Team:Groningen/Modeling

From 2012.igem.org

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|'''Possible Modeling Targets'''
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|'''Modeling Targets'''
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'''''Germination'''''
'''''Germination'''''
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# Effects of h2o and L-alanine concentrations on germination rate.
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#* Effects of h2o and L-alanine concentrations on germination rate.
'''''Volatile production'''''
'''''Volatile production'''''
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# Concentration and production rates as a function of temperature, volume, type of meat, geometry. (EX_amine, EX_nh4, EX_h)
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#* Concentration and production rates as a function of temperature, volume, type of meat, geometry.  
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'''''Normal operation'''''
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'''''Life Support'''''
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# Receptor sensitivities
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# What nutrients are required to support growth?
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#* Binding rate as a function of volatile concentration (TAAR5)
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# What is the growth rate (doubling time) vs. temperature using the minimum media?
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# Diffusion rates
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# What metabolites are required for lycopene production?
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#* Through the membrane (nh4_diffusion, h_diffusion)
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# What are the rates of consumption for various temperatures as the biomass grows?
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#* Through ion channels (nh4_ion)
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# What is the total amount of nutrients required to support X amount of biomass?
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# Reaction rates through the signaling pathways as a function of metabolite concentrations (path1,path2,path3)
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'''''Signaling Functionality'''''
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# Carotenoid pathway precursor concentrations as a function of the signaling pathways. (IPP,DMAPP)
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# What will the cell do in the presence of large concentration of ammonium?
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# Reaction rates of the carotenoid pathway metabolites (crtE, crtB, crtI, crtY)
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# Is TnrA a function of glutamine concentration, or the rate of NH4 conversion into glutamine?
# Opacity as a function of lycopene concentration
# Opacity as a function of lycopene concentration
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'''''OMIX visualization through reaction pathways'''''
 
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Revision as of 20:50, 13 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


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. What nutrients are required to support growth?
  2. What is the growth rate (doubling time) vs. temperature using the minimum media?
  3. What metabolites are required for lycopene production?
  4. What are the rates of consumption for various temperatures as the biomass grows?
  5. 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
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