Computer Simulation of Metabolism
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