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General Information info

Manuscript title Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.
PubMed ID 21092096
Journal Microbial Cell Factories
Year 2010
Authors Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu
Affiliations Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan
Keywords Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution
Full text article Downloadarticle Kadir_2010.pdf
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain K-12 BW25113 and ppc, pyk mutants
Data type time-series data of metabolites
Data units g/L
Execution date not specified

Experimental Details info

Temperature (0C) 37.0
pH 7.0
Carbon source glucose,
Culture mode batch
Process condition aerobic
Dilution rate (h-1)
Working volume (L) 1.0
Biomass concentration (g/L) not specified
Medium composition

M9 sythetic medium: 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 40 mM (NH4)zSO4 and 4 g/l of glucose. Components filter-sterilized separatory and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml vitamin B1 (1 mgl stock), 1 ml 0.1 mM CaCl2, and 10 ml trace element solution containing (per liter): 0.55g CaCl2 1g FeCl3, 0.1 mg/l MnCl2.4H2O, 0.17 g ZnCl2, 0.043 g CuCl2.2H2O, 0.06 g CoCl2.2H2O, and 0.06 g Na2MoO4.2H2O).

General protocol information Sampling method: 5ml from the culture broth

Quenching procedure: 15ml of 60% (v/v) aqueous methanol containing 70mM HEPES at -80ºC

Extraction technique: enzymatic, perchloric acid

Sample analyzing method: enzymatic

Methods description - Notes

Cells were separated from the culture by centrifugation at 10,000 ×g for 15 min at 0°C. To extract intracellular metabolites from the cell pellet, 500 ml of 50% methanol was added, and the cells were re-suspended by vortexing the mixture. Then 2 ml of 35% of perchloric acid was added, which was pre-cooled on ice, and vortexed again for 10 s. After one freeze-thaw cycle, proteins and cell fragments were removed by centrifugation at 12,000 ×g for 30 min at 0°C. Clear suparnatant was neutralized by adding collected supernatant, and then 895 μm of 5 M K2KO3 was added. Precipitated perchlorates were removed by another centrifugation step (12,000 ×g at 0°C for 10 min), the clear supernatant was collected, and they were stored as 200 μm aliquots at -20°C for analysis.

Data file
Downloadmetabolites KIMODATAID38_v1.xlsx
Alternative format(s)
KIMODATAID38_wt_timeseries.csv
KIMODATAID38_pyk_timeseries.csv
KIMODATAID38_ppc_timseries.csv
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Organism


Related Data: AccessID 52 | AccessID 104


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 2013-04-24 14:37:13 UTC

Updated 2018-07-21 11:34:43 UTC

Version 1

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




Associated Models


Here we can find relevant models associated with Data EntryID 38:

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
38
Authors: Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata

Original paper: Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli

E. coli Central Carbon Metabolism Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680\u20114 Kawazu, Iizuka, Fukuoka 820\u20118502, Japan","article_file_name":null,"authors":"Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata","biomodels_id":"","category":"Metabolism","combine_archive_content_type":"application/octet-stream","combine_archive_file_name":"COMBINE_KIMOMODELID38.omex","combine_archive_file_size":6603649,"combine_archive_updated_at":"2018-07-23T21:38:00Z","comments":"MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ","control":"2018-07-20T16:47:46Z","dilution_rate":"0.2, 0.4, 0.5 and 0.7","id":38,"journal":"Microbial Cell Factories","keywords":"Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme","main_organism":"Escherichia coli","manuscript_title":"Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli","model_name":"E. coli Central Carbon Metabolism","model_type":"ordinary differential equations","organism_id":null,"project_name":"","pubmed_id":"27329289","review_journal_id":null,"sbml_file_name":"Jahan_2016.pdf","software":"MATLAB2007 or higher","used_for":"---\n- Model building\n- Model validation\n","year":2016} Administrator KiMoSys
45
Authors: Hiroyuki Kurata and Yurie Sugimoto

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

Batch kinetic model of Escherichia coli Metabolism ordinary differential equations Model building 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":null,"dilution_rate":"\u2014","id":45,"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":"Batch 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","year":2018} Administrator KiMoSys



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