Applied Metagenomics
Stokes Baker, University of Detroit Mercy
The long-term objective of the proposal is to develop a metagenomics course that will support the goals of the ReBUILDetroit program at the University of Detroit Mercy. Genomics technologies are now revolutionizing biomedical research due to advancements in next genera¬tion sequencing (NGS) technologies. As a result, undergraduates that have significant exposure to metagenomics will be better prepared to enter graduate school. To meet the objective, high-impact activities that have been shown to increase retention among underrepresented minorities (URM) and women will be built into the pedagogical approaches. A new course-based undergraduate research experience (CURE) course, entitled "Applied Metagenomics", will be created where undergraduates will be conducting authentic research that directly impacts their local community. Students will work on common projects and write laboratory reports in a cooperative manner within their learning communities. This course will advance public health because a diverse pool of future biomedical researchers will gain expertise in an emerging technology. The course involves using 16S rRNA metagenomics to evaluate the potential public health impacts of ponds found in city parks. The students will collect samples, isolate bacterial DNA, and make 16S rRNA gene libraries. A new NGS technology (the MinION by Oxford Nanopore, Oxford UK) will be used to sequence the students' libraries. The students will use the supercomputing resources provided by Argonne National Laboratory to publicly archive their data (thus directly contributing to the scientific community) and to analyze their data. The effectiveness of the instructional materials and pedagogies will be evaluated using standardized instruments and contemplation writing assignments. The results and instructional materials will be disseminated in peer-reviewed venues.