Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada.
The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China.
J Exp Biol. 2020 Dec 17;223(Pt 24):jeb191262. doi: 10.1242/jeb.191262.
'Omics' methods, such as transcriptomics, proteomics, lipidomics or metabolomics, yield simultaneous measurements of many related molecules in a sample. These approaches have opened new opportunities to generate and test hypotheses about the mechanisms underlying biochemical and physiological phenotypes. In this Commentary, we discuss general approaches and considerations for successfully integrating omics into comparative physiology. The choice of omics approach will be guided by the availability of existing resources and the time scale of the process being studied. We discuss the use of whole-organism extracts (common in omics experiments on small invertebrates) because such an approach may mask underlying physiological mechanisms, and we consider the advantages and disadvantages of pooling samples within biological replicates. These methods can bring analytical challenges, so we describe the most easily analyzed omics experimental designs. We address the propensity of omics studies to digress into 'fishing expeditions' and show how omics can be used within the hypothetico-deductive framework. With this Commentary, we hope to provide a roadmap that will help newcomers approach omics in comparative physiology while avoiding some of the potential pitfalls, which include ambiguous experiments, long lists of candidate molecules and vague conclusions.
“组学”方法，如转录组学、蛋白质组学、脂质组学或代谢组学，可同时测量样本中许多相关分子。这些方法为生成和测试关于生化和生理表型背后机制的假设提供了新的机会。在这篇评论中，我们讨论了成功地将组学整合到比较生理学中的一般方法和注意事项。组学方法的选择将取决于现有资源的可用性和研究过程的时间尺度。我们讨论了使用整个生物体提取物（在小型无脊椎动物的组学实验中很常见），因为这种方法可能掩盖潜在的生理机制，并且我们考虑了在生物学重复内汇集样本的优缺点。这些方法可能会带来分析挑战，因此我们描述了最容易分析的组学实验设计。我们讨论了组学研究倾向于偏离“钓鱼探险”的倾向，并展示了如何在假设演绎框架内使用组学。通过这篇评论，我们希望提供一个路线图，帮助比较生理学领域的新手使用组学，同时避免一些潜在的陷阱，包括模糊的实验、候选分子的长列表和模糊的结论。
