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General Information info

Manuscript title Dynamic modeling of the central carbon metabolism of Escherichia coli.
PubMed ID 17590932
Journal Biotechnology and Bioengineering
Year 2002
Authors Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss
Affiliations Institute of Biochemical Engineering, University of Stuttgart
Keywords dynamic model, Escherichia coli, intracellular metabolites, transient conditions, control and stability analysis
Full text article Downloadarticle Chassagnole_2002.pdf
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain K-12 W3110
Data type time-series data of metabolites
Data units mM
Execution date not specified

Experimental Details info

Temperature (0C) 35.0
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h-1) 0.1
Working volume (L) 1.5
Biomass concentration (g/L) 8.7
Medium composition

Synthetic mineral medium: 4.0 g/L Na2SO4, 5.36 g/L (NH4)2SO4, 1.0 g/L NHCl, 7.3 g/L K2HPO4, 1.8 g/L NaH2PO4 H2O, 120 g/L (NH4)2-H-citrate, 4.0 mL/L MgSO4 (1M), 6.0 ml/L trace element solution, 0.02 g/L thiamine, 20.0 g/L glucose.

General protocol information Sampling method: manually every 3 seconds with vacuum-sealed, precooled glass tubes containing the quenching solution

Quenching procedure: liquid nitrogen (-196 ºC) and perchloric acid

Extraction technique: perchloric acid

Sample analyzing method: enzymatic, HPLC/HIC

Methods description - Notes

The concentrations of the extracellular metabolites (glucose, acetate) and most of the intracellular metabolites were determined as describe previously [1]. Improved analysis of the adenine nucleotides was summarized by Mailinger et al. [2] and Meyer et al. [3]. The metabolites and cometabolites from the pentose-phosphate pathway (6PG, NADP+, and NADPH) were measured according to Vaseghi et al. [4].
See also Figure 1 of the original model.

-------------References------------
[1] Theobals U., Mailinger W., Baltes M., Rizzi M., Reuss M., 1997. In vivo analysis of metabolic dynamics in Saccharomyces cerevisae: I. Experimental observations. Biotechnol Bioeng. 55: 305-316. http://doi.org/crtbrx
[2] Mailinger W., Baumeister A., Reuss M., Rizzi M., 1998. Rapid and highly automated determination of adenine and pyridine nucleotides in extracts of Saccharomyces cerevisae using a micro robotic sample preparation-HPLC system. J. Biotechnol. 63: 155-166. http://doi.org/bvbfcn
[3] Meyer S., Noisommit-Rizzi N., Reuss M., Neubauer P., 1999. Optimized analysis of intracellular adenosine and guanosine phosphate in Escherichia coli. Anal Biochem. 271: 43-52. http://doi.org/c7nb99
[4] Vaseghi S., Baumeister A., Rizzi M., Reuss M., 1999. In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisae. Metab Eng. 1: 128-140. http://doi.org/bvvrdg

Data file
Downloadmetabolites KIMODATAID30_v1.xlsx
Alternative format(s)
KIMODATAID30_metab_timeseries.csv
KIMODATAID30_cometab_timeseries.csv
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Organism


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Submission and curation info

Entered by Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data

Created 2013-03-06 18:00:37 UTC

Updated 2015-07-27 10:28:11 UTC

Version 1

Status (reviewed) 2013-12-06 17:17:38 UTC




Associated Models


Here we can find relevant models associated with Data EntryID 30:

Model
EntryID
Model name Category Model Type Data used for Access Json
13
Authors: Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss

Original paper: Dynamic modeling of the central carbon metabolism of Escherichia coli.

Chassagnole2002_Carbon_Metabolism Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"Institute of Biochemical Engineering, University of Stuttgart ","article_file_name":null,"authors":"Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss","biomodels_id":"BIOMD0000000051","category":"Metabolism","combine_archive_content_type":"application/omex+xml","combine_archive_file_name":"COMBINE_KIMOMODELID13.omex","combine_archive_file_size":249522,"combine_archive_updated_at":"2014-06-30T17:38:01Z","comments":"Original model source: in BioModels database.","control":"2014-03-19T14:31:21Z","dilution_rate":"0.1","id":13,"journal":"Biotechnology and Bioengineering","keywords":"dynamic model, Escherichia coli, parameter fitting, flux control coefficients","main_organism":"Escherichia coli","manuscript_title":"Dynamic modeling of the central carbon metabolism of Escherichia coli.","model_name":"Chassagnole2002_Carbon_Metabolism","model_type":"ordinary differential equations","organism_id":30,"project_name":"","pubmed_id":"17590932","review_journal_id":null,"sbml_file_name":"Chassagnole_2002.pdf","software":"","used_for":"---\n- Model building\n- Model validation\n","year":2002} Administrator KiMoSys



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