Dataset Information

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

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.

SUBMITTER: Lopatto D

PROVIDER: S-EPMC7048401 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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

Lopatto David D Rosenwald Anne G AG DiAngelo Justin R JR Hark Amy T AT Skerritt Matthew M Wawersik Matthew M Allen Anna K AK Alvarez Consuelo C Anderson Sara S Arrigo Cindy C Arsham Andrew A Barnard Daron D Bazinet Christopher C Bedard James E J JEJ Bose Indrani I Braverman John M JM Burg Martin G MG Burgess Rebecca C RC Croonquist Paula P Du Chunguang C Dubowsky Sondra S Eisler Heather H Escobar Matthew A MA Foulk Michael M Furbee Emily E Giarla Thomas T Glaser Rivka L RL Goodman Anya L AL Gosser Yuying Y Haberman Adam A Hauser Charles C Hays Shan S Howell Carina E CE Jemc Jennifer J Johnson M Logan ML Jones Christopher J CJ Kadlec Lisa L Kagey Jacob D JD Keller Kimberly L KL Kennell Jennifer J Key S Catherine Silver SCS Kleinschmit Adam J AJ Kleinschmit Melissa M Kokan Nighat P NP Kopp Olga Ruiz OR Laakso Meg M MM Leatherman Judith J Long Lindsey J LJ Manier Mollie M Martinez-Cruzado Juan C JC Matos Luis F LF McClellan Amie Jo AJ McNeil Gerard G Merkhofer Evan E Mingo Vida V Mistry Hemlata H Mitchell Elizabeth E Mortimer Nathan T NT Mukhopadhyay Debaditya D Myka Jennifer Leigh JL Nagengast Alexis A Overvoorde Paul P Paetkau Don D Paliulis Leocadia L Parrish Susan S Preuss Mary Lai ML Price James V JV Pullen Nicholas A NA Reinke Catherine C Revie Dennis D Robic Srebrenka S Roecklein-Canfield Jennifer A JA Rubin Michael R MR Sadikot Takrima T Sanford Jamie Siders JS Santisteban Maria M Saville Kenneth K Schroeder Stephanie S Shaffer Christopher D CD Sharif Karim A KA Sklensky Diane E DE Small Chiyedza C Smith Mary M Smith Sheryl S Spokony Rebecca R Sreenivasan Aparna A Stamm Joyce J Sterne-Marr Rachel R Teeter Katherine C KC Thackeray Justin J Thompson Jeffrey S JS Peters Stephanie Toering ST Van Stry Melanie M Velazquez-Ulloa Norma N Wolfe Cindy C Youngblom James J Yowler Brian B Zhou Leming L Brennan Janie J Buhler Jeremy J Leung Wilson W Reed Laura K LK Elgin Sarah C R SCR

Journal of microbiology & biology education 20200228 1

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 lin ...[more]

PMID: 32148609

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Project description:Genetic analysis in model systems can provide a rich context for conceptual understanding of gene structure, regulation, and function. With an intent to create a rich learning experience in molecular genetics, we developed a semester-long course-based undergraduate research experience (CURE) using the CRISPR-Cas9 gene editing system to disrupt specific genes in the zebrafish. The course was offered to freshman students; nine students worked in four groups (two to three members per group) to design, synthesize, and test the nuclease activity of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/sgRNAs for targeted disruption of specific genes in the zebrafish. Each group worked with a gene with an already known mutant phenotype that can be visually scored and a gene that had not been studied in zebrafish previously. Embedded in the course were a series of workshop-styled units or tutorials, including tours to core facilities. The focus was on introducing and developing skills that could be accommodated within the span of a semester. Each group successfully cloned at least one plasmid-encoding CRISPR/sgRNA template, visually analyzed injected embryos, and performed genotyping assays to detect CRISPR-Cas9 activity. In-class discussions, a final end-of-semester written test, and group oral presentations were assessed for an understanding of the CRISPR-Cas9 system, application of the CRISPR-Cas9 system as a gene manipulation tool, and experimental methods used to create plasmid vectors and synthesize sgRNA. In addition, poster presentations were evaluated by faculty, graduate students, and senior undergraduate students at a University research exposition. Self-reflections in the form of group conversations were video recorded. All students (9/9) distinctly showed learning gains after completing the activity, but the extent of the gains was variable, as seen from results of a written test and poster presentation assessment. Qualitative analysis of evaluations and self-reporting data indicated several gains, suggesting that all students found many aspects of the CURE valuable and gained project-specific (conceptual) and transferrable skills (science process and science identity).

Project description:Course-based undergraduate research experiences (CUREs) are an effective means of transforming the learning and teaching of science by involving students in the scientific process. The potential importance of the microbiome in shaping both environmental health and disease makes investigations of microbiomes an excellent teaching tool for undergraduate microbiology. Here, we present a CURE based on the microbiome of the bean beetle (Callosobruchus maculatus), a model system for undergraduate laboratory education. Despite the extensive research literature on bean beetles, little is known about their microbiome, making them an ideal system for a discovery-based CURE. In the CURE, students acquire microbiological technical skills by characterizing both culturable and unculturable members of the beetle gut-microbial community. Students plate beetle gut homogenates on different media, describe the colonies that are formed to estimate taxonomic diversity, extract DNA from colonies of interest, PCR amplify the16S rRNA gene for Sanger sequencing, and use the NCBI-nBLAST database to taxonomically classify sequences. Additionally, students extract total DNA from beetle gut homogenates for high-throughput paired-end sequencing and perform bioinformatic and statistical analyses of bacterial communities using a combination of open-access data processing software. Each activity allows students to engage with studies of microbiomes in a real-world context, to apply concepts and laboratory techniques to investigate either student or faculty-driven research questions, and to gain valuable experiences working with large high-throughput datasets. The CURE is designed such that it can be implemented over either 6-weeks (half semester) or 12-weeks (full semester), allowing for flexibility within the curriculum. Furthermore, student-generated data from the CURE (including bacterial colony phenotypic data, full-length 16S rRNA gene sequences from cultured isolates, and bacterial community sequences from gut homogenates) has been compiled in a continuously curated open-access database on the Bean Beetle Microbiome Project website, facilitating the generation of broader research questions across laboratory classrooms.

Dataset Information

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

Publications

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

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