Discovery through research provides real-world challenge and reward that promotes student learning. Parallel implementation of research projects in a teaching lab environment multiples both the challenges and the rewards. The practical complications to exploring the unknown by implementing discovery research in the teaching lab include organizing multiple parallel projects, communicating protocols effectively, collecting data systematically, and controlling for data quality. We have developed an online resource called GENI (Guiding Education through Novel Investigations) to provide biochemistry protocols and data collection tools that can be used in teaching labs to better answer research questions in the context of undergraduate teaching labs. GENI protocols and tools guide undergraduates to produce high-quality, organized data and conclusions that can be peer-reviewed and published. Protocols and data collection tools on the GENI website guided students through a three-week bioinformatics project in a biochemistry course with more than 50 students. The research question was initiated by a bacterial genome that contained duplicate, highly divergent genes for the final step in the proline biosynthesis pathway, which may participate in the osmotic stress reponse. Genes homologous to both paralogs were found in many related bacteria with complete genomes in public databases. Each student lab group was assigned a different gene and tasked with exploring the source organism's genome, looking for signs of stress-induced operons, analyzing the primary sequence, building a homology model online with I-TASSER, evaluating the quality of the model, and analyzing the model structure with tools such as PyMol. Each hypothesized on the quaternary structure, solubility, and cofactor binding of their assigned gene. In a subsequent Molecular Biology course, also facilitated by GENI, students are able to test these hypotheses, connecting the two disciplines for greater educational depth. [Partial support for this work was provided by the National Science Foundation's Transforming Undergraduate Education in Science, Technology, Engineering and Mathematics (TUES) program under Award No. 1322848.]

Discovery in large undergraduate biochemistry labs through homology modeling and functional annotation of paralogous genes

251st National Meeting (2016)

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