Evolutionary Systems Biology最新文献

Modeling complex biological systems: Tackling the parameter curse through evolution 复杂生物系统建模:通过进化解决参数诅咒

Evolutionary Systems Biology Pub Date : 2021-02-25 DOI: 10.32942/osf.io/safm4

P. Hogeweg

引用次数: 1

Addressing evolutionary questions with synthetic biology 用合成生物学解决进化问题

Evolutionary Systems Biology Pub Date : 2021-02-08 DOI: 10.31219/osf.io/6msvq

F. Baier, Y. Schaerli

{"title":"Addressing evolutionary questions with synthetic biology","authors":"F. Baier, Y. Schaerli","doi":"10.31219/osf.io/6msvq","DOIUrl":"https://doi.org/10.31219/osf.io/6msvq","url":null,"abstract":"Synthetic biology emerged as an engineering discipline to design and construct artificial biological systems. Synthetic biological designs aim to achieve specific biological behavior, which can be exploited for biotechnological, medical and industrial purposes. In addition, mimicking natural systems using well-characterized biological parts also provides powerful experimental systems to study evolution at the molecular and systems level. A strength of synthetic biology is to go beyond nature’s toolkit, to test alternative versions and to study a particular biological system and its phenotype in isolation and in a quantitative manner. Here, we review recent work that implemented synthetic systems, ranging from simple regulatory circuits, rewired cellular networks to artificial genomes and viruses, to study fundamental evolutionary concepts. In particular, engineering, perturbing or subjecting these synthetic systems to experimental laboratory evolution provides a mechanistic understanding on important evolutionary questions, such as: Why did particular regulatory networks topologies evolve and not others? What happens if we rewire regulatory networks? Could an expanded genetic code provide an evolutionary advantage? How important is the structure of genome and number of chromosomes? Although the field of evolutionary synthetic biology is still in its teens, further advances in synthetic biology provide exciting technologies and novel systems that promise to yield fundamental insights into evolutionary principles in the near future.","PeriodicalId":12324,"journal":{"name":"Evolutionary Systems Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89088982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Robustness and evolvability in transcriptional regulation 转录调控的稳健性和进化性

Evolutionary Systems Biology Pub Date : 2021-02-05 DOI: 10.31219/osf.io/ef3m6

José Aguilar-Rodríguez, J. Payne

引用次数: 1

Direction and Constraint in Phenotypic Evolution: Dimension Reduction and Global Proportionality in Phenotype Fluctuation and Responses 表型进化的方向和约束:表型波动和响应的降维和全局比例

Evolutionary Systems Biology Pub Date : 2021-02-05 DOI: 10.1007/978-3-030-71737-7_3

K. Kaneko, C. Furusawa

引用次数: 1

Dynamical Modularity of the Genotype-Phenotype Map 基因型-表型图谱的动态模块化

Evolutionary Systems Biology Pub Date : 2021-02-02 DOI: 10.31219/osf.io/vfz4t

Johannes Jaeger, Nick Monk

{"title":"Dynamical Modularity of the Genotype-Phenotype Map","authors":"Johannes Jaeger, Nick Monk","doi":"10.31219/osf.io/vfz4t","DOIUrl":"https://doi.org/10.31219/osf.io/vfz4t","url":null,"abstract":"An organism’s phenotype can be thought of as consisting of a set of discrete traits, able to evolve relatively independently of each other. This implies that the developmental processes generating these traits—the underlying genotype-phenotype map—must also be functionally organised in a modular manner. The genotype-phenotype map lies at the heart of evolutionary systems biology. Recently, it has become popular to define developmental modules in terms of the structure of gene regulatory networks. This approach is inherently limited: gene networks often do not have structural modularity. More generally, the connection between structure and function is quite loose. In this chapter, we discuss an alternative approach based on the concept of dynamical modularity, which overcomes many of the limitations of structural modules. A dynamical module consists of the activities of a set of genes and their interactions that generate a specific dynamic behaviour. These modules can be identified and characterised by phase-space analysis of data-driven models. We showcase the power and the promise of this new approach using several case studies. Dynamical modularity forms an important component of a general theory of the evolution of regulatory systems and the genotype-phenotype map they define.","PeriodicalId":12324,"journal":{"name":"Evolutionary Systems Biology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85775120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Of Evolution, Systems and Complexity 论进化、系统和复杂性

Evolutionary Systems Biology Pub Date : 2021-01-01 DOI: 10.1007/978-3-030-71737-7_1

G. Beslon, Vincent Liard, David P. Parsons, Jonathan Rouzaud-Cornabas

引用次数: 4

Experimental Evolution to Understand the Interplay Between Genetics and Adaptation 实验进化以理解遗传和适应之间的相互作用

Evolutionary Systems Biology Pub Date : 2021-01-01 DOI: 10.1007/978-3-030-71737-7_6

Jana Helsen, Rob Jelier

引用次数: 1

Understanding the Genotype-Phenotype Map: Contrasting Mathematical Models 理解基因型-表型图谱:对比数学模型

Evolutionary Systems Biology Pub Date : 2021-01-01 DOI: 10.1007/978-3-030-71737-7_10

I. Salazar-Ciudad, Miquel Marin-Riera, Miguel Brun-Usan

引用次数: 1

Life’s Attractors Continued: Progress in Understanding Developmental Systems Through Reverse Engineering and In Silico Evolution 生命的吸引力继续:通过逆向工程和计算机进化理解发育系统的进展

Evolutionary Systems Biology Pub Date : 2021-01-01 DOI: 10.1007/978-3-030-71737-7_4

Anton Crombach, Johannes Jaeger

引用次数: 1

Evolutionary Systems Biology: Advances, Questions, and Opportunities 进化系统生物学:进展、问题和机遇

Evolutionary Systems Biology Pub Date : 2021-01-01 DOI: 10.1007/978-3-030-71737-7

引用次数: 1