Download Evolutionary Systems Biology by Maureen A. O’Malley (auth.), Orkun S. Soyer (eds.) PDF

By Maureen A. O’Malley (auth.), Orkun S. Soyer (eds.)

The e-book goals to introduce the reader to the rising box of Evolutionary platforms Biology, which techniques classical structures biology questions inside of an evolutionary framework. An evolutionary technique may well let figuring out the importance of saw range, discover “evolutionary layout rules” and expand predictions made in version organisms to others. moreover, evolutionary structures biology can generate new insights into the adaptive panorama via combining molecular platforms biology versions and evolutionary simulations. This perception can permit the improvement of extra distinct mechanistic evolutionary hypotheses.

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Therefore, many approaches to understand the function of genome-scale metabolic networks focus on coarser-grained representations of 2 Metabolic Networks and Their Evolution 31 such networks. An especially prominent and fruitful approach in this area is called flux balance analysis (FBA), which requires only stoichiometric information about individual reactions, and which can predict the biosynthetic abilities of a network under some general assumptions (Box 1). Box 1: Constraint-based modeling and flux balance analysis (FBA) An important goal of systems biology is to predict a metabolic phenotype, the identity of the molecules that a metabolic network can synthesize, as well as their rate of synthesis, from a metabolic genotype, the set of enzymes encoded by a genome and their regulation.

Oberhardt MA, Puchalka J, dos Santos VAPM, Papin JA (2011) Reconciliation of genomescale metabolic reconstructions for comparative systems analysis. PLOS Comput Biol 7(3):e1001116 101. de Silva E, Stumpf MPH (2005) Complex networks and simple models in biology. J R Interface 2:419–430 102. Stumpf MPH, Kelly WP, Thorne T, Wiuf C (2007) Evolution at the system level: the natural history of protein interaction networks. Trends Ecol Evol 22:366–373 103. Wagner A (2011) Genotype networks shed light on evolutionary constraints.

It is often observed for organisms living in environments that undergo little change, such as endoparasitic or endosymbiotic single-celled organisms, which live inside other organisms. Examples include Buchnera aphidicola, an endosymbiotic relative of E. coli, which lives inside the cells of aphids [65, 66]. Buchnera provides its host with essential amino acids in an association that has persisted for many million years [66]. During this time the genome of Buchnera has lost many genes, and its metabolic network has lost many chemical reactions [67].

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