DataEntryID 107
    General information
      Manuscript title: Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/12802531
      Journal: Appl Micriobiol Biotechnology
      Year: 2004
      Authors: Al Zaid Siddiquee K, Arauzo-Bravo MJ, Shimizu K.
      Affiliations: Department of Biochemical Engineering and Science, Kyushu Institute of Technology,Iizuka, 820–8502 Fukuoka, Japan
      Keywords: Dilution Ratem Intracellular Metabolite, Metabolic Flux Analysis, Oxidative Pentose Phosphate Pathway, Proteinogenic Amino Acid 
      Full text article: no file uploaded
      Project name: not specified

    Experiment description
      Organism: Escherichia coli
      Strain: BW25113 and pyk mutant
      Data type: flux measurements
      Data units: (mmol/g-dry cell weight/h)
      Execution date: not specified

    Experimental details
      Temperature (°C): 37
      pH: 7.0
      Carbon source: glucose
      Culture mode: chemostat
      Process condition: aerobic
      Dilution rate (h⁻¹): 0.1
      Working volume: 0.5 L
      Biomass concentration (g/L): see worksheet.
      Medium composition: Minimal medium consisting of 5 g glucose per liter, 48 mM Na2HPO4,22mMKH2PO4, 10 mM NaCl, and40 mM (NH4)SO4, was used. For minimal medium, the following components were filter-sterilized separately and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml 0.1 mM CaCl2, 1ml vitamin B1 (1 mg/l stock) and 10 ml trace element solution containing (per liter): 0.55 g CaCl2, 1 g FeCl3, 0.1 g 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: Type analysis list: 13C constrained MFA; Platform list: NMR, GC-MS;
      Methods description: The isotopomer balance systems were described using isotopomer mapping matrices [1] and solved through an iterative scheme, based on the approach of [1]. The isotopomers of the proteinogenic amino acids were used to generate NMR synthetic patterns. For the representation of the metabolic fluxes, the forward v and backward v fluxes associated with each bidirectional reaction step were transformed into a net v [2]. A non-linear mapping from exchange fluxes to exchange coefficients v exch[0,1] was made to overcome the numerical problems arising from very large parameters values [3]. Please see more details in the original publication.                                                                                                                                                                             -----------------------------------References------------------------------
[1] Schmidt K, Carlsen M, Nielsen J, Villadsen J (1997). Biotechnol Bioeng 55:831–840. http://doi.org/dfb3d5
[2] Schmidt K, Nielsen J, Villadsen J (1999).  J Biotechnol 71:175–190. http://doi.org/bjxbj5                                                                                                                                                                                                                                 [3] Wiechert W, Siefke C, de Graff AA, Marx A (1997). Biotechnol Bioeng 55:118–135. http://doi.org/fn584s
      Data file: http://kimosys.org/repository/107/download?parameter=1229; 
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    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2018-07-21 20:09:18 UTC
      Updated: 2020-04-24 16:10:36 UTC
      Version: 1
      Status: (reviewed) 2018-07-21 20:19:41 UTC
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