A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties
TLDR
Using techniques based on linear programming, the construction and analysis of a genome-scale metabolic model of Arabidopsis (Arabidopsis thaliana) primarily derived from the annotations in the Aracyc database is described.Abstract:
We describe the construction and analysis of a genome-scale metabolic model of Arabidopsis (Arabidopsis thaliana) primarily derived from the annotations in the Aracyc database. We used techniques based on linear programming to demonstrate the following: (1) that the model is capable of producing biomass components (amino acids, nucleotides, lipid, starch, and cellulose) in the proportions observed experimentally in a heterotrophic suspension culture; (2) that approximately only 15% of the available reactions are needed for this purpose and that the size of this network is comparable to estimates of minimal network size for other organisms; (3) that reactions may be grouped according to the changes in flux resulting from a hypothetical stimulus (in this case demand for ATP) and that this allows the identification of potential metabolic modules; and (4) that total ATP demand for growth and maintenance can be inferred and that this is consistent with previous estimates in prokaryotes and yeast.read more
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Current status and applications of genome-scale metabolic models.
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Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
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AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
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References
More filters
Journal ArticleDOI
A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
TL;DR: This assay is very reproducible and rapid with the dye binding process virtually complete in approximately 2 min with good color stability for 1 hr with little or no interference from cations such as sodium or potassium nor from carbohydrates such as sucrose.
Journal ArticleDOI
The minimal gene complement of Mycoplasma genitalium
Claire M. Fraser,Jeannine D. Gocayne,Owen White,Mark Raymond Adams,Rebecca A. Clayton,Robert D. Fleischmann,Carol J. Bult,Anthony R. Kerlavage,Granger G. Sutton,Jenny M. Kelley,Janice L. Fritchman,Janice Weidman,Keith V. Small,Mina Sandusky,Joyce Fuhrmann,David Nguyen,Teresa Utterback,D. Saudek,Cheryl Phillips,Joseph M. Merrick,J F Tomb,Brian Dougherty,Kenneth F. Bott,Ping Chuan Hu,Thomas Lucier,Scott N. Peterson,Hamilton O. Smith,Clyde A. Hutchison,J. Craig Venter +28 more
TL;DR: Comparison of the Mycoplasma genitalium genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.
Journal ArticleDOI
Lipid extraction of tissues with a low-toxicity solvent
Atsushi Hara,Norman S. Radin +1 more
TL;DR: An improved method for extracting the lipids from tissues consists of the use of hexane:isopropanol, followed by a wash of the extract with aqueous sodium sulfate to remove nonlipid contaminants.
Book
The Regulation of Cellular Systems
TL;DR: The basic equations of metabolic control analysis are rewritten in terms of co-response coefficients and internal response coefficients to describe the interaction of optimization methods and the interrelation with evolution.
Journal ArticleDOI
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
TL;DR: It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined.