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Team:ETH Zurich/Parameter
From 2013.igem.org
(Difference between revisions)
| Line 17: | Line 17: | ||
<td>4.9 x 10<sup>-6</sup> cm<sup>2</sup>/s</td> | <td>4.9 x 10<sup>-6</sup> cm<sup>2</sup>/s</td> | ||
<td>AHL diffusion constant</td> | <td>AHL diffusion constant</td> | ||
| - | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Stewart2003"/> Stewart P.S., 2003</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 23: | Line 23: | ||
<td>0.9</td> | <td>0.9</td> | ||
<td> Reduced diffusion coefficient</td> | <td> Reduced diffusion coefficient</td> | ||
| - | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Fatin2004"/>Fatin-Rouge <i>et al.</i>, 2004</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 29: | Line 29: | ||
<td>0.01 min<sup>-1</sup></td> | <td>0.01 min<sup>-1</sup></td> | ||
<td>AHL synthesis rate</td> | <td>AHL synthesis rate</td> | ||
| - | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 35: | Line 35: | ||
<td>0.01 min<sup>-1</sup></td> | <td>0.01 min<sup>-1</sup></td> | ||
<td>AHL degradation rate (intracellular)</td> | <td>AHL degradation rate (intracellular)</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005"/>Basu <i>et al.</i>, 2005</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 41: | Line 41: | ||
<td>4.8135 x 10<sup>-4</sup> min<sup>-1</sup></td> | <td>4.8135 x 10<sup>-4</sup> min<sup>-1</sup></td> | ||
<td>AHL extracellular decay</td> | <td>AHL extracellular decay</td> | ||
| - | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Horswill2007"/>Horswill <i>et al.</i>, 2007</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 47: | Line 47: | ||
<td>2</td> | <td>2</td> | ||
<td>Diffusion rate across the cell membrane</td> | <td>Diffusion rate across the cell membrane</td> | ||
| - | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 53: | Line 53: | ||
<td>1</td> | <td>1</td> | ||
<td>Average diffusion rate for all cells</td> | <td>Average diffusion rate for all cells</td> | ||
| - | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 59: | Line 59: | ||
<td>1 μM/min</td> | <td>1 μM/min</td> | ||
<td>LuxI synthesis rate</td> | <td>LuxI synthesis rate</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 77: | Line 77: | ||
<td>0.005 μ M/min</td> | <td>0.005 μ M/min</td> | ||
<td>LuxR synthesis rate</td> | <td>LuxR synthesis rate</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005 </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 83: | Line 83: | ||
<td>0.01 min<sup>-1</sup></td> | <td>0.01 min<sup>-1</sup></td> | ||
<td>LuxR degradation rate</td> | <td>LuxR degradation rate</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Manefield2002">Manefield <i>et al.</i>, 2002</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 89: | Line 89: | ||
<td>0.5 μM<sup>-3</sup>min<sup>-1</sup></td> | <td>0.5 μM<sup>-3</sup>min<sup>-1</sup></td> | ||
<td>LuxR/AHL dimerization</td> | <td>LuxR/AHL dimerization</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 95: | Line 95: | ||
<td>0.0231 min<sup>-1</sup></td> | <td>0.0231 min<sup>-1</sup></td> | ||
<td>Dimer LuxR/AHL degradation rate</td> | <td>Dimer LuxR/AHL degradation rate</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 101: | Line 101: | ||
<td>0.01 μM</td> | <td>0.01 μM</td> | ||
<td>LuxR/AHL activation coefficient</td> | <td>LuxR/AHL activation coefficient</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 107: | Line 107: | ||
<td>1</td> | <td>1</td> | ||
<td>Hill coefficient</td> | <td>Hill coefficient</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 113: | Line 113: | ||
<td> 2 μM min<sup>-1</sup></td> | <td> 2 μM min<sup>-1</sup></td> | ||
<td>GFP synthesis rate</td> | <td>GFP synthesis rate</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 125: | Line 125: | ||
<td>4.4432 x 10<sup>-4</sup> min<sup>-1</sup> </td> | <td>4.4432 x 10<sup>-4</sup> min<sup>-1</sup> </td> | ||
<td>GFP degradation rate</td> | <td>GFP degradation rate</td> | ||
| - | <td> <a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td> <a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Corish1999">Corish and Tyler-Smith, 1999 </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 137: | Line 137: | ||
<td>9.6270<sup>-5</sup> s<sup>-1</sup></td> | <td>9.6270<sup>-5</sup> s<sup>-1</sup></td> | ||
<td>GusA degradation (half-life 55<sup>o</sup>C 2 hr)</td> | <td>GusA degradation (half-life 55<sup>o</sup>C 2 hr)</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Jefferson1995">Jefferson, 1995</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 167: | Line 167: | ||
<td>9.6270<sup>-5</sup> s<sup>-1</sup></td> | <td>9.6270<sup>-5</sup> s<sup>-1</sup></td> | ||
<td>AES degradation (half-life 55<sup>o</sup>C 2 hr)</td> | <td>AES degradation (half-life 55<sup>o</sup>C 2 hr)</td> | ||
| - | <td><a href="https://2013.igem.org/Team:ETH_Zurich/ | + | <td><a href="https://2013.igem.org/Team:ETH_Zurich/Paarameter#Jefferson1995">Jefferson, 1995</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
Revision as of 16:19, 27 October 2013
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 | 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 | 0.01 μM | LuxR/AHL activation coefficient | Basu et al., 2005 |
| η | 1 | Hill coefficient | Basu et al., 2005 |
| αGFP | 2 μM min-1 | GFP synthesis rate | Basu et al., 2005 |
| kGFP | 0.025 | GFP basal expression | estimated |
| 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 |
| η1 | 1.7 | Hill coefficient | estimated from experimental data |
| kGusA | 0.025 | 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 |
| η2 | 0.8 | Hill coefficient | estimated from experimental data |
| kAES | 0.025 | AES 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]
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]
