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General Information info

Manuscript title Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis.
PubMed ID 22319437
Journal PLOS Computational Biology
Year 2012
Authors Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang
Affiliations Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, Missouri, United States of America
Keywords Shewanella oneidensis, dynamic metabolism, extracellular
Full text article Downloadarticle Feng_2012.pdf
Project name not specified

Experiment Description info

Organism Shewanella oneidensis
Strain MR-1 (ATCC 70050)
Data type time-series data of metabolites
Data units (g/L) and (mM)
Execution date not specified

Experimental Details info

Temperature (0C) 30.0
pH not specified
Carbon source lactate,
Culture mode batch
Process condition aerobic
Dilution rate (h-1)
Working volume (L) 0.1
Biomass concentration (g/L) ≈ 0.3 - 0.5
Medium composition

defined medium

General protocol information Sampling method: manually at different time

Quenching procedure:

Extraction technique: not used

Sample analyzing method: enzymatic

Methods description - Notes

The growth curve was monitored by dried biomass weight. The concentrations of lactate and acetate in the medium were measured using enzyme kits (r-Biopharm, Darmstadt, Germany). The concentration of pyruvate in the medium was measured with the enzyme assay developed by Marbach and Weli [1].

--------------------References-------------------
[1] Marbach EP, Weli MH (1967). Rapid enzymatic measurement of blood lactate and pyruvate. Use and significance of metaphosphoric acid as a common precipitant. Clin Chem 13: 314–325.

Data file
Downloadmetabolites KIMODATAID77_v0.xlsx
Alternative format(s)
KIMODATAID77_metabolites_timeseries.csv
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Organism


Related Data: AccessID 66


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 2013-07-03 16:40:55 UTC

Updated 2014-05-09 15:22:14 UTC

Version 0

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




Associated Models


Here we can find relevant models associated with Data EntryID 77:

Model
EntryID
Model name Category Model Type Data used for Access Json
30
Authors: Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang

Original paper: Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.

Kinetic model of Shewanella oneidensis MR-1 Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"","article_file_name":null,"authors":"Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang","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":"2014-04-11T17:54:44Z","dilution_rate":"\u2014","id":30,"journal":"PLOS Computational Biology","keywords":"DFBA, kinetic model","main_organism":"Shewanella oneidensis","manuscript_title":"Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.","model_name":"Kinetic model of Shewanella oneidensis MR-1 ","model_type":"ordinary differential equations","organism_id":77,"project_name":"","pubmed_id":"22319437","review_journal_id":null,"sbml_file_name":"Feng_2012.pdf","software":"http://www.matlab.com (MATLAB)","used_for":"---\n- Model building\n- Model validation\n","year":2012} Administrator KiMoSys



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