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General Information
Manuscript title Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.
PubMed ID 21092096
Journal Microbial Cell Factories
Year 2010
Authors Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu
Affiliations Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
Keywords Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution
Full text article Kadir_2010.pdf
Project name not specified


Experiment Description
Organism Escherichia coli
Strain K-12 BW25113 and ppc, pck, pyk mutants
Data type flux measurements
Data units (mmol/g-dry cell weight/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) 0.2
Working volume (L) 1.0
Biomass concentration (g/L) not specified
Medium composition

M9 sythetic medium: 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 40 mM (NH4)zSO4 and 4 g/l of glucose. Components filter-sterilized separatory and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml vitamin B1 (1 mgl stock), 1 ml 0.1 mM CaCl2, and 10 ml trace element solution containing (per liter): 0.55g CaCl2 1g FeCl3, 0.1 mg/l MnCl2.4H2O, 0.17 g ZnCl2, 0.043 g CuCl2.2H2O, 0.06 g CoCl2.2H2O, and 0.06 g Na2MoO4.2H2O).

General protocol information Flux analysis method: 13C constrained MFA

Platform: GC-MS

Methods description - Notes

13C-labeling experiments and sample preparation: The biomass sample was kept on ice for 2-3 minutes, and the sample was centrifuged at 6,000 rpm at 2°C for 15 minutes [1]. The cell pellets were washed three times with 20 mM Tris-HCl at pH 7.6 and suspended in 10 ml of 6 M HC ...

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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: 2018-07-21 11:27:22 UTC

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

Version: 1

Status: (reviewed) 2018-07-21 11:38:32 UTC

Views: 5

Downloads: 0




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EntryID
Model name Category Model Type Data used for Access Json
41 Continuous kinetic model of Escherichia coli Metabolism ordinary differential equations Model building and Model validation {"id":41,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"Continuous kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":"2018-07-24T15:46:04.831Z","main_organism":"Escherichia coli","year":2018,"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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