Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism.
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Analysis of metabolic networks using linear optimization theory allows one to quantify and understand the limitations imposed on the cell by its metabolic stoichiometry, and to understand how the flux through each pathway influences the overall behavior of metabolism.About:
This article is published in Journal of Theoretical Biology.The article was published on 1992-02-21 and is currently open access. It has received 255 citations till now.read more
Citations
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Journal ArticleDOI
A protocol for generating a high-quality genome-scale metabolic reconstruction.
TL;DR: This protocol provides a helpful manual for all stages of the reconstruction process and presents a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction.
Journal ArticleDOI
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
TL;DR: A predictive algorithm is formulated in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures.
Journal ArticleDOI
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
TL;DR: The flux balance methodology allows the quantitative interpretation of metabolic physiology, gives an interpretation of experimental data, provides a guide to metabolic engineering, enables optimal medium formulation, and provides a method for bioprocess optimization.
Journal ArticleDOI
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.
Pedro Mendes,Douglas B. Kell +1 more
TL;DR: A generic approach to combine numerical optimization methods with biochemical kinetic simulations is described, suitable for use in the rational design of improved metabolic pathways with industrial significance and for solving the inverse problem of metabolic pathways.
Journal ArticleDOI
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.
References
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Book ChapterDOI
mRNA structure and function.
TL;DR: The chapter attempts to discover and study the nuclear proteins responsible for genetic regulation and concludes that the study of eukaryotic mRNA is truly coming of age.
Journal ArticleDOI
Pyruvate Metabolism in Mitochondria from Rat Liver
Jörg W. Stucki,Paul Walter +1 more
TL;DR: Rat liver mitochondria were incubated in the presence of [2-14C]pyruvate, HCO3−, ATP and phosphate and it was concluded that the pools of malate and oxaloacetate within the matrix cannot be fully equilibrated and it is proposed that the transport of malates out of the mitochondria restricts the passage of this metabolite through the citric acid cycle.
Book ChapterDOI
On the Analysis of Metabolic Networks
Jacob J. Blum,Robert B. Stein +1 more
TL;DR: When flux values from network analysis are interpreted in the light of information on the in vitro behavior of the enzymes involved and on the concentrations of ligands in the relevant subcellular compartments, one may expect to acquire a deeper understanding of the regulation of metabolism in the living cell.
Journal ArticleDOI
Turnover rates and intracellular pool size distribution of citrate cycle intermediates in normal, diabetic and fat-fed rats estimated by computer analysis from specific activity decay data of 14C-labeled citrate cycle acids.
TL;DR: A state of non-equilibration of isotope exists for the acetyl-CoA and acetylcarnitine, citrate, malate, aspartate, glutamate and α-ketoglutarate pools distributed between cytoplasmic and mitochondrial compartments.
Journal ArticleDOI
Malate-citrate cycle during glycolysis and glutaminolysis in Ehrlich ascites tumor cells
Josefa Perez-Rodriguez,Francisca Sánchez-Jiménez,F. Javier Márquez,Miguel Ángel Medina,Ana R. Quesada,Ignacio Núñez de Castro +5 more
TL;DR: The results suggest that in this strain, the malate-citrate shuttle is not an effective pathway for transferring glycolytic reducing equivalents from cytosol to mitochondria, and the glucose metabolism depressed the oxidative processes in Ehrlich ascites tumor mitochondria not only alone, but also in the presence of glutamine.