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General Information info

Manuscript title Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.
PubMed ID 15158257
Journal FEMS Microbiology Letters
Year 2004
Authors Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu
Affiliations Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
Keywords ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis
Full text article Downloadarticle Peng_2004.pdf
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain BW25113 and ppc mutant
Data type flux measurements
Data units (mmol/g-dry cell weight/h)
Execution date not specified

Experimental Details info

Temperature (0C) 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) see worksheet.
Medium composition

M9 minimal medium as described previously [3].

General protocol information Flux analysis method: 13C constrained MFA

Platform: NMR, GC-MS

Methods description - Notes

The fluxes of Pgi, Pyk, CS were chosen as the net free fluxes, and 11 exchange fluxes (Pgi, Eno, Rpi, Rpe, Tkt1, Tkt2, Tal, ICDH, Fum, Mdh, Ppc/Pck) were considered. In both cases, the free fluxes were obtained by minimizing the error criterion originating from the weighted residuals of the metabolite balances as well as the weighted residuals between the estimated and the measured GC-MS and 2D NMR signals [1]. The modified minimization algorithm [2] was used to compute the intracellular fluxes. A set of intracellular fluxes was then determined as the best fit to the experimentally determined data using a parameter fitting approach.
--------------------References---------------
[1] Dauner M. Bailey, J. Sauer U. (2001). Biotechnol. Bioeng. 76, 132–143. http://doi.org/ffkpm2
[2] Araúzo-Bravo M.J., Shimizu K. (2003). J. Biotechnol. 105, 117–133. http://doi.org/cpnw8k [3] Zhao J., Shimizu K. (2002). J. Biotechnol. 101, 101–117. http://doi.org/cdjhrn

Data file
Downloadfluxes KIMODATAID105_v2.xlsx
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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 2018-07-21 14:36:12 UTC

Updated 2018-07-26 10:37:05 UTC

Version 2

Status (reviewed) 2018-07-21 14:43:53 UTC




Associated Models


Here we can find relevant models associated with Data EntryID 105:

Model
EntryID
Model name Category Model Type Data used for Access Json
16
Authors: Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu

Original paper: Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.

glycolysis Escherichia coli model Metabolism ordinary differential equations Model validation Visto4 {"affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","article_file_name":null,"authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","biomodels_id":"","category":"Metabolism","combine_archive_content_type":null,"combine_archive_file_name":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"comments":"","control":"2018-07-21T20:34:09Z","dilution_rate":"\u2014","id":16,"journal":"Microbial Cell Factories","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","main_organism":"Escherichia coli","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","model_name":"glycolysis Escherichia coli model","model_type":"ordinary differential equations","organism_id":38,"project_name":"","pubmed_id":"21092096","review_journal_id":null,"sbml_file_name":"Kadir_2010.pdf","software":"http://www.matlab.com (MATLAB)","used_for":"---\n- Model validation\n","year":2010} Administrator KiMoSys
41
Authors: Hiroyuki Kurata and Yurie Sugimoto

Original paper: Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures

Continuous kinetic model of Escherichia coli Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","article_file_name":null,"authors":"Hiroyuki Kurata and Yurie Sugimoto","biomodels_id":"","category":"Metabolism","combine_archive_content_type":null,"combine_archive_file_name":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","control":"2018-07-24T15:46:04Z","dilution_rate":"0.2, 0.4, 0.5 and 0.7","id":41,"journal":"Journal of Bioscience and Bioengineering","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","main_organism":"Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","model_name":"Continuous kinetic model of Escherichia coli","model_type":"ordinary differential equations","organism_id":null,"project_name":"","pubmed_id":"29054464","review_journal_id":null,"sbml_file_name":"Kurata_2018.pdf","software":"MATLAB (MathWorks)","used_for":"---\n- Model building\n- Model validation\n","year":2018} Administrator KiMoSys



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