From 2007.igem.org

Introduction

blabla

Model Parameters

Parameter	Value	Description	Comments		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
Degradation constants
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
Dissociation constants
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?
Hill cooperativity
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?

Hill cooperativity

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

[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