DataEntryID 90
    General information
      Manuscript title: Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/24909362
      Journal: Metabolic Engineering
      Year: 2014
      Authors: Aditi Swarup, Jimg Lu, Kathleen C. DeWoody, Maciek R. Antoniewicz
      Affiliations: Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark DE 19716, USA
      Keywords: Extremophile, Thermophilic bacterium, Optimal growth, Metabolic network model, Isotopic labeling
      Full text article: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcTBFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--96458a3cb7ef05ab836db524fd0205efbddae37c/Swarup_2014.pdf
      Project name: not specified

    Experiment description
      Organism: Thermus thermophilus
      Strain: HB8 (ATCC 27634)
      Data type: flux measurements
      Data units: % substrate uptake
      Execution date: not specified

    Experimental details
      Temperature (°C): 70
      pH: 7.9
      Carbon source: glucose
      Culture mode: batch
      Process condition: aerobic
      Dilution rate (h⁻¹): —
      Working volume: 0.01 L
      Biomass concentration (g/L): 0.39 (g/L)/OD600 cell dry weight and 25.3 g/C-mol for the molecular weight of dry biomass
      Medium composition: Glucose stock solutions were prepared at 20 wt% in distilled water. The optimized minimum medium contained (per liter of medium): 0.50 g K2HPO4, 0.30 g KH2PO4, 0.50 g NH4Cl, 0.50 g NaCl, 0.20 g MgCl2.6H2O, 0.04 g CaSO4.2H2O, 40 mL of 1 M Tris, 5 mL of Wolfe׳s minerals, and 5 mL of Wolfe׳s vitamins.
      General protocol information: Type analysis list: 13C constrained MFA; Platform list: GC-MS;
      Methods description: 13C-Metabolic flux analysis - 13C –MFA was performed using the Metran software [1,2], which is based on the elementary metabolite units (EMU) framework [3,4]. Fluxes were estimated by minimizing the variance-weighted sum of squared residuals (SSR) between the experimentally measured and model predicted mass isotopomer distributions of amino acids using non-linear least-squares regression [5]. Flux estimation was repeated 10 times starting with random initial values for all fluxes to find a global solution. At convergence, accurate 95% confidence intervals were computed for all estimated fluxes by evaluating the sensitivity of the minimized SSR to flux variations [5].                                                                                                                                                                               Metabolic network model - A metabolic network model of T. thermophilus central carbon metabolism was constructed for 13C–MFA based on KEGG and PathwayTools metabolic pathway databases [6,7,8]. The model includes all major metabolic pathways of central carbon metabolism. A lumped biomass reaction was used to describe the drain of precursor metabolites and co-factors required for cell growth. The complete model is provided in the original paper.

----------------References-----------------
[1] S.B. Crown, M.R. Antoniewicz,Metab. Eng., 20 (2013), pp. 42–48. http://doi.org/7td
[2] H. Yoo, M.R. Antoniewicz, G. Stephanopoulos, J.K. Kelleher, J. Biol. Chem., 283 (2008), pp. 20621–20627. http://doi.org/fsrtj5
[3] M.R. Antoniewicz, J.K. Kelleher, G. Stephanopoulos, Metab. Eng., 9 (2007), pp. 68–86. http://doi.org/b97p7s
[4] J.D. Young, J.L. Walther, M.R. Antoniewicz, H. Yoo, G. Stephanopoulos, Biotechnol. Bioeng., 99 (2008), pp. 686–699. http://doi.org/crmdfw
[5] M.R. Antoniewicz, J.K. Kelleher, G. Stephanopoulos, Metab. Eng., 8 (2006), pp. 324–337. http://doi.org/fbgz85
[6] R. Caspi, T. Altman, K. Dreher, C.A. Fulcher, P. Subhraveti, I.M. Keseler, A. Kothari, M. Krummenacker, M. Latendresse, L.A. Mueller, Q. Ong, S. Paley, A. Pujar, A.G. Shearer, M. Travers, D. Weerasinghe, P. Zhang, P.D. Karp, Nucleic Acids Res., 40 (2012), pp. http://doi.org/ckb6fjD742–D753
[7] M. Kanehisa, S. Goto, Nucleic Acids Res., 28 (2000), pp. 27–30. http://doi.org/b9st54
[8] M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, M. Tanabe, Nucleic Acids Res., 40 (2012), pp. D109–D114. http://doi.org/c4vgkr                                                                                                  
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      Entered by: Administrator KiMoSys
      Created: 2015-09-22 12:48:07 UTC
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