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General Information
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 Feng_2012.pdf
Project name not specified


Experiment Description
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
Temperature (°C) 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 Marba ...

--------------------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.

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Data file
KIMODATAID77_v0.xlsx
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 KIMODATAID77_metabolites_timeseries.csv Preview
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Plain text: metadataDataEntryID77.txt
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Related Data: AccessID 66


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: 2013-07-03 16:40:55 UTC

Updated: 2020-04-24 16:10:34 UTC

Version: 0

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

Views: 300

Downloads: 138



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 Kinetic model of Shewanella oneidensis MR-1 Metabolism ordinary differential equations Model building and Model validation {"id":30,"organism_id":77,"comments":"","sbml_file_name":"Feng_2012.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"22319437","dilution_rate":"—","name_of_model":"Kinetic model of Shewanella oneidensis MR-1 ","manuscript_title":"Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.","authors":"Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang","journal":"PLOS Computational Biology","affiliation":"","project_name":"","biomodels_id":"","keywords":"DFBA, kinetic model","software":"http://www.matlab.com (MATLAB)","control":"2014-04-11T17:54:44.161Z","main_organism":"Shewanella oneidensis","year":2012,"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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