Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger,Richard Que,Ronan M. T. Fleming,Ines Thiele,Jeffrey D. Orth,Adam M. Feist,Daniel C. Zielinski,Aarash Bordbar,Nathan E. Lewis,Sorena Rahmanian,Joseph Kang,Daniel R. Hyduke,Bernhard O. Palsson +12 more
TLDR
The constraint-based reconstruction and analysis toolbox as discussed by the authors is a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraintbased approach and allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules.Abstract:
The manner in which microorganisms utilize their metabolic processes can be predicted using constraint-based analysis of genome-scale metabolic networks. Herein, we present the constraint-based reconstruction and analysis toolbox, a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraint-based approach. Specifically, this software allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules. Functions enabling these calculations are included in the toolbox, allowing a user to input a genome-scale metabolic model distributed in Systems Biology Markup Language format and perform these calculations with just a few lines of code. The results are predictions of cellular behavior that have been verified as accurate in a growing body of research. After software installation, calculation time is minimal, allowing the user to focus on the interpretation of the computational results.read more
Citations
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Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation.
TL;DR: A computational multi-scale workflow that combines whole-body physiologically based pharmacokinetic (PBPK) models and organ-specific genome-scale metabolic network (GSMN) models through shared reactions of the xenobiotic metabolism is presented.
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Enhancing fatty acid production in Escherichia coli by Vitreoscilla hemoglobin overexpression.
TL;DR: It is revealed the fatty acid over-producing strain is sensitive to metabolic burden and oxygen influx, and thus a careful evaluation of the cost-benefit tradeoff with the guidance of fluxome analysis will be fundamental for the rational design of synthetic biology strains.
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A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp. PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry.
TL;DR: Production of ethylene, the most widely used petrochemical produced exclusively from fossil fuels, in the model cyanobacterium Synechocystis sp.
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Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways
Hong Zeng,Aidong Yang +1 more
TL;DR: This FBA-based model is able to quantitatively predict the onset and extent of the overflow metabolism in various E. coli strains, enabled by three linearly-correlated (as opposed to uniquely determinable) proteomic cost parameters.
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Fed-batch production of l-tryptophan from glycerol using recombinant Escherichia coli.
TL;DR: Fed‐batch production of l‐tryptophan from glycerol was shown for the first time with recombinant E. coli.
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