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

我的实验室研究生化适应，以发现让许多加拿大动物以惊人的方式自我适应的分子机制--冻结并存活的青蛙，冬眠数月的小型哺乳动物，整个冬天在没有氧气的水下生活的海龟，等等。所有这些现象都有独特的分子特征，但也有共同的元素，我的实验室探索了它们生存的秘密的分子机制。这项工作不仅扩大了我们对新陈代谢是如何调节的以及新陈代谢可以扩展到的极限的理解，而且还具有潜在的生物医学应用；例如，用于器官保存或在患者治疗中使用可诱导的麻木。我的实验室目前感兴趣的两个问题是microRNAs和蛋白质稳定性，以及它们如何有助于动物适应。MicroRNAs是从DNA转录而来的小RNA分子，但不编码蛋白质产物；相反，它们在调节编码蛋白质的较大RNA分子是否翻译成蛋白质方面发挥着主要作用。因此，microRNAs类型和数量的变化可能会对有机体对压力的反应产生重大影响。我的实验室设计了一个计算机程序(SMIRP)来搜索非哺乳动物的基因组并对所有的microRNA序列进行分类；然后我们使用这些信息来确定哪些microRNA在压力条件下发生了变化，进而确定哪些蛋白质编码基因受到了影响。尽管我们已经证明了SMIRP的成功，但由于我们计算机的计算能力有限，SMIRP目前需要6-8个月才能完成单个基因组的编目。在识别出新的microRNA序列后，我们量化其丰度的压力响应变化的能力也受到限制，因为我的20人实验室依赖于一台可以完成这项任务的qPCR机。因此，这一应用程序有两个要求：(A)两个强大的计算机工作站来识别动物基因组中的miRNAs；这将减少80%-95%的计算时间；(B)两个先进的qPCR机器来量化miRNA对压力的反应。所选的qPCR温箱还被设计成具有双重功能，因为它们还将用于在差示扫描荧光模式下精确分析蛋白质在热/冷、变性剂和稳定剂以及纳米颗粒等污染物中展开的情况。这为我实验室的另一边服务，我的实验室研究酶和其他蛋白质是如何构成的，以适应和保护细胞新陈代谢，以应对极端环境条件。

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.