UC Davis

Gene regulatory systems contribute to an organism’s fitness by providing a way to dynamically tune cellular responses in response to fluctuating environmental conditions. In this work, we compare the regulatory tuning of genes involved in the catabolism of glucose, maltose, and sucrose in the metabolically versatile halophilic archaeon Halogeometricum borinquense through functional transcriptomic profiling, targeted qRT-PCR, and sugar utilization assays. This work provides the first transcriptomic study for this organism, preliminarily characterizes the unique and shared responses of H. borinquense to single- and multiple-sugar growth conditions, identifies key metabolic regulatory points in the organism, and advances the discussion of archaeal carbon catabolite repression (CCR) by identifying putative targets of CCR that can be probed in future work to further explore underlying mechanisms.

Halophilic organisms are also suitable for use in educational settings. Here, I present the development and study examining the impact of a quantitative biology-focused Course Based Undergraduate Research Experience (CURE) on the development of student interest in and self-efficacy for quantitative biology. Students in the course isolate halophilic organisms from environmental samples, quantitatively characterize their growth, and thereafter sequence the genomes of the isolates. We found that although students initially reported high math-biology values, we saw improvements with regard to students seeing higher value in using quantitative calculations in biology and increased interest in pursuing future quantitative experiences (e.g., coursework, occupation).

Lastly, I present collaborative research that explores how students express affect when they engage with one another in the context of an online course textbook-based annotation and discussion forum. This work includes efforts to use machine learning to predict student affect and better understand student confusion, to increase student engagement with the course content by seeding forums, and to create and validate a limited emoji-hashtag pair set that enables more reliable student-driven affect tagging of forum posts.