DataEntryID 99
    General information
      Manuscript title: A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/23831062
      Journal: FEBS Letters
      Year: 2013
      Authors: Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W. Hayes, Daniel Jameson, David S. Broomhead, Stephen G. Oliver, Simon J. Gaskell, John E.G. McCarthy, Norman W. Paton, Hans V. Westerhoff, Douglas B. Kell, Pedro Mendes
      Affiliations: Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK
      Keywords: Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling
      Full text article: https://www.kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcjRFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--83aa95be6c5b8986eda3d15002240aa59b0cfd4b/Smallbone_2013.pdf
      Project name: —

    Experiment description
      Organism: Saccharomyces cerevisiae
      Strain: Y23925
      Data type: metabolites at steady-state
      Data units: molecules/cell
      Execution date: not specified

    Experimental details
      Temperature (°C): not specified
      pH: not specified
      Carbon source: glucose
      Culture mode: chemostat
      Process condition: aerobic
      Dilution rate (h⁻¹): µmax
      Working volume: not specified L
      Biomass concentration (g/L): monitored by measuring the electrical capacitance of the culture.
      Medium composition: not specified
      General protocol information: Sampling Method: 10 ml of culture.; Quenching: 10 ml of culture solution into 40 ml of a 60:40 methanol/water solution [1] stored at a temperature of −47 °C [2]. Immediate separation of cells was performed by applying centrifugation (4000 g for 5 min) followed by removal of the quenching solution. ; Extraction list: freezing-thawing in methanol, methanol-water; Analysis list: GC-MS, LC-MS;
      Methods description: Samples were analysed using two analytical platforms. Fructose‐1,6‐bisphosphate was quantified applying ultra-performance liquid chromatography mass spectrometry (UPLC‐MS) (Waters Acquity UPLC coupled to a ThermoFisher hybrid electrospray LTQ‐Orbitrap mass spectrometer (ThermoFisher Scientific, http://www.thermofisher.com/)) and the standard addition method for accurate quantification. Other metabolites were quantified applying GC–MS (Agilent 6890 Gas Chromatograph coupled to a Leco Pegasus III electron impact‐time‐of‐flight mass spectrometer (Leco, http://www.leco.com/)) and the external calibration method for accurate quantification. The concentrations determined in the extracted samples were reported as the number of molecules per cell. The gas chromatographic separation of 2‐phosphoglycerate and 3‐phosphoglycerate is technically demanding and was not achieved during this study. Therefore, the combined concentration of both metabolites was reported rather than separate concentrations for each metabolite.  Concentrations were calculated relative to an effective cytoplasmic volume of 5 fl.
-----------------References--------------------
[1] W.B. Dunn , C.L. Winder. Methods Enzymol., 500, (2011), 277– 297. http://doi.org/dfwnv3                                                                                                                                                                                                                                                                                                                           [2] M. Martins , W. Sha , C. Evans , S. Martino-Catt , P. Mendes , V. Shulaev. Yeast, 24, (2007), 181– 188. http://doi.org/c2qv8f
      Data file: http://kimosys.org/repository/99/download?parameter=1213; 
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    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2018-07-16 15:49:58 UTC
      Updated: 2020-04-24 16:10:35 UTC
      Version: 2
      Status: (reviewed) 2018-07-16 15:57:33 UTC
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      Downloads: 54