Details:

Alternative Title:
J Theor Biol
Publisher's site:
http://dx.doi.org/10.1016/j.jtbi.2013.12.009
Personal Author:
Birch, Elsa W. ; Udell, Madeleine ; Covert, Markus W.
Birch, Elsa W. ; Udell, Madeleine ; Covert, Markus W. Less -
Description:
We present two modifications of the flux balance analysis (FBA) metabolic modeling framework which relax implicit assumptions of the biomass reaction. Our flexible flux balance analysis (flexFBA) objective removes the fixed proportion between reactants, and can therefore produce a subset of biomass reactants. Our time-linked flux balance analysis (tFBA) simulation removes the fixed proportion between reactants and byproducts, and can therefore describe transitions between metabolic steady states. Used together, flexFBA and tFBA model a time scale shorter than the regulatory and growth steady state encoded by the biomass reaction. This combined short-time FBA method is intended for integrated modeling applications to enable detailed and dynamic depictions of microbial physiology such as whole-cell modeling. For example, when modeling Escherichia coli, it avoids artifacts caused by low-copy-number enzymes in single-cell models with kinetic bounds. Even outside integrated modeling contexts, the detailed predictions of flexFBA and tFBA complement existing FBA techniques. We show detailed metabolite production of in silico knockouts used to identify when correct essentiality predictions are made for the wrong reason.
Subject:
[+]
Animals
Article
Biomass
Computer Simulation
Gene Knockout Techniques
Integrated Modeling
Metabolic Networks And Pathways
Metabolism
Models, Biological

Source:
J Theor Biol. 2013; 345:12-21.
Pubmed ID:
24361328
Pubmed Central ID:
PMC3933926
Document Type:
Journal Article
Funding:
5DP1LM01150-05/DP/NCCDPHP CDC HHS/United States ; DP1 LM011510/LM/NLM NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States
5DP1LM01150-05/DP/NCCDPHP CDC HHS/United States ; DP1 LM011510/LM/NLM NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States Less -
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:5784718bdebde6d0cf2ca98440550a318e30f80fc8f78cbfa6c53bb6f9415b05
File Type:

Supporting Files

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