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，以发现允许许多加拿大动物以惊人的方式适应自己的分子机制-青蛙冻结固体并存活，冬眠数月的小型哺乳动物，整个冬天在没有氧气的情况下生活在水下的海龟，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。这项工作不仅扩展了我们对代谢如何调节以及它可以延伸的极限的理解，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诱导性麻痹。我的实验室目前的两个兴趣是microRNA和蛋白质稳定性，以及它们如何有助于动物适应。MicroRNA是从DNA转录的小RNA分子，但不编码蛋白质产物;相反，它们在调节较大的蛋白质编码RNA分子是否翻译成蛋白质方面发挥主要作用。因此，microRNA的类型和数量的变化可以对生物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序列进行编目;然后我们使用这些信息来确定哪些microRNA在应激条件下发生了变化，并暗示哪些蛋白质编码基因受到了影响。虽然我们已经证明了它的成功，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。在确定了新的microRNA序列之后，我们在量化其丰度的应激反应变化方面的能力也受到限制，因为我的>20人实验室依赖于一台可以完成这项任务的qPCR机器。因此，该应用有两个要求：（a）两个强大的计算机工作站来识别动物基因组中的miRNA;这将减少80- 95%的计算时间，以及（B）两个先进的qPCR机器来量化miRNA对压力的反应。所选的qPCR热循环仪也被设计为双重功能，因为它们也将用于差示扫描荧光测定模式，以精确分析蛋白质解折叠对热/冷、变性剂与稳定剂以及污染物（如纳米颗粒）的响应。这服务于我实验室的另一边，研究酶和其他蛋白质是如何结构化的，以适应和保护细胞代谢，以应对极端的环境条件。

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.