ETHZ/Parameters

From 2007.igem.org

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== Model Parameters ==
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[http://www.pnas.org/cgi/content/abstract/104/8/2643 &#91;1&#93; Weber W et al.] <i>"A synthetic time-delay circuit in mammalian cells and mice"</i>, P Natl Acad Sci USA 104(8):2643-2648, 2007<br />
[http://www.pnas.org/cgi/content/abstract/104/8/2643 &#91;1&#93; Weber W et al.] <i>"A synthetic time-delay circuit in mammalian cells and mice"</i>, P Natl Acad Sci USA 104(8):2643-2648, 2007<br />

Revision as of 10:09, 13 October 2007

Introduction

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Model Parameters

Parameter Value Description Comments
c1max 0.01 [mM/h] max. transcription rate of constitutive promoter (per gene) promoter no. J23105; Reference: Estimate
c2max 0.01 [mM/h] max. transcription rate of luxR-activated promoter (per gene) Reference: Estimate
lhi 25 high-copy plasmid number Reference: Estimate
llo 5 low-copy plasmid number Reference: Estimate
aQ2,R 0.1 - 0.2 basic production of Q2/R-inhibited genes Reference: Conclusions after discussion
aQ2 0.1 - 0.2 basic production of Q2-inhibited genes Reference: Conclusions after discussion
aQ1,S 0.1 - 0.2 basic production of Q1/S-inhibited genes Reference: Conclusions after discussion
aQ1 0.1 - 0.2 basic production of Q1-inhibited genes Reference: Conclusions after discussion
aQ2,S 0.1 - 0.2 basic production of Q2/S-inhibited genes Reference: Conclusions after discussion
aQ1,R 0.1 - 0.2 basic production of Q1/R-inhibited genes Reference: Conclusions after discussion
dR 2.31e-3 [per sec] degradation of lacI Ref. [10]
dS 1e-5 [pro sec]/2.31e-3 [per sec] degradation of tetR Ref. [9]/ Ref. [10]
dL 1e-3 - 1e-4 [per sec] degradation of luxR Ref: [6]
dQ1 7e-4 [per sec] degradation of cI Ref. [7]
dQ2 degradation of p22cII
dYFP 6.3e-3 [per min] degradation of YFP suppl. mat. to Ref. [8] corresponding to a half life of 110min
dGFP 6.3e-3 [per min] degradation of GFP in analogy to YFP
dRFP 6.3e-3 [per min] degradation of RFP in analogy to YFP
dCFP 6.3e-3 [per min] degradation of CFP in analogy to YFP
KR 0.1 - 1 [pM] lacI repressor dissociation constant Ref. [2]
KIR 1.3 [µM] IPTG-lacI repressor dissociation constant Ref. [2]
KS 179 [pM] tetR repressor dissociation constant Ref. [1]
KIS 893 [pM] aTc-tetR repressor dissociation constant Ref. [1]
KL 55 - 520 [nM] luxR activator dissociation constant Ref: [6]
KIL 0.09 - 1 [µM] AHL-luxR activator dissociation constant Ref: [6]
KQ1
  • 8 [pM]
  • 50 [nM]
cI repressor dissociation constant
  • Ref. [12]
  • starting with values of Ref. [6] and using Ref. [3]
KQ2 0.577 [µM] p22cII repressor dissociation constant Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?
nR 1 lacI repressor Hill cooperativity Ref. [5]
nIR 2 IPTG-lacI repressor Hill cooperativity Ref. [5]
nS 3 tetR repressor Hill cooperativity Ref. [3]
nIS 2 (1.5-2.5) aTc-tetR repressor Hill cooperativity Ref. [3]
nL 2 luxR activator Hill cooperativity Ref: [6]
nIL 1 AHL-luxR activator Hill cooperativity Ref. [3]
nQ1 2 cI repressor Hill cooperativity Ref. [12]
nQ2 4 p22cII repressor Hill cooperativity Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?

References

[1] Weber W et al. "A synthetic time-delay circuit in mammalian cells and mice", P Natl Acad Sci USA 104(8):2643-2648, 2007
[2] Setty Y et al. "Detailed map of a cis-regulatory input function", P Natl Acad Sci USA 100(13):7702-7707, 2003
[3] Braun D et al. "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
[4] Fung E et al. "A synthetic gene--metabolic oscillator", Nature 435:118-122, 2005 (supplementary material)
[5] Iadevaia S and Mantzais NV "Genetic network driven control of PHBV copolymer composition", J Biotechnol 122(1):99-121, 2006
[6] Goryachev AB et al. "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
[7] Arkin A et al. "Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells", Genetics 149: 1633-1648, 1998
[8] Colman-Lerner A et al. "Yeast Cbk1 and Mob2 Activate Daughter-Specific Genetic Programs to Induce Asymmetric Cell Fates", Cell 107(6): 739-750, 2001 (supplementary material)
[9] Becskei A and Serrano L "Engineering stability in gene networks by autoregulation", Nature 405: 590-593, 2000
[10] Tuttle et al. "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
[11] McMillen LM et al. "Synchronizing genetic relaxation oscillators by intercell signaling", P Natl Acad Sci USA 99(2):679-684, 2002
[12] Basu S et al. "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005