Experimental systems biology approaches reveal interaction mechanisms in model multispecies communities

Mainstreaming Caenorhabditis elegans in experimental evolution

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.3055 ◽

2014 ◽

Vol 281 (1778) ◽

pp. 20133055 ◽

Cited By ~ 38

Author(s):

Jeremy C. Gray ◽

Asher D. Cutter

Keyword(s):

Life History ◽

Systems Biology ◽

Caenorhabditis Elegans ◽

Experimental Evolution ◽

Life History Theory ◽

Evolutionary Process ◽

Biological Knowledge ◽

Experimental Systems ◽

Research Areas ◽

Mating System Evolution

Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host–pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis , detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.

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Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production

10.2172/1178803 ◽

2015 ◽

Author(s):

Elefterios Papoutsakis

Keyword(s):

Systems Biology ◽

Bioenergy Production ◽

Experimental Systems

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Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Behavioral and Brain Sciences ◽

10.1017/s0140525x18002911 ◽

2019 ◽

Vol 42 ◽

Author(s):

J. Alfredo Blakeley-Ruiz ◽

Carlee S. McClintock ◽

Ralph Lydic ◽

Helen A. Baghdoyan ◽

James J. Choo ◽

...

Keyword(s):

Systems Biology ◽

High Resolution ◽

Experimental Design ◽

Integrated Systems ◽

Microbiome Research ◽

Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

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