgRNA design using bioinformatics tools (e.g., Benchling, CRISPRScan, ChopChop). In Phase 2, a double-stranded DNA (dsDNA) that will be used as a template for sgRNA synthesis is prepared. Phase 3 involves the synthesis of sgRNA by T7 RNA polymerase-driven transcription followed by quantitative and qualitative analysis of the synthesized RNA. During Phase 4, the nuclease activity of the sgRNA-Cas9 ribonucleoprotein complex on the PCR-amplified genomic target region is tested . CRISPR = clustered regularly interspaced short palindromic repeats; sgRNA = single guide RNA.

Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1702
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v20i1.1702.f3-jmbe-20-19
FIGURE 3
Sample gels prepared and analyzed by undergraduate students in a summer course demonstrating nuclease assay of CRISPR-Cas9. The gel image in the left panel shows the efficacy of various sgRNA guides (C1–C4), along with various experimental controls to demonstrate the conditions required for optimal nuclease activity. The gel in the right panel shows nuclease activity at different concentrations of the sgRNA guide. CRISPR = clustered regularly interspaced short palindromic repeats; sgRNA = single guide RNA.
jmbe/20/1/jmbe-20-19f3_thmb.gif
jmbe/20/1/jmbe-20-19f3.gif
Image of FIGURE 3

Click to view

FIGURE 3

Sample gels prepared and analyzed by undergraduate students in a summer course demonstrating nuclease assay of CRISPR-Cas9. The gel image in the left panel shows the efficacy of various sgRNA guides (C1–C4), along with various experimental controls to demonstrate the conditions required for optimal nuclease activity. The gel in the right panel shows nuclease activity at different concentrations of the sgRNA guide. CRISPR = clustered regularly interspaced short palindromic repeats; sgRNA = single guide RNA.

Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1702
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v20i1.1702.f4-jmbe-20-19
FIGURE 4
Example of implementation plan in an undergraduate laboratory. sgRNA = single guide RNA; RT-PCR = reverse transcriptase PCR.
jmbe/20/1/jmbe-20-19f4_thmb.gif
jmbe/20/1/jmbe-20-19f4.gif
Image of FIGURE 4

Click to view

FIGURE 4

Example of implementation plan in an undergraduate laboratory. sgRNA = single guide RNA; RT-PCR = reverse transcriptase PCR.

Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1702
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