Biochemical adaptation: Analytics to drive next-generation research on novel microRNAs and proteins responsive to environmental stress

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My lab studies biochemical adaptation to discover the molecular mechanisms that allow many Canadian animals to adapt themselves in amazing ways – frogs that freeze solid and survive, small mammals that hibernate for months, turtles that live underwater without oxygen all winter, and many more. All these phenomena have unique molecular characteristics but also elements in common and my lab probes the molecular mechanisms that are the secrets to their survival. This work not only extends our understanding of how metabolism is regulated and the limits to which it can be stretched but also holds potential biomedical applications; e.g. for organ preservation or the use of inducible torpor in patient treatment. Two current interests of my lab are microRNAs and protein stability and how these contribute to animal adaptation. MicroRNAs are small RNA molecules that are transcribed from DNA but do not code for protein products; instead, they play major roles in regulating whether or not the larger protein-coding RNA molecules get translated into protein. Hence, changes in the types and amounts of microRNAs can have a major impact on an organism’s response to stress. My lab designed a computer program (SMIRP) to search non-mammalian genomes and catalogue all microRNA sequences; we then use the information to determine which microRNAs change under stress conditions and, by implication, which protein-coding genes are affected. Although we have proven its success, SMIRP is currently taking 6-8 months to complete the catalogue of a single genome, due to the limited computational power of our computers. Having identified new microRNA sequences, we are also limited in our ability to quantify stress-responsive changes in their abundance because my >20 person lab is dependent on one qPCR machine that can do this task. Hence, this application has two requests: (a) two powerful computer workstations to identify miRNAs in animal genomes; these will reduce computational time by 80-95%, and (b) two advanced qPCR machines to quantify miRNA responses to stress. The chosen qPCR thermocylers are also designed to do double-duty because they will also be used to in a differential scanning fluorometry mode to precisely analyze protein unfolding in response to heat/cold, denaturants vs stabilizers, and contaminants such as nanoparticles. This serves the other side of my lab which studies how enzymes and other proteins are structured to both adapt and protect cell metabolism to deal with extreme environmental conditions.