"

From 2012.igem.org

Fig. m2. Reactions involved between ammonium uptake and TnrA.

References

1. SubtiWiki, http://subtiwiki.uni-goettingen.de/wiki/index.php
2. K. Gunka, F.M. Commichau, “Control of glutamate homeostasis in Bacillus subtilis: a complex interplay between ammonium assimilation, glutamate biosynthesis and degradation,” Molecular Biology, under review (2012).
3. N.A. Doroshchuk, M.S. Gelfand, D.A. Rodlanov, “Regulation of Nitrogen Metabolism in Gram-Positive Bacteria,” Molecular Biology, vol. 40(5), pp. 829-836, (2006).
4. Study Guide, Chem153C, University of California, Los Angeles. http://vohweb.chem.ucla.edu/voh/classes%5Cspring10%5C153CID28%5C11AminoAcidBiosynthesisSQA.pdf

Possible Modeling Targets

Germination

1. Effects of h2o and L-alanine concentrations on germination rate.

Volatile production

1. Concentration and production rates as a function of temperature, volume, type of meat, geometry. (EX_amine, EX_nh4, EX_h)

Normal operation

1. Receptor sensitivities
   • Binding rate as a function of volatile concentration (TAAR5)
2. Diffusion rates
   • Through the membrane (nh4_diffusion, h_diffusion)
   • Through ion channels (nh4_ion)
3. Reaction rates through the signaling pathways as a function of metabolite concentrations (path1,path2,path3)
4. Carotenoid pathway precursor concentrations as a function of the signaling pathways. (IPP,DMAPP)
5. Reaction rates of the carotenoid pathway metabolites (crtE, crtB, crtI, crtY)
6. Opacity as a function of lycopene concentration

OMIX visualization through reaction pathways