Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

David Lopatto¹, Anne G Rosenwald², Justin R DiAngelo³, Amy T Hark⁴, Matthew Skerritt⁵, Matthew Wawersik⁶, Anna K Allen⁷, Consuelo Alvarez⁸, Sara Anderson⁹, Cindy Arrigo¹⁰, Andrew Arsham¹¹, Daron Barnard¹², Christopher Bazinet¹³, James E J Bedard¹⁴, Indrani Bose¹⁵, John M Braverman¹⁶, Martin G Burg¹⁷, Rebecca C Burgess¹⁸, Paula Croonquist¹⁹, Chunguang Du²⁰, Sondra Dubowsky²¹, Heather Eisler²², Matthew A Escobar²³, Michael Foulk²⁴, Emily Furbee²⁵, Thomas Giarla²⁶, Rivka L Glaser¹⁸, Anya L Goodman²⁷, Yuying Gosser²⁸, Adam Haberman²⁹, Charles Hauser³⁰, Shan Hays³¹, Carina E Howell³², Jennifer Jemc³³, M Logan Johnson³⁴, Christopher J Jones³⁵, Lisa Kadlec³⁶, Jacob D Kagey³⁷, Kimberly L Keller³⁸, Jennifer Kennell³⁹, S Catherine Silver Key⁴⁰, Adam J Kleinschmit⁴¹, Melissa Kleinschmit⁴¹, Nighat P Kokan⁴², Olga Ruiz Kopp⁴³, Meg M Laakso⁴⁴, Judith Leatherman⁴⁵, Lindsey J Long⁴⁶, Mollie Manier⁴⁷, Juan C Martinez-Cruzado⁴⁸, Luis F Matos⁴⁹, Amie Jo McClellan⁵⁰, Gerard McNeil⁵¹, Evan Merkhofer⁵², Vida Mingo⁵³, Hemlata Mistry⁵⁴, Elizabeth Mitchell²¹, Nathan T Mortimer⁵⁵, Debaditya Mukhopadhyay⁵⁶, Jennifer Leigh Myka⁵⁷, Alexis Nagengast⁵⁸, Paul Overvoorde⁵⁹, Don Paetkau⁶⁰, Leocadia Paliulis⁶¹, Susan Parrish⁶², Mary Lai Preuss⁶³, James V Price⁴³, Nicholas A Pullen⁴⁵, Catherine Reinke⁶⁴, Dennis Revie⁶⁵, Srebrenka Robic⁶⁶, Jennifer A Roecklein-Canfield⁶⁷, Michael R Rubin⁶⁸, Takrima Sadikot⁶⁹, Jamie Siders Sanford⁷⁰, Maria Santisteban⁷¹, Kenneth Saville⁷², Stephanie Schroeder⁶³, Christopher D Shaffer⁷³, Karim A Sharif⁷⁴, Diane E Sklensky⁷⁵, Chiyedza Small⁷⁶, Mary Smith⁷⁷, Sheryl Smith⁷⁸, Rebecca Spokony⁷⁹, Aparna Sreenivasan⁸⁰, Joyce Stamm⁸¹, Rachel Sterne-Marr²⁶, Katherine C Teeter⁸², Justin Thackeray⁸³, Jeffrey S Thompson⁸⁴, Stephanie Toering Peters⁸⁵, Melanie Van Stry⁷⁵, Norma Velazquez-Ulloa⁸⁶, Cindy Wolfe⁸⁷, James Youngblom⁸⁸, Brian Yowler⁸⁹, Leming Zhou⁹⁰, Janie Brennan⁹¹, Jeremy Buhler⁹², Wilson Leung⁷³, Laura K Reed⁹³, Sarah C R Elgin⁷³

Affiliations

¹ Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, IA 50112, USA.
² Biology, Georgetown University, Washington, DC 20057, USA.
³ Division of Science, Penn State Berks, Reading, PA 19610, USA.
⁴ Biology, Muhlenberg College, Allentown, PA 18104, USA.
⁵ Science, SUNY Corning Community College, Corning, NY 14830, USA.
⁶ Biology, College of William and Mary, Williamsburg, VA 23187, USA.
⁷ Biology, Howard University, Washington, DC 20059, USA.
⁸ Biology, Longwood University, Farmville, VA 23909, USA.
⁹ Biosciences, Minnesota State University Moorhead, Moorhead, MN 56563, USA.
¹⁰ Biology, New Jersey City University, Jersey City, NJ 07305, USA.
¹¹ Biology, Bemidji State University, Bemidji, MN 56601, USA.
¹² Biology, Worcester State University, Worcester, MA 01602, USA.
¹³ Biological Sciences, St. John's University, Queens, NY 11439, USA.
¹⁴ Biology, University of the Fraser Valley, Abbotsford, BC, V2S 7M8, Canada.
¹⁵ Biology, Western Carolina University, Cullowhee, NC 28723, USA.
¹⁶ Biology, Saint Joseph's University, Philadelphia, PA 19131, USA.
¹⁷ Biomedical Sciences and Cell & Molecular Biology, Grand Valley State University, Allendale, MI 49401, USA.
¹⁸ Biological Sciences, Stevenson University, Owings Mills, MD 21117, USA.
¹⁹ Biology, Anoka-Ramsey Community College, Coon Rapids, MN 55433, USA.
²⁰ Biology, Montclair State University, Montclair, NJ 07043, USA.
²¹ Biology, McLennan Community College, Waco, TX 76708, USA.
²² Biology, University of the Cumberlands, Williamsburg, KY 40769, USA.
²³ Biological Sciences, California State University San Marcos, CA 92096, USA.
²⁴ Biology, Mercyhurst University, Erie, PA 16546, USA.
²⁵ Biology, Washington and Jefferson College, Washington, PA 15301, USA.
²⁶ Biology, Siena College, Loudonville, NY 12211, USA.
²⁷ Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
²⁸ Student Research and Scholarship, City College CUNY, New York, NY 10031, USA.
²⁹ Biology, University of San Diego, San Diego, CA 92110, USA.
³⁰ Biology, St. Edward's University, Austin, TX 78704, USA.
³¹ Biology, Western Colorado University, Gunnison, CO 81231, USA.
³² Biological Sciences, Lock Haven University, Lock Haven, PA 17745, USA.
³³ Biology, Loyola University Chicago, Chicago, IL 60660, USA.
³⁴ Biology, Notre Dame College, South Euclid, OH 44121, USA.
³⁵ Biological Sciences, Moravian College, Bethlehem, PA 18018, USA.
³⁶ Biology, Wilkes University, Wilkes-Barre, PA 18766, USA.
³⁷ Biology, University of Detroit Mercy, Detroit, MI 48221, USA.
³⁸ Biology, William Woods University, Fulton, MO 65251, USA.
³⁹ Biology, Vassar College, Poughkeepsie, NY 12604, USA.
⁴⁰ Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA.
⁴¹ Natural and Applied Science, University of Dubuque, Dubuque, IA 52001, USA.
⁴² Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217, USA.
⁴³ Biology, Utah Valley University, Orem, UT 84058, USA.
⁴⁴ Biology, Eastern University, St. Davids, PA 19087, USA.
⁴⁵ Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA.
⁴⁶ Biology, Oklahoma Christian University, Oklahoma City, OK 73136, USA.
⁴⁷ Biological Sciences, George Washington University, Washington, DC 20052, USA.
⁴⁸ Biología, University of Puerto Rico at Mayagüez, Mayagüez, PR 00680, USA.
⁴⁹ Biology, Eastern Washington University, Cheney, WA 99004, USA.
⁵⁰ Science and Mathematics, Bennington College, Bennington, VT 05201, USA.
⁵¹ Biology, York College / CUNY, Jamaica, NY 11451, USA.
⁵² Natural Sciences, Mount Saint Mary College, Newbergh, NY 12550, USA.
⁵³ Biology, Columbia College, Columbia, SC 29203, USA.
⁵⁴ Biology and Biochemistry, Widener University, Chester, PA 19013, USA.
⁵⁵ Biological Sciences, Illinois State University, Normal, IL 61790, USA.
⁵⁶ Molecular Biology, Biochemistry, and Bioinformatics, Towson University, Towson, MD 21252, USA.
⁵⁷ Biology, Gateway Community and Technical College, Florence, KY 41042, USA.
⁵⁸ Chemistry and Biochemistry, Widener University, Chester, PA 19013, USA.
⁵⁹ Biology, Macalester College, St. Paul, MN 55105, USA.
⁶⁰ Biology, Saint Mary's College, Notre Dame, IN 46556, USA.
⁶¹ Biology, Bucknell University, Lewisburg, PA 17837, USA.
⁶² Biology, McDaniel College, Westminster, MD 21157, USA.
⁶³ Biological Sciences, Webster University, St. Louis, MO 63119, USA.
⁶⁴ Biology, Linfield College, McMinnville, OR 97128, USA.
⁶⁵ Biology, California Lutheran University, Thousand Oaks, CA 91360, USA.
⁶⁶ Biology, Agnes Scott College, Decatur, GA 30030, USA.
⁶⁷ Chemistry, Simmons College, Boston, MA 02115, USA.
⁶⁸ Biology, University of Puerto Rico at Cayey, Cayey, PR 00736, USA.
⁶⁹ Biology, Washburn University, Topeka, KS 66621, USA.
⁷⁰ Biology, Ohio Northern University, Ada, OH 45810, USA.
⁷¹ Biology, University of North Carolina at Pembroke, Pembroke, NC 28372, USA.
⁷² Biology, Albion College, Albion, MI 49224, USA.
⁷³ Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
⁷⁴ Biology, Massasoit Community College, Brockton, MA 02302, USA.
⁷⁵ Biology, Lane College, Jackson, TN 38301, USA.
⁷⁶ Biology, Medgar Evers College, CUNY, Brooklyn, NY 11225, USA.
⁷⁷ Biology, North Carolina A & T State University, Greensboro, NC 27411, USA.
⁷⁸ Biology, Arcadia, University, Glenside, PA 19038, USA.
⁷⁹ Natural Sciences, Baruch College, CUNY, New York, NY 10010, USA.
⁸⁰ Biology, School of Natural Sciences, California State University, Monterey Bay, Seaside, CA 93950, USA.
⁸¹ Biology, University of Evansville, Evansville, IN 47722, USA.
⁸² Biology, Northern Michigan University, Marquette, MI 49855, USA.
⁸³ Biology, Clark University, Worcester, MA 01610, USA.
⁸⁴ Biology, Denison University, Granville, OH 43023, USA.
⁸⁵ Biology, Wartburg College, Waverly, IA 50677, USA.
⁸⁶ Biology, Lewis & Clark College, Portland, OR 97219, USA.
⁸⁷ Biology, Kentucky Wesleyan College, Owensboro, KY 42301, USA.
⁸⁸ Biological Sciences, California State University Stanislaus, Turlock, CA 95382, USA.
⁸⁹ Biology, Grove City College, Grove City, PA 16127, USA.
⁹⁰ Health Information Management, University of Pittsburgh, Pittsburgh, PA 15213, USA.
⁹¹ Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
⁹² Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
⁹³ Biological Sciences, University of Alabama Tuscaloosa, AL 35487, USA.

PMID: 32148609
PMCID: PMC7048401
DOI: 10.1128/jmbe.v21i1.2005

Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

David Lopatto et al. J Microbiol Biol Educ. 2020.

. 2020 Feb 28;21(1):21.1.6.

doi: 10.1128/jmbe.v21i1.2005. eCollection 2020.

Authors

Affiliations

¹ Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, IA 50112, USA.
² Biology, Georgetown University, Washington, DC 20057, USA.
³ Division of Science, Penn State Berks, Reading, PA 19610, USA.
⁴ Biology, Muhlenberg College, Allentown, PA 18104, USA.
⁵ Science, SUNY Corning Community College, Corning, NY 14830, USA.
⁶ Biology, College of William and Mary, Williamsburg, VA 23187, USA.
⁷ Biology, Howard University, Washington, DC 20059, USA.
⁸ Biology, Longwood University, Farmville, VA 23909, USA.
⁹ Biosciences, Minnesota State University Moorhead, Moorhead, MN 56563, USA.
¹⁰ Biology, New Jersey City University, Jersey City, NJ 07305, USA.
¹¹ Biology, Bemidji State University, Bemidji, MN 56601, USA.
¹² Biology, Worcester State University, Worcester, MA 01602, USA.
¹³ Biological Sciences, St. John's University, Queens, NY 11439, USA.
¹⁴ Biology, University of the Fraser Valley, Abbotsford, BC, V2S 7M8, Canada.
¹⁵ Biology, Western Carolina University, Cullowhee, NC 28723, USA.
¹⁶ Biology, Saint Joseph's University, Philadelphia, PA 19131, USA.
¹⁷ Biomedical Sciences and Cell & Molecular Biology, Grand Valley State University, Allendale, MI 49401, USA.
¹⁸ Biological Sciences, Stevenson University, Owings Mills, MD 21117, USA.
¹⁹ Biology, Anoka-Ramsey Community College, Coon Rapids, MN 55433, USA.
²⁰ Biology, Montclair State University, Montclair, NJ 07043, USA.
²¹ Biology, McLennan Community College, Waco, TX 76708, USA.
²² Biology, University of the Cumberlands, Williamsburg, KY 40769, USA.
²³ Biological Sciences, California State University San Marcos, CA 92096, USA.
²⁴ Biology, Mercyhurst University, Erie, PA 16546, USA.
²⁵ Biology, Washington and Jefferson College, Washington, PA 15301, USA.
²⁶ Biology, Siena College, Loudonville, NY 12211, USA.
²⁷ Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
²⁸ Student Research and Scholarship, City College CUNY, New York, NY 10031, USA.
²⁹ Biology, University of San Diego, San Diego, CA 92110, USA.
³⁰ Biology, St. Edward's University, Austin, TX 78704, USA.
³¹ Biology, Western Colorado University, Gunnison, CO 81231, USA.
³² Biological Sciences, Lock Haven University, Lock Haven, PA 17745, USA.
³³ Biology, Loyola University Chicago, Chicago, IL 60660, USA.
³⁴ Biology, Notre Dame College, South Euclid, OH 44121, USA.
³⁵ Biological Sciences, Moravian College, Bethlehem, PA 18018, USA.
³⁶ Biology, Wilkes University, Wilkes-Barre, PA 18766, USA.
³⁷ Biology, University of Detroit Mercy, Detroit, MI 48221, USA.
³⁸ Biology, William Woods University, Fulton, MO 65251, USA.
³⁹ Biology, Vassar College, Poughkeepsie, NY 12604, USA.
⁴⁰ Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA.
⁴¹ Natural and Applied Science, University of Dubuque, Dubuque, IA 52001, USA.
⁴² Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217, USA.
⁴³ Biology, Utah Valley University, Orem, UT 84058, USA.
⁴⁴ Biology, Eastern University, St. Davids, PA 19087, USA.
⁴⁵ Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA.
⁴⁶ Biology, Oklahoma Christian University, Oklahoma City, OK 73136, USA.
⁴⁷ Biological Sciences, George Washington University, Washington, DC 20052, USA.
⁴⁸ Biología, University of Puerto Rico at Mayagüez, Mayagüez, PR 00680, USA.
⁴⁹ Biology, Eastern Washington University, Cheney, WA 99004, USA.
⁵⁰ Science and Mathematics, Bennington College, Bennington, VT 05201, USA.
⁵¹ Biology, York College / CUNY, Jamaica, NY 11451, USA.
⁵² Natural Sciences, Mount Saint Mary College, Newbergh, NY 12550, USA.
⁵³ Biology, Columbia College, Columbia, SC 29203, USA.
⁵⁴ Biology and Biochemistry, Widener University, Chester, PA 19013, USA.
⁵⁵ Biological Sciences, Illinois State University, Normal, IL 61790, USA.
⁵⁶ Molecular Biology, Biochemistry, and Bioinformatics, Towson University, Towson, MD 21252, USA.
⁵⁷ Biology, Gateway Community and Technical College, Florence, KY 41042, USA.
⁵⁸ Chemistry and Biochemistry, Widener University, Chester, PA 19013, USA.
⁵⁹ Biology, Macalester College, St. Paul, MN 55105, USA.
⁶⁰ Biology, Saint Mary's College, Notre Dame, IN 46556, USA.
⁶¹ Biology, Bucknell University, Lewisburg, PA 17837, USA.
⁶² Biology, McDaniel College, Westminster, MD 21157, USA.
⁶³ Biological Sciences, Webster University, St. Louis, MO 63119, USA.
⁶⁴ Biology, Linfield College, McMinnville, OR 97128, USA.
⁶⁵ Biology, California Lutheran University, Thousand Oaks, CA 91360, USA.
⁶⁶ Biology, Agnes Scott College, Decatur, GA 30030, USA.
⁶⁷ Chemistry, Simmons College, Boston, MA 02115, USA.
⁶⁸ Biology, University of Puerto Rico at Cayey, Cayey, PR 00736, USA.
⁶⁹ Biology, Washburn University, Topeka, KS 66621, USA.
⁷⁰ Biology, Ohio Northern University, Ada, OH 45810, USA.
⁷¹ Biology, University of North Carolina at Pembroke, Pembroke, NC 28372, USA.
⁷² Biology, Albion College, Albion, MI 49224, USA.
⁷³ Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
⁷⁴ Biology, Massasoit Community College, Brockton, MA 02302, USA.
⁷⁵ Biology, Lane College, Jackson, TN 38301, USA.
⁷⁶ Biology, Medgar Evers College, CUNY, Brooklyn, NY 11225, USA.
⁷⁷ Biology, North Carolina A & T State University, Greensboro, NC 27411, USA.
⁷⁸ Biology, Arcadia, University, Glenside, PA 19038, USA.
⁷⁹ Natural Sciences, Baruch College, CUNY, New York, NY 10010, USA.
⁸⁰ Biology, School of Natural Sciences, California State University, Monterey Bay, Seaside, CA 93950, USA.
⁸¹ Biology, University of Evansville, Evansville, IN 47722, USA.
⁸² Biology, Northern Michigan University, Marquette, MI 49855, USA.
⁸³ Biology, Clark University, Worcester, MA 01610, USA.
⁸⁴ Biology, Denison University, Granville, OH 43023, USA.
⁸⁵ Biology, Wartburg College, Waverly, IA 50677, USA.
⁸⁶ Biology, Lewis & Clark College, Portland, OR 97219, USA.
⁸⁷ Biology, Kentucky Wesleyan College, Owensboro, KY 42301, USA.
⁸⁸ Biological Sciences, California State University Stanislaus, Turlock, CA 95382, USA.
⁸⁹ Biology, Grove City College, Grove City, PA 16127, USA.
⁹⁰ Health Information Management, University of Pittsburgh, Pittsburgh, PA 15213, USA.
⁹¹ Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
⁹² Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
⁹³ Biological Sciences, University of Alabama Tuscaloosa, AL 35487, USA.

PMID: 32148609
PMCID: PMC7048401
DOI: 10.1128/jmbe.v21i1.2005

Abstract

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students' learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our "formative frustration" hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of "formative frustration" is an important aspect for a successful CURE.

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Figures

**FIGURE 1**
The GEP mirror of the UCSC Genome Browser for *Drosophila mojavensis* (Sept 2008 GEP/dot assembly), with lines of evidence supporting the presence of a protein-coding gene in this region. The genome sequence is shown in the top line (Improved Sequence), with multiple lines of evidence supporting the presence of a gene mapped against that sequence. There are apparent contradictions in these evidence tracks. The BLASTx alignment track indicates that the region at 93000–12000 of *D. mojavensis* shows significant similarity to protein sequences for two isoforms of the *D. melanogaster* gene *Sox102F* (Sequence Homology track). Computer-based gene predictors indicate a gene in this region (Gene Predictions tracks), but vary on the number, size, and location of predicted exons. RNA-Seq data appear to support the presence of three or four exons, yet TopHat and Cufflinks differ on the number and location of intron splice sites. The region from 7500 to 8000 might contain an exon of *Sox102F* (predicted by N-SCAN), or it might be a separate gene (predicted by Genscan and SGP) as there is some RNA-Seq data, but little or no conservation is indicated in this region. Students must reconcile these differences to generate the best-supported gene models for this region of the *D. mojavensis* genome.

**FIGURE 2**
Faculty observe that setbacks in the research process promote student learning. Results from *NVivo* analysis of comments from the Formative Failure faculty survey (Appendix 2) on the effects on student learning from course setbacks (survey question 9.D: problems affecting all students in the class, N=161) and student setbacks (survey question 10.D: problems encountered by individual students, N=134). The percent of faculty responses that were positive (blue), negative (orange), or neutral (no effect; grey) are shown. GEP = Genomics Education Partnership.

**FIGURE 3**
Faculty are more likely to let their students risk failure in GEP research projects than in wet bench or field work lab courses and research projects. Faculty were asked how likely they were to let students fail in performance of wet bench lab work (coursework and research), field work (coursework or research), and GEP research activities. The degree of willingness to risk failure was evaluated as 1 (very likely) to 3 (not at all). Note that many GEP faculty members do not do field work, so the number of responses in that category is lower. (Percentages do not sum to 100%, as “not applicable” responses are not shown.) GEP = Genomics Education Partnership.

**FIGURE 4**
Genomics-based CUREs can support an iterative learning process. A collaborative Learning Environment (1) supports the entire process, which includes a defined learning objective (2), a formative strategy (3), and iterative experimentation (4). Adapted with permission from (10).

See this image and copyright information in PMC

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Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

Affiliations

Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

Authors

Affiliations

Abstract

Figures

References

Grants and funding

LinkOut - more resources

Full Text Sources