Team:Groningen/Modeling

From 2012.igem.org

(Difference between revisions)
m
Line 3: Line 3:
{|align="center"
{|align="center"
<br>
<br>
-
|[[File:Groningen2012 JP 20120509 bsc Reaction Map v0.png|center|680px]]
+
|[[File:Groningen2012 JP 20120611 NH4-TnrA Relationship.png|680px|center]]
|-
|-
-
|
+
{|align="center"
-
{|align="center"  
+
|Fig. m2. Reactions involved between ammonium uptake and TnrA.
-
|Fig. m1. OMIX diagram of the reactions and metabolites involved in active b. salus carnis.
+
|}
|}
 +
 +
References
 +
# SubtiWiki, http://subtiwiki.uni-goettingen.de/wiki/index.php
 +
# 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).
 +
# 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).
 +
# Study Guide, Chem153C, University of California, Los Angeles. http://vohweb.chem.ucla.edu/voh/classes%5Cspring10%5C153CID28%5C11AminoAcidBiosynthesisSQA.pdf
 +
 +
|-
|-
-
|'''Modeling Targets'''
+
|'''Possible Modeling Targets'''
<br>
<br>
'''''Germination'''''
'''''Germination'''''

Revision as of 18:56, 12 June 2012





Groningen2012 JP 20120611 NH4-TnrA Relationship.png
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

Retrieved from "http://2012.igem.org/Team:Groningen/Modeling"