Journal ArticleDOI
Dynamic metabolic flux analysis--tools for probing transient states of metabolic networks.
TLDR
Predictive models are thus established that can be used to optimize bioprocessing conditions and identify useful genetic manipulations by combining network analysis with a kinetic model.About:
This article is published in Current Opinion in Biotechnology.The article was published on 2013-12-01. It has received 93 citations till now. The article focuses on the topics: Flux balance analysis & Metabolic network modelling.read more
Citations
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Journal ArticleDOI
Methods and advances in metabolic flux analysis: a mini-review.
TL;DR: This mini-review discusses and classify the various methods of MFA that have been developed, which include stoichiometric MFA, 13C metabolic flux analysis, isotopic non-stationary 13Cmetabolic fluxAnalysis, dynamic metabolic fluxanalysis, and 13C dynamic metabolism flux analysis.
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A guide to 13C metabolic flux analysis for the cancer biologist.
TL;DR: A practical guide for investigators interested in getting started with 13C-MFA is provided, which includes best practices, pitfalls, alternative approaches, and new developments, especially new user-friendly software that allows researchers without extensive training in mathematics, statistics, or coding to perform 13C -MFA.
Journal ArticleDOI
Multivariate modular metabolic engineering for pathway and strain optimization.
Bradley W. Biggs,Brecht De Paepe,Christine Nicole S. Santos,Marjan De Mey,Parayil Kumaran Ajikumar +4 more
TL;DR: In this technique, key enzymes are organized into distinct modules and simultaneously varied based on expression to balance flux through a pathway, which has the potential to systematize and revolutionize the field of metabolic engineering and industrial biotechnology.
Journal ArticleDOI
Quantifying Protein Synthesis and Degradation in Arabidopsis by Dynamic 13CO2 Labeling and Analysis of Enrichment in Individual Amino Acids in Their Free Pools and in Protein.
TL;DR: The rates of protein synthesis and degradation during leaf development, during growth at high temperature, and compared synthesis rates of Rubisco large and small subunits of in the light and dark are investigated.
Journal ArticleDOI
High-resolution 13C metabolic flux analysis.
TL;DR: A GC–MS method for 13C metabolic flux analysis with data analysis using Metran software that can be completed in 4 d and quantifies metabolic fluxes with a standard deviation of ≤2%, a substantial improvement over previous implementations.
References
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What is flux balance analysis
TL;DR: This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.
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OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization
TL;DR: The computational OptKnock framework is introduced for suggesting gene deletion strategies leading to the overproduction of chemicals or biochemicals in E. coli, and hints at a growth selection/adaptation system for indirectly evolving overproducing mutants.
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Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli
TL;DR: In this article, two different formulations of dynamic flux balance analysis were used to simulate the batch growth of E. coli on glucose, and the predictions were found to qualitatively match experimental data.
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The biomass objective function
TL;DR: Fundamental issues associated with its formulation and use are reviewed and use to compute optimal growth states are reviewed.
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An Elementary Metabolite Unit (EMU) Based Method of Isotopically Nonstationary Flux Analysis
TL;DR: This work applied elementary metabolite unit (EMU) theory to NMFA, dramatically reducing computational difficulty, and introduced block decoupling, a new method that systematically and comprehensively divides EMU systems of equations into smaller subproblems to further reduce computational difficulty.