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  • Introduction
  • Effects of Varying Rates and Pool Sizes - A Sample Program
  • Consideration of Multiple Compartments
  • Consideration of Cycles - The GS/GOGAT Cycle
  • Compounds Receiving Several 13C Atoms from 13CO2
  • Isotopomers of the Citric Acid Cycle Supplied with 3-13C-Pyruvate
  • Modeling Radioactive Precursor Uptake Kinetics
  • Simulation of The Pathway of DMSP Biosynthesis in Enteromorpha intestinalis
  • Simulation of The Pathway of Synthesis of DMSP in Spartina alterniflora
  • Making Rates Linearly or Hyperbolically Responsive to Pool Size Changes
  • Metabolic Engineering of Glycine Betaine Synthesis - Metabolism of 14C-Choline in Transgenic Tobacco Expressing Choline Monooxygenase in the Chloroplast
  • Considering Feedback Inhibition
  • Modeling Allosteric Behavior - Cooperative Substrate Binding
  • Links to Other Metabolic Modeling Resources on the www
  • References
  • Sponsors
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    Computer Simulation of Metabolism

    References

    The following articles have used the computer simulation tools described here:

    Nuccio, M.L., McNeil, S.D., Ziemak, M.J., Hanson, A.D., Jain, R.K., Selvaraj, G. 2000. Choline import into chloroplasts limits glycine betaine synthesis in tobacco: analysis of plants engineered with a chloroplastic or a cytosolic pathway. Metab. Eng. 2: 300-311.

    McNeil, S.D., Rhodes, D., Russell, B.L., Nuccio, M.L., Shachar-Hill, Y., Hanson, A.D. 2000. Metabolic modeling identifies key constraints on an engineered glycine betaine synthesis pathway in tobacco. Plant Physiology 124: 153-162.

    McNeil, S.D., Nuccio, M.L., Rhodes, D., Shachar-Hill, Y., Hanson, A.D. 2000. Radiotracer and computer modeling evidence that phosphobase methylation is the main route of choline synthesis in tobacco. Plant Physiology 123: 371-380.

    Kocsis, M.G., Nolte, K.D., Rhodes, D., Shen, T.L., Gage, D.A. and Hanson, A.D. 1998. Dimethylsulfoniopropionate biosynthesis in Spartina alterniflora Loisel.: evidence that S-methylmethionine and dimethylsulfoniopropylamine are intermediates. Plant Physiology 117: 273-281.

    Gage, D.A., Rhodes, D., Nolte, K.D., Hicks, W.A., Leustek, T., Cooper, A.J.L. and Hanson, A.D. 1997. A new route for synthesis of dimethylsulphoniopropionate in marine algae. Nature 387: 891-894.

    Mayer, R.R., Cherry, J.H. and Rhodes, D. 1990. Effects of heat shock on amino acid metabolism of cowpea cells. Plant Physiology 94: 796-810.

    Rhodes, D. and Handa, S. 1989. Amino acid metabolism in relation to osmotic adjustment. In (J.H. Cherry, ed.) "Environmental Stress in Plants. Biochemical and Physiological Mechanisms", NATO ASI Series G: Ecological Sciences, Vol 19, Springer-Verlag, Berlin, pp. 41-62.

    Rhodes, D., Handa, S. and Bressan, R.A. 1986. Metabolic changes associated with adaptation of plant cells to water stress. Plant Physiology 82: 890-903.

    Hanson, A.D. and Rhodes, D. 1983. 14C Tracer evidence for synthesis of choline and betaine via phosphoryl base intermediates in salinized sugar beet leaves. Plant Physiology 71: 692-700.

    Hitz, W.D., Rhodes, D. and Hanson, A.D. 1981. Radiotracer evidence implicating phosphoryl and phosphatidyl bases as intermediates in betaine synthesis by water-stressed barley leaves. Plant Physiology 68: 814-822.

    Rhodes, D., Sims, A.P. and Folkes, B.F. 1980. Pathway of ammonia assimilation in illuminated Lemna minor. Phytochemistry 19: 357-365.

    For additional references on computer simulation, labeling, metabolic engineering, modeling, metabolic flux analysis, and allied topics, please see:

    HORT640 - Metabolic Plant Physiology - References

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    David Rhodes
    Department of Horticulture & Landscape Architecture
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    Last Update: 8/20/03