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General Information
Manuscript title Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.
PubMed ID 19690571
Journal Molecular Systems Biology
Year 2009
Authors Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz
Affiliations Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA
Keywords E. coli, ammonia assimilation, nitrogen upshift
Full text article Yuan_2009.pdf
Project name not specified


Experiment Description
Organism Escherichia coli
Strain NCM 3722 and mutants
Data type time-series data of metabolites
Data units mM
Execution date not specified


Experimental Details
Temperature (°C) 37.0
pH ≈ 7.0
Carbon source glucose,
Culture mode batch
Process condition anaerobic
Dilution rate (h⁻¹)
Working volume (L) not specified
Biomass concentration (g/L) not specified
Medium composition

Minimal salts media with 10 mM NH4Cl and 0.4 % glucose.

General protocol information Sampling method: filter cultures were prepared by passing 5 ml of exponentially growing liquid batch culture through membrane filters.

Quenching procedure: filters were submerged directly into -75 ºC methanol or -20 ºC 40:40:20 acetonitrile:methanol:water with 0.1 % formic acid.

Extraction technique: methanol

Sample analyzing method: LC-ESI-MS

Methods description - Notes

Detailed protocols for preparing filter cultures and extracting metabolites have been published [1,2].
Metabolite measurement - Cell extracts were analyzed by LC-electrospray ionization (ESI)-MS/MS on a Thermo Quantum triple quadrupole mass spectrometer operating in se ...

-----------References-------------
[1] Bennett B, Yuan J, Kimball E, Rabinowitz J (2008) Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat Protoc 3: 1299–1311. http://doi.org/dx4wxn
[2] Yuan J, Bennett B, Rabinowitz J (2008) Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nature Protoc 3: 1328–1340. http://doi.org/cprs6m
[3] Lu W, Bennett BD, Rabinowitz JD (2008). Analytical strategies for LC-MS-based targeted metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 871: 236–242. http://doi.org/bc7n2m
[4] Kraml CM, Zhou D, Byrne N, McConnell O (2005) Enhanced chromatographic resolution of amine enantiomers as carbobenzyloxy derivatives in high-performance liquid chromatography and supercritical fluid chromatography. J Chromatogr A 1100: 108–115. http://doi.org/fwnt9q

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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: 2013-06-12 13:00:46 UTC

Updated: 2020-04-24 16:10:33 UTC

Version: 0

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

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Downloads: 0




Associated Models

Here we can find relevant models associated with Data EntryID 63:

Model
EntryID
Model name Category Model Type Data used for Access Json
25 Nitrogen assimilation model Metabolism ordinary differential equations Model building and Model validation {"id":25,"organism_id":63,"comments":"","sbml_file_name":"Yuan_2009.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"19690571","dilution_rate":"—","name_of_model":"Nitrogen assimilation model","manuscript_title":"Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.","authors":"Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz","journal":"Molecular Systems Biology","affiliation":"Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA","project_name":"","biomodels_id":"","keywords":"E. coli, ammonia assimilation, nitrogen upshift, differential equations, sensitivity analysis","software":"written in C++","control":"2014-04-11T17:38:32.527Z","main_organism":"Escherichia coli","year":2009,"combine_archive_file_name":"COMBINE_KIMOMODELID25.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":645413,"combine_archive_updated_at":"2014-06-30T17:56:44.644Z","review_journal_id":null,"doi":null} Administrator KiMoSys



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