Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism.
Reads0
Chats0
TLDR
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
More filters
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
More filters
Journal ArticleDOI
Transient responses of hybridoma metabolism to changes in the oxygen supply rate in continuous culture
TL;DR: The increase in cell concentration following the return to 10% DO was preceded by increased biosynthetic activity, as evidenced by transiently reduced yields of lactate from glucose, and alanine and ammonia from glutamine.
Journal ArticleDOI
Control of lipid metabolism in cultured cells.
TL;DR: Intracellular cholesterol content is regulated by rates of uptake, hydrolysis and excretion as well as by biosynthesis.
Journal ArticleDOI
Quantitative analysis of intermediary metabolism in hepatocytes incubated in the presence and absence of glucagon with a substrate mixture containing glucose, ribose, fructose, alanine and acetate.
TL;DR: Hepatocytes were isolated from the livers of fed rats and incubated, in the presence and absence of 100 nM-glucagon, with a substrate mixture containing glucose, alanine, glutamate, lipid glycerol and fatty acids, and a structural metabolic model incorporating all reactions of the glycolytic, gluconeogenic, and pentose phosphate pathways was analysed.
Journal ArticleDOI
The upper and lower limits of the mechanistic stoichiometry of mitochondrial oxidative phosphorylation. Stoichiometry of oxidative phosphorylation.
TL;DR: Measurements in rat liver mitochondria when the rate of phosphorylation was systematically varied by three specific means suggest that the mechanistic P/O ratio is 1.75 for succinate oxidation and 2-hydroxybutyrate oxidation, which must be equal to or greater than the Mechanistic stoichiometry.
Journal ArticleDOI
Quantitative analysis of flux along the gluconeogenic, glycolytic and pentose phosphate pathways under reducing conditions in hepatocytes isolated from fed rats.
J M Crawford,J J Blum +1 more
TL;DR: An improved method of computer analysis of the equations describing the flow of label through each carbon atom of each metabolite under steady-state conditions was used to compute values for the 34 independent flux parameters in this model and a good fit was obtained, thereby permitting good estimates of most of the fluxes in the pathways under consideration.