ETHZ/Parameters
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Revision as of 10:11, 13 October 2007
Introduction
blabla
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 |
| cI repressor dissociation constant |
|
| 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
[http://www.pnas.org/cgi/content/abstract/104/8/2643 [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
[http://www.pnas.org/cgi/content/full/100/13/7702?ck=nck [2] Setty Y et al.] "Detailed map of a cis-regulatory input function", P Natl Acad Sci USA 100(13):7702-7707, 2003
[http://ieeexplore.ieee.org/iel5/9711/30654/01416417.pdf [3] Braun D et al.] "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
[http://www.nature.com/nature/journal/v435/n7038/suppinfo/nature03508.html [4] Fung E et al.] "A synthetic gene--metabolic oscillator", Nature 435:118-122, 2005 (supplementary material)
[http://dx.doi.org/10.1016/j.jbiotec.2005.08.030 [5] Iadevaia S and Mantzais NV] "Genetic network driven control of PHBV copolymer composition", J Biotechnol 122(1):99-121, 2006
[http://dx.doi.org/10.1016/j.biosystems.2005.04.006 [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
[http://www.genetics.org/cgi/content/abstract/149/4/1633 [7] Arkin A et al.] "Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells", Genetics 149: 1633-1648, 1998
[http://download.cell.com/supplementarydata/cell/107/6/739/DC1/index.htm [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)
[http://www.nature.com/nature/journal/v405/n6786/abs/405590a0.html [9] Becskei A and Serrano L] "Engineering stability in gene networks by autoregulation", Nature 405: 590-593, 2000
[http://www.biophysj.org/cgi/content/full/89/6/3873?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=89&firstpage=3873&resourcetype=HWCIT [10] Tuttle et al.] "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
[http://www.pnas.org/cgi/reprint/99/2/679 [11] McMillen LM et al.] "Synchronizing genetic relaxation oscillators by intercell signaling", P Natl Acad Sci USA 99(2):679-684, 2002
[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html [12] Basu S et al.] "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005
