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General Information
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 Haus_2011.pdf
Project name not specified


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


Experimental Details
Temperature (°C) 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 ...

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Data file
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 KIMODATAID42_third_forward_timeseries.csv Preview
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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: 2013-05-03 10:45:33 UTC

Updated: 2020-04-24 16:10:31 UTC

Version: 0

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

Views: 415

Downloads: 229



Associated Models

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Model
EntryID		 Model name Category Model Type Data used for Access Json
19 first forward shift Metabolism ordinary differential equations Model building {"id":19,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"first forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":" http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:25:43.341Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID19.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401646,"combine_archive_updated_at":"2014-06-30T20:38:42.907Z","review_journal_id":null,"doi":null} Administrator KiMoSys
20 second forward shift Metabolism ordinary differential equations Model building {"id":20,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"second forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":"http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:26:19.201Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID20.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401633,"combine_archive_updated_at":"2014-06-30T20:39:10.028Z","review_journal_id":null,"doi":null} Administrator KiMoSys
21 third forward shift Metabolism ordinary differential equations Model building {"id":21,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"third forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":"http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:24:43.452Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID21.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401643,"combine_archive_updated_at":"2014-06-30T20:39:32.642Z","review_journal_id":null,"doi":null} Administrator KiMoSys
22 reverse forward shift Metabolism ordinary differential equations Model building {"id":22,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"reverse forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":"http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:27:26.964Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID22.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401628,"combine_archive_updated_at":"2014-06-30T20:39:48.510Z","review_journal_id":null,"doi":null} Administrator KiMoSys



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