{"title":"Phenotypic systems biology for organisms: Concepts, methods and case studies.","authors":"Takao K Suzuki","doi":"10.2142/biophysico.bppb-v19.0011","DOIUrl":null,"url":null,"abstract":"<p><p>Design principles of phenotypes in organisms are fundamental issues in physical biology. So far, understanding \"systems\" of living organisms have been chiefly promoted by understanding the underlying biomolecules such as genes and proteins, and their intra- and inter-relationships and regulations. After a long period of sophistication, biophysics and molecular biology have established a general framework for understanding 'molecular systems' in organisms without regard to species, so that the findings of fly studies can be applied to mouse studies. However, little attention has been paid to exploring \"phenotypic systems\" in organisms, and thus its general framework remains poorly understood. Here I review concepts, methods, and case studies using butterfly and moth wing patterns to explore phenotypes as systems. First, I present a unifying framework for phenotypic traits as systems, termed multi-component systems. Second, I describe how to define components of phenotypic systems, and also show how to quantify interactions among phenotypic parts. Subsequently, I introduce the concept of the macro-evolutionary process, which illustrates how to generate complex traits. In this point, I also introduce mathematical methods, \"phylogenetic comparative methods\", which provide stochastic processes along molecular phylogeny as bifurcated paths to quantify trait evolution. Finally, I would like to propose two key concepts, macro-evolutionary pathways and genotype-phenotype loop (GP loop), which must be needed for the next directions. I hope these efforts on phenotypic biology will become one major target in biophysics and create the next generations of textbooks. This review article is an extended version of the Japanese article, Biological Physics in Phenotypic Systems of Living Organisms, published in SEIBUTSU-BUTSURI Vol. 61, p. 31-35 (2021).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2022-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c3/e5/19_e190011.PMC9159793.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biophysics and Physicobiology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.2142/biophysico.bppb-v19.0011","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2022/1/1 0:00:00","PubModel":"eCollection","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
Design principles of phenotypes in organisms are fundamental issues in physical biology. So far, understanding "systems" of living organisms have been chiefly promoted by understanding the underlying biomolecules such as genes and proteins, and their intra- and inter-relationships and regulations. After a long period of sophistication, biophysics and molecular biology have established a general framework for understanding 'molecular systems' in organisms without regard to species, so that the findings of fly studies can be applied to mouse studies. However, little attention has been paid to exploring "phenotypic systems" in organisms, and thus its general framework remains poorly understood. Here I review concepts, methods, and case studies using butterfly and moth wing patterns to explore phenotypes as systems. First, I present a unifying framework for phenotypic traits as systems, termed multi-component systems. Second, I describe how to define components of phenotypic systems, and also show how to quantify interactions among phenotypic parts. Subsequently, I introduce the concept of the macro-evolutionary process, which illustrates how to generate complex traits. In this point, I also introduce mathematical methods, "phylogenetic comparative methods", which provide stochastic processes along molecular phylogeny as bifurcated paths to quantify trait evolution. Finally, I would like to propose two key concepts, macro-evolutionary pathways and genotype-phenotype loop (GP loop), which must be needed for the next directions. I hope these efforts on phenotypic biology will become one major target in biophysics and create the next generations of textbooks. This review article is an extended version of the Japanese article, Biological Physics in Phenotypic Systems of Living Organisms, published in SEIBUTSU-BUTSURI Vol. 61, p. 31-35 (2021).
生物体表型的设计原理是物理生物学的基本问题。迄今为止,对生物体 "系统 "的认识主要是通过了解基因和蛋白质等基本生物大分子及其内部和相互之间的关系和调控来实现的。经过长期的发展,生物物理学和分子生物学已经建立了不分物种理解生物体内 "分子系统 "的总体框架,因此,对蝇蛆的研究结果可以应用于对小鼠的研究。然而,人们很少关注生物体内 "表型系统 "的探索,因此对其总体框架的了解仍然很少。在此,我将回顾利用蝴蝶和飞蛾翅膀模式探索表型系统的概念、方法和案例研究。首先,我提出了表型特征作为系统的统一框架,即多组分系统。其次,我介绍了如何定义表型系统的组成部分,并展示了如何量化表型各部分之间的相互作用。随后,我介绍了宏观进化过程的概念,说明了如何产生复杂的性状。在这一点上,我还介绍了数学方法--"系统进化比较方法",它提供了分子系统进化的随机过程,作为量化性状进化的分叉路径。最后,我想提出两个关键概念,即宏观进化路径和基因型-表型循环(GP 循环),这两个概念是下一步发展方向所必须的。我希望这些关于表型生物学的努力能成为生物物理学的一个主要目标,并创造出下一代教科书。本评论文章是日文文章《生物体表型系统中的生物物理学》(Biological Physics in Phenotypic Systems of Living Organisms)的扩展版,发表于《SEIBUTSU-BUTSURI》第 61 卷第 31-35 页(2021 年)。