Extending the Fly-CURE into an Upper-Level Undergraduate Bioinformatics Course
Authors: Kayla Bieser 1; Richard Tillett 2; Jacob Kagey 3; Karen Bieluch 4; Nikolaos Tsotakos 5
Affiliations: 1) Nevada State College; 2) University of Nevada Las Vegas; 3) University of Detroit Mercy; 4) University of Maine; 5) Penn State Harrisburg
Keywords: f. classroom undergraduate research experience (CURE)
The Fly-CURE is a Course-based Undergraduate Research Experience (CURE) in which undergraduate genetics students from multiple US institutions characterize and conduct deficiency mapping of mutants in Drosophila melanogaster. A Flp/FRT EMS screen was conducted in the Drosophila eye in the context of blocked apoptosis to screen for conditional mutants that alter control of cell growth and development. The goal is to identify and map the mutation to a genomic region and/or gene on 2R. However, the gene and molecular location of some mutants have proven difficult to map utilizing these complementation techniques. To identify the mutations, we conducted whole genome sequencing (WGS) and bioinformatics analysis utilizing stocks of heterozygous EMS mutated flies with an unknown mutational locus, but in some instances with a known genetic region mapped. A bioinformatics workflow was successfully established and verified utilizing four EMS mutants identified in the initial screen and a control stock representing their pre-EMS genetic background. When combined with deficiency mapping data, this methodology successfully identified mutated SNPs. To broaden participation and interest in bioinformatics, a scaffolded curriculum with the Fly-CURE was created at Nevada State College, a 4-year HSI. A 400-level bioinformatics course was implemented with a virtual format in Fall 2020 utilizing GitHub for course content and an app was developed in the CyVerse Discovery Environment for terminal and data access. A modification of Data Carpentries Genomics curriculum was utilized to introduce bash, the Unix command line and genomics methods, followed by a tailored hands-on pipeline for student analysis of WGS data collected from mutant flies the students had previously studied in the Fly-CURE. To-date, 49 students have completed the course and analyzed the genomes of 14 EMS mutant Drosophila, with eight mutations having been conclusively determined via this methodology. Preliminary assessment data supports that most students had little to no prior experience in bioinformatics and made significant gains in their understanding of file structures, Unix tools, Next Gen Sequencing, and their understanding of bioinformatics and how it relates to studying real world problems. The scaffolding of curriculum from genetics into bioinformatics allowed for greater understanding and buy-in by the students. Future goals include expansion of the curriculum to other institutions.