Implementation of a CRISPR/Cas9 course‐based undergraduate research experience (CURE) in the biochemistry curriculum at a small private college

Abstract

In this course‐based undergraduate research experience (CURE), thirty students enroll in biochemistry per year and participate in a novel CRISPR/Cas9 project in collaboration with the Environmental Protection Agency (EPA) research labs in Duluth, MN. Genes of interest in fathead minnows and zebrafish are mutated to assess the validity of adverse outcome pathways based on the existing toxicological data. This work provides all biochemistry and biology majors at the College of Saint Scholastica (CSS) with an opportunity for project ownership and the consequent growth of scientific identity.During the first semester biochemistry course, Biochemistry I, the focus is on enhancing students' understanding of the relationship between protein structure and function. Through a series of assignments, they gain experience using uniprot.org, Clustal Omega, BLAST, and PubMed. Students propose a region of their assigned fathead gene for CRISPR/Cas9 targeting and supply evidence supporting their choice. After discussing their proposals in small groups with others assigned to the same target, they prepare individual reports summarizing their findings and plan for mutation.In Biochemistry II, students apply the data collected during the first semester to design CRISPR/Cas9 guide strands. Online bioinformatic tools are used for this purpose, and in fathead minnows, guide strands are vetted against the zebrafish genome to verify a lack of off‐target hits since the fathead genome assembly is incomplete. Students also tour the EPA research labs, meeting the scientists on the collaborative research team and learning about their work. Fish samples from previous CRISPR/Cas9 experiments are brought back to campus and students screen for mutants by extracting DNA, amplifying via PCR, and submitting the samples for sequencing. The class analyzes the sequence data using TIDE: Tracking of Indels by Decomposition (tide.nki.nl), an algorithm that delivers mutation information by position and percentage. Results from the yearlong CURE are summarized in a formal lab report and poster presentation, affording an opportunity to synthesize and reflect on the data generated throughout the yearlong experience. Implementation of this program at CSS has allowed for a significant increase in research participation by biochemistry and biology majors.Support or Funding InformationU.S. Environmental Protection Agency, Office of Research and Development, Mid‐Continent Ecology Division, Duluth, MN The College of St. Scholastica, Faculty Development Committee Research Grant.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.