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General Information
Manuscript title Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.
PubMed ID 17379776
Journal Science
Year 2007
Authors Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita
Affiliations Institute for Advanced Biosciences, Keio University
Keywords Escherichia coli, perturbations response, chemostat, single knockouts
Full text article no file uploaded
Project name not specified


Experiment Description
Organism Escherichia coli
Strain WT K-12 BW25113 and mutants
Data type flux measurements
Data units (mmol/gDW/h)
Execution date not specified


Experimental Details
Temperature (°C) 37.0
pH 7.0
Carbon source glucose
Culture mode chemostat
Process condition aerobic
Dilution rate (h⁻¹) 0.1, 0.2, 0.4, 0.5 and 0.7
Working volume (L) 1.0
Biomass concentration (g/L) See Supplementary files of the original article (Tabel S3).
Medium composition

Synthetic medium: 48mM Na2HPO4, 22mM KH2PO4, 10mM NaCl, 45mM (NH4)2SO4, 4g/L glucose, 1mM MgSO4, 1mg/L thiamin.HCL, 5.6 mg/L CaCl2, 8 mg/L FeCl3, 1 mg/L MnCl2.4H2O, 1.7 mg/L ZnCl2, 0.43 mg/L CuCl2.2H2O, 0.6 mg/L CoCl2.2H2O and 0.6 mg/L Na2MoO4.2H2O

General protocol information Flux analysis method: 13C constrained MFA

Platform: GC-MS

Methods description - Notes

13C-labeling experiment - for metabolic flux analysis, 13C-labeling experiments were initiated after taking samples for transcriptome, proteome and metabolome analysis. For experiments with gene disruptants, the feed medium containing 4 g/l of natural glucose was replaced by ...

--------------------References---------------
[1] J. Zhao, K. Shimizu, J. Biotechnol. 101, 101 (2003). http://doi.org/cdjhrn
[2] M. Li, P. Y. Ho, S. Yao, K. Shimizu, J. Biotechnol. 122, 254 (2006). http://doi.org/cr7qpd

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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: 2013-04-22 11:42:01 UTC

Updated: 2020-04-24 16:10:28 UTC

Version: 3

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

Views: 538

Downloads: 71




Associated Models

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EntryID
Model name Category Model Type Data used for Access Json
36 Kinetic model of Escherichia coli core metabolism Metabolism ordinary differential equations Model building and Model validation {"id":36,"organism_id":null,"comments":"","sbml_file_name":"Khodayari_2014.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"24928774","dilution_rate":"","name_of_model":"Kinetic model of Escherichia coli core metabolism","manuscript_title":"A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.","authors":"Ali Khodayari, Ali R. Zomorrodi, James C.Liao, Costas D. Maranas","journal":"Metabolic Engineering","affiliation":"Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA","project_name":"","biomodels_id":"","keywords":"ensemble modeling, kinetic modeling, metabolic network","software":"http://www.matlab.com (MATLAB)","control":null,"main_organism":"Escherichia coli","year":2014,"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
38 E. coli Central Carbon Metabolism Metabolism ordinary differential equations Model building and Model validation {"id":38,"organism_id":null,"comments":"MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ","sbml_file_name":"Jahan_2016.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"27329289","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"E. coli Central Carbon Metabolism","manuscript_title":"Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli","authors":"Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan","project_name":"","biomodels_id":"","keywords":"Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme","software":"MATLAB2007 or higher","control":"2018-07-20T16:47:46.311Z","main_organism":"Escherichia coli","year":2016,"combine_archive_file_name":"COMBINE_KIMOMODELID38.omex","combine_archive_content_type":"application/octet-stream","combine_archive_file_size":6603649,"combine_archive_updated_at":"2018-07-23T21:38:00.461Z","review_journal_id":null,"doi":null} Administrator KiMoSys
41 Continuous kinetic model of Escherichia coli Metabolism ordinary differential equations Model building and Model validation {"id":41,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"Continuous kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":"2018-07-24T15:46:04.831Z","main_organism":"Escherichia coli","year":2018,"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
42 kinetic model of the central carbon metabolism of E. coli Metabolism ordinary differential equations Model building {"id":42,"organism_id":null,"comments":"For the analysis and evaluation of the kinetic model, the solver ode15s was used.","sbml_file_name":"Mannan_2015.PDF","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"26469081","dilution_rate":"0.2","name_of_model":"kinetic model of the central carbon metabolism of E. coli ","manuscript_title":"Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.","authors":"Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco","journal":"Plos One","affiliation":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ","project_name":"","biomodels_id":"","keywords":"E. coli, Bistability, Central Metabolism","software":"MATLAB® R2007b (version 7.5.0)","control":null,"main_organism":"Escherichia coli","year":2015,"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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