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Team:ETH Zurich/Parameter
From 2013.igem.org
Parameters
Overview of the parameters used in the models.
| Parameter | Value | Description | Reference |
|---|---|---|---|
| DAHL | 4.9 x 10-6 cm2/s | AHL diffusion constant | Stewart P.S., 2003 |
| Cagar | 0.9 | Reduced diffusion coefficient | Fatin-Rouge et al., 2004 |
| αAHL | 0.01 min-1 | AHL synthesis rate | Garcia-Ojalvo et. al., 2004 |
| dAHL | 0.01 min-1 | AHL degradation rate (intracellular) | Basu et al., 2005 |
| dAHL,e | 4.8135 x 10-4 min-1 | AHL extracellular decay | Horswill et al., 2007 |
| ηAHL | 2 | Diffusion rate across the cell membrane | Garcia-Ojalvo et. al., 2004 |
| ηext | 1.3333 | Average diffusion rate for all cells | Garcia-Ojalvo et. al., 2004 |
| αLuxI | 1 μM/min | LuxI synthesis rate | Basu et al., 2005 |
| dLuxI | 0.0167 min-1 | LuxI degradation rate | MIT iGEM 2010 |
| k | 0.888 h-1 | Cell growth rate | estimated from experimental data |
| αLuxR | 0.005 μ M/min | LuxR synthesis rate | Basu et al., 2005 |
| dLuxR | 0.01 min-1 | LuxR degradation rate | Manefield et al., 2002 |
| ρR | 0.5 μM-3min-1 | LuxR/AHL dimerization | Basu et al., 2005 |
| dR | 0.0231 min-1 | Dimer LuxR/AHL degradation rate | Basu et al., 2005 |
| KR | 0.013 nM | LuxR/AHL activation coefficient | estimated from experimental data (scaled) |
| n | 1 | Hill coefficient | Basu et al., 2005 |
| αGFP | 2 μM min-1 | GFP synthesis rate | Basu et al., 2005 |
| dGFP | 4.4432 x 10-4 min-1 | GFP degradation rate | Corish and Tyler-Smith, 1999 |
| αGusA | 1 μM min-1 | GusA synthesis rate | estimated |
| dGusA | 9.6270-5 s-1 | GusA degradation (half-life 55oC 2 hr) | Jefferson, 1995 |
| KR1 | 4.45 nM | AHL activation coefficient | estimated from experimental data |
| n1 | 1.7 | Hill coefficient | estimated from experimental data |
| kleaky | 0.0375 | GusA basal expression | estimated |
| αAES | 1 μM min-1 | AES synthesis rate | estimated |
| dAES | 9.6270-5 s-1 | AES degradation (half-life 55oC 2 hr) | Jefferson, 1995 |
| KR2 | 12555 nM | AHL activation coefficient | estimated from experimental data |
| n2 | 0.8 | Hill coefficient | estimated from experimental data |
| kGFP | 0.0375 | Hydrolases basal expression | estimated |
References
Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R.; Nature; 2005 Apr; 434: 1130-1134.
A synthetic multicellular system for programmed pattern formation.
[http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html Nature]
Corish P, Tyler-Smith C; Protein Engineering. 199; 12(12): 1053-1040.
Attenuation of green fluorescent protein half-life in mammalian cells.
[http://peds.oxfordjournals.org/content/12/12/1035.full peds]
Farias T, Mandrich L, Rossi M, Manco G; Protein Pept Lett. 2007; 14(2):165-9. Biochemical and thermostability features of acetyl esterase Aes from Escherichia coli. [http://www.ncbi.nlm.nih.gov/pubmed/17305603 PubMed]
Fatin-Rouge N., Starchev K., Buffle J.; Biophysical Journal. 2004 May; 86:2710–2719.
Size Effects on Diffusion Processes within Agarose Gels
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304142/ PMC]
Garcia-Ojalvo J., Elowitz M.B., Strogatz S.H.; PNAS; 2004 Jul; 101(30): 10955–10960.
Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing.
[http://www.pnas.org/content/101/30/10955.long PNAS]
Horswill A.R., Stoodley P., Stewart P.S., Parsek M.R.; Anal Bioanal Chem.; 2007 Jan; 387(2): 371–380.
The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797063/ PMC]
Jefferson RA; US 5432081 A. 1995 Jul. Host cells transformed with the E. coli glucoronide permease gene
Manefield M., Rasmussen T.B., Henzter M., Andersen J.B., Steinberg P., Kjelleberg S., Givskov M.; Microbiology . 2002 Apr; 148(4):1119-1127
Halogenated furanones inhibit quorum sensing through accelerated LuxR turnover
[http://www.ncbi.nlm.nih.gov/pubmed/11932456 PubMed]
Stewart P.S.; Journal of Bacteriology; 2003 Mar.; 185(5): 1485-1491.
Diffusion in Biofilms.
[http://jb.asm.org/content/185/5/1485.full JB]
