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Optimal Selection Of Metabolic Fluxes For In Vivo Measurement. I. Development Of Mathematical Methods, Joanne M. (Savinell) Belovich, Bernhard O. Palsson
Optimal Selection Of Metabolic Fluxes For In Vivo Measurement. I. Development Of Mathematical Methods, Joanne M. (Savinell) Belovich, Bernhard O. Palsson
Chemical & Biomedical Engineering Faculty Publications
The measurement of uptake and secretion rates is often not sufficient to allow the calculation of all internal metabolic fluxes. Measurements of internal fluxes are needed and these additional measurements are used in conjunction with mass-balance equations to calculate the complete metabolic flux map. A method is presented that identifies the fluxes that should be selected for experimental measurement, and the fluxes that can be computed using the mass-balance equations. The criterion for selecting internal metabolic fluxes for measurement is that the values of the computed fluxes should have low sensitivity to experimental error in the measured fluxes. A condition …
Optimal Selection Of Metabolic Fluxes For In Vivo Measurement. Ii. Application To Escherichia Coli And Hybridoma Cell Metabolism, Joanne M. (Savinell) Belovich, Berhard O. Palsson
Optimal Selection Of Metabolic Fluxes For In Vivo Measurement. Ii. Application To Escherichia Coli And Hybridoma Cell Metabolism, Joanne M. (Savinell) Belovich, Berhard O. Palsson
Chemical & Biomedical Engineering Faculty Publications
A method of analysis was presented in part I of this series for determining the fluxes in a biochemical network that are the optimal choices for experimental measurement. This algorithm is applied to two important biological models: Escherichia coli and a hybridoma cell line (167.4G5.3). Our results show that potentially poor choices for in vivo measurement of metabolic fluxes exist for both model systems. For the subset of reactions in E. coli that was studied, the condition number of the augmented stoichiometric matrix reveals that a 60-fold amplification of experimental error during computations is possible. The biochemical network of the …
Network Analysis Of Intermediary Metabolism Using Linear Optimization. I. Development Of Mathematical Formalism, Joanne M. (Savinell) Belovich, Bernhard O. Palsson
Network Analysis Of Intermediary Metabolism Using Linear Optimization. I. Development Of Mathematical Formalism, Joanne M. (Savinell) Belovich, Bernhard O. Palsson
Chemical & Biomedical Engineering Faculty Publications
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. A stoichiometric matrix accounting for the major pathways involved in energy and mass transformations in the cell was used in our analysis. The auxiliary parameters of linear optimization, the so-called shadow prices, identify the intermediates and cofactors that cause the growth to be limited on each nutrient. This formalism was used to examine how well the cell balances its needs for …