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General Information info

Manuscript title A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.
PubMed ID 21247470
Journal BMC Systems Biology
Year 2011
Authors Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer
Affiliations University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics
Keywords Clostridium acetobutylicum, continuous culture, effect of pH, solvent production
Full text article Downloadarticle Haus_2011.pdf
Project name not specified

Experiment Description info

Organism Clostridium acetobutylicum
Strain ATCC824
Data type time-series data of metabolites
Data units mM
Execution date not specified

Experimental Details info

Temperature (0C) 37.0
pH 5.7 and 4.5
Carbon source glucose,
Culture mode chemostat
Process condition anaerobic
Dilution rate (h-1) 0.1
Working volume (L) 1.0
Biomass concentration (g/L) not specified
Medium composition

4% (wt/vol) glucose in the supplying medium

General protocol information Sampling method: 2 ml of C. acetobutylicum cell suspensions were collected and quickly sedimented at 16,000 g for 30s at 4°C in a benchtop centrifuge.

Quenching procedure:

Extraction technique: not used

Sample analyzing method: GC-MS

Methods description - Notes

Separation took place in a Chromosorb 101 column (length, 2 m; 80 to 100 mesh) at 155 to 197°C (rate of temperature increase, 9°C/min) with N2 as the carrier gas (flow rate, 30 ml/min). Injector temperature was 195°C, and the detector temperature was 230°C. Signal analysis was performed by using the program Maestro II.

Data file
Downloadmetabolites KIMODATAID42_v0.xlsx
Alternative format(s)
KIMODATAID42_third_forward_timeseries.csv
KIMODATAID42_second_forward_timeseries.csv
KIMODATAID42_reverse_timeseries.csv
KIMODATAID42_first_forward_timeseries.csv
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Organism



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 2013-05-03 10:45:33 UTC

Updated 2014-05-02 22:11:47 UTC

Version 0

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




Associated Models


Here we can find relevant models associated with Data EntryID 42:

Model
EntryID
Model name Category Model Type Data used for Access Json
19
Authors: Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer

Original paper: A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.

first forward shift Metabolism ordinary differential equations Model building Visto4 {"affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics","article_file_name":null,"authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-J\u00f6rg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","biomodels_id":"","category":"Metabolism","combine_archive_content_type":"application/omex+xml","combine_archive_file_name":"COMBINE_KIMOMODELID19.omex","combine_archive_file_size":401646,"combine_archive_updated_at":"2014-06-30T20:38:42Z","comments":"","control":"2014-04-11T17:25:43Z","dilution_rate":"0.1","id":19,"journal":"BMC Systems Biology","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","main_organism":"Clostridium acetobutylicum","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","model_name":"first forward shift","model_type":"ordinary differential equations","organism_id":42,"project_name":"","pubmed_id":"21247470","review_journal_id":null,"sbml_file_name":"Haus_2011.pdf","software":" http://www.sbtoolbox.org (SBToolbox)","used_for":"---\n- Model building\n","year":2011} Administrator KiMoSys
20
Authors: Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer

Original paper: A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.

second forward shift Metabolism ordinary differential equations Model building Visto4 {"affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics","article_file_name":null,"authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-J\u00f6rg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","biomodels_id":"","category":"Metabolism","combine_archive_content_type":"application/omex+xml","combine_archive_file_name":"COMBINE_KIMOMODELID20.omex","combine_archive_file_size":401633,"combine_archive_updated_at":"2014-06-30T20:39:10Z","comments":"","control":"2014-04-11T17:26:19Z","dilution_rate":"0.1","id":20,"journal":"BMC Systems Biology","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","main_organism":"Clostridium acetobutylicum","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","model_name":"second forward shift","model_type":"ordinary differential equations","organism_id":42,"project_name":"","pubmed_id":"21247470","review_journal_id":null,"sbml_file_name":"Haus_2011.pdf","software":"http://www.sbtoolbox.org (SBToolbox)","used_for":"---\n- Model building\n","year":2011} Administrator KiMoSys
21
Authors: Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer

Original paper: A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.

third forward shift Metabolism ordinary differential equations Model building Visto4 {"affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics","article_file_name":null,"authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-J\u00f6rg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","biomodels_id":"","category":"Metabolism","combine_archive_content_type":"application/omex+xml","combine_archive_file_name":"COMBINE_KIMOMODELID21.omex","combine_archive_file_size":401643,"combine_archive_updated_at":"2014-06-30T20:39:32Z","comments":"","control":"2014-04-11T17:24:43Z","dilution_rate":"0.1","id":21,"journal":"BMC Systems Biology","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","main_organism":"Clostridium acetobutylicum","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","model_name":"third forward shift","model_type":"ordinary differential equations","organism_id":42,"project_name":"","pubmed_id":"21247470","review_journal_id":null,"sbml_file_name":"Haus_2011.pdf","software":"http://www.sbtoolbox.org (SBToolbox)","used_for":"---\n- Model building\n","year":2011} Administrator KiMoSys
22
Authors: Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer

Original paper: A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.

reverse forward shift Metabolism ordinary differential equations Model building Visto4 {"affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics","article_file_name":null,"authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-J\u00f6rg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","biomodels_id":"","category":"Metabolism","combine_archive_content_type":"application/omex+xml","combine_archive_file_name":"COMBINE_KIMOMODELID22.omex","combine_archive_file_size":401628,"combine_archive_updated_at":"2014-06-30T20:39:48Z","comments":"","control":"2014-04-11T17:27:26Z","dilution_rate":"0.1","id":22,"journal":"BMC Systems Biology","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","main_organism":"Clostridium acetobutylicum","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","model_name":"reverse forward shift","model_type":"ordinary differential equations","organism_id":42,"project_name":"","pubmed_id":"21247470","review_journal_id":null,"sbml_file_name":"Haus_2011.pdf","software":"http://www.sbtoolbox.org (SBToolbox)","used_for":"---\n- Model building\n","year":2011} Administrator KiMoSys



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