"

From 2012.igem.org

Fig. m1. 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

Modeling Targets

Germination

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

Volatile production

• Concentration and production rates as a function of temperature, volume, type of meat, geometry.

Life Support

1. How much glutamine is required to keep GS active till there is extracellular ammonium available?
2. What nutrients are required to support growth?
3. What is the growth rate (doubling time) vs. temperature using the minimum media?
4. What metabolites are required for lycopene production?
5. What are the rates of consumption for various temperatures as the biomass grows?
6. What is the total amount of nutrients required to support X amount of biomass?

Signaling Functionality

1. What will the cell do in the presence of large concentration of ammonium?
2. Is TnrA a function of glutamine concentration, or the rate of NH4 conversion into glutamine?
3. Opacity as a function of lycopene concentration