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General Information
Manuscript title Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method.
PubMed ID 12568740
Journal Journal of Biotechnology
Year 2003
Authors Jiao Zhao, Kazuyuki Shimizu
Affiliations Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan
Keywords Mass isotopomer analysis, Metabolic flux analysis, Carbon source, Genetic algorithm, Levenberg-Marquardt algorithm, Escherichia coli K12
Full text article no file uploaded
Project name not specified


Experiment Description
Organism Escherichia coli
Strain K-12
Data type flux measurements
Data units (mmol/g.h)
Execution date not specified


Experimental Details
Temperature (°C) 37
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h⁻¹) 0.11 and 0.22
Working volume (L) 0.9
Biomass concentration (g/L) not specified
Medium composition

Minimal medium: 2 g of sodium acetate or 4 g of glucose per liter, 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, and 30 mM (NH4)2SO4. The following components were sterilized separately and then added (per liter of final medium): 1 ml of 1 M MgSO4, 1 ml of 0.1 mM CaCl2, 1 ml of 1 mg of vitamin B1 per liter (filter sterilized), and 10 ml of trace element solution containing (per liter) 0.55 g of CaCl2, 1 g of FeCl3, 0.1 g of MnCl2·4H2O, 0.17 g of ZnCl2, 0.043 g of CuCl2·2H2O, 0.06 g of CoCl2·6H2O, and 0.06 g of Na2MoO4·2H2O.

General protocol information Flux analysis method: 13C constrained MFA

Platform: GC-MS

Methods description - Notes

Labeling experiments were initiated after the culture reached a steady state, which was inferred from the stable oxygen and carbon dioxide concentrations in the fermentor off-gas and stable optical density in the effluent medium for at least twice as long as the residence ti ...

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Submission and curation

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: 2018-07-23 10:04:17 UTC

Updated: 2020-04-24 16:10:36 UTC

Version: 1

Status: (reviewed) 2018-07-23 10:04:51 UTC

Views: 4

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EntryID
Model name Category Model Type Data used for Access Json
43 Singh2006_TCA_Ecoli_acetate Metabolism ordinary differential equations Model validation {"id":43,"organism_id":null,"comments":"Original model source: in BioModels database.","sbml_file_name":"Singh_2006.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"16887020","dilution_rate":"","name_of_model":"Singh2006_TCA_Ecoli_acetate","manuscript_title":"Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets","authors":"Vivek Kumar Singh and Indira Ghosh","journal":"Theoretical Biology and Medical Modelling","affiliation":"Bioinformatics Centre, University of Pune, India","project_name":"","biomodels_id":"BIOMD0000000221","keywords":"Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux","software":"Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)","control":null,"main_organism":"Escherichia coli","year":2006,"combine_archive_file_name":"COMBINE_KIMOMODELID43.omex","combine_archive_content_type":"application/octet-stream","combine_archive_file_size":253672,"combine_archive_updated_at":"2018-07-27T10:28:17.660Z","review_journal_id":null,"doi":null} Administrator KiMoSys
44 Singh2006_TCA_Ecoli_glucose Metabolism ordinary differential equations Model validation {"id":44,"organism_id":null,"comments":"Original model source: in BioModels database.","sbml_file_name":"Singh_2006.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"16887020","dilution_rate":"","name_of_model":"Singh2006_TCA_Ecoli_glucose","manuscript_title":"Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets","authors":"Vivek Kumar Singh and Indira Ghosh","journal":"Theoretical Biology and Medical Modelling","affiliation":"Bioinformatics Centre, University of Pune, India","project_name":"","biomodels_id":"BIOMD0000000222","keywords":"Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux","software":"Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)","control":null,"main_organism":"Escherichia coli","year":2006,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys



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