Team:ETH Zurich/Parameter

From 2013.igem.org

(Difference between revisions)
 
(80 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:ETH_Zurich/Templates}}
{{:Team:ETH_Zurich/Templates}}
 +
{{:Team:ETH_Zurich/Templates/stylesheet}}
-
<table border="1">
+
<h1>Parameters</h1>
 +
<html>
 +
<p>Overview of the parameters used in the models.</p>
 +
<script src="sorttable.js"></script>
 +
<table style="font-size:12px" class="sortable" border="1">
<tr>
<tr>
-
<th>Header 1</th>
+
<th width="150" height="30">Parameter</th>
-
<th>Header 2</th>
+
<th>Value</th>
-
<th>Header 3</th>
+
<th width="250" height="30">Description</th>
-
<th>Header 4</th>
+
<th width="200" height="30">Reference</th>
</tr>
</tr>
<tr>
<tr>
-
<td>row 1, cell 1</td>
+
<td>D<sub>AHL</sub></td>
-
<td>row 1, cell 2</td>
+
<td>4.9 x 10<sup>-6</sup> cm<sup>2</sup>/s</td>
-
<td>row 1, cell 3</td>
+
<td>AHL diffusion constant</td>
-
<td>row 1, cell 4</td>
+
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Stewart2003"/> Stewart P.S., 2003</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 2, cell 1</td>
+
<td>C<sub>agar</sub></td>
-
<td>row 2, cell 2</td>
+
<td>0.9</td>
-
<td>row 2, cell 3</td>
+
<td> Reduced diffusion coefficient</td>
-
<td>row 2, cell 4</td>
+
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Fatin2004"/>Fatin-Rouge <i>et al.</i>, 2004</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 3, cell 1</td>
+
<td>&alpha;<sub>AHL</sub></td>
-
<td>row 3, cell 2</td>
+
<td>0.01 min<sup>-1</sup></td>
-
<td>row 3, cell 3</td>
+
<td>AHL synthesis rate</td>
-
<td>row 3, cell 4</td>
+
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 4, cell 1</td>
+
<td>d<sub>AHL</sub></td>
-
<td>row 4, cell 2</td>
+
<td>0.01 min<sup>-1</sup></td>
-
<td>row 4, cell 3</td>
+
<td>AHL degradation rate (intracellular)</td>
-
<td>row 4, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005"/>Basu <i>et al.</i>, 2005</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 5, cell 1</td>
+
<td>d<sub>AHL,e</sub></td>
-
<td>row 5, cell 2</td>
+
<td>4.8135 x 10<sup>-4</sup> min<sup>-1</sup></td>
-
<td>row 5, cell 3</td>
+
<td>AHL extracellular decay</td>
-
<td>row 5, cell 4</td>
+
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Horswill2007"/>Horswill <i>et al.</i>, 2007</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 6, cell 1</td>
+
<td>&eta;<sub>AHL</sub></td>
-
<td>row 6, cell 2</td>
+
<td>2</td>
-
<td>row 6, cell 3</td>
+
<td>Diffusion rate across the cell membrane</td>
-
<td>row 6, cell 4</td>
+
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 7, cell 1</td>
+
<td>&eta;<sub>ext</sub></td>
-
<td>row 7, cell 2</td>
+
<td>1.3333</td>
-
<td>row 7, cell 3</td>
+
<td>Average diffusion rate for all cells</td>
-
<td>row 7, cell 4</td>
+
<td><a href = "https://2013.igem.org/Team:ETH_Zurich/Parameter#Garcia2004"/> Garcia-Ojalvo <i>et. al.</i>, 2004 </td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 8, cell 1</td>
+
<td>&alpha;<sub>LuxI</sub></td>
-
<td>row 8, cell 2</td>
+
<td>1 &mu;M/min</td>
-
<td>row 8, cell 3</td>
+
<td>LuxI synthesis rate</td>
-
<td>row 8, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 9, cell 1</td>
+
<td>d<sub>LuxI</sub></td>
-
<td>row 9, cell 2</td>
+
<td>0.0167 min<sup>-1</sup></td>
-
<td>row 9, cell 3</td>
+
<td>LuxI degradation rate</td>
-
<td>row 9, cell 4</td>
+
<td><a href="https://2010.igem.org/Team:MIT_tmodel"> MIT iGEM 2010</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 10, cell 1</td>
+
<td>k</td>
-
<td>row 10, cell 2</td>
+
<td>0.888 h<sup>-1</sup></td>
-
<td>row 10,cell 3</td>
+
<td>Cell growth rate</td>
-
<td>row 10, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Modeling/Reaction_Diffusion_OOHL#growthRate">estimated from experimental data</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 11, cell 1</td>
+
<td>&alpha;<sub>LuxR</sub></td>
-
<td>row 11, cell 2</td>
+
<td>0.005 &mu; M/min</td>
-
<td>row 11, cell 3</td>
+
<td>LuxR synthesis rate</td>
-
<td>row 11, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005 </td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 13, cell 1</td>
+
<td>d<sub>LuxR</sub></td>
-
<td>row 13, cell 2</td>
+
<td>0.01 min<sup>-1</sup></td>
-
<td>row 13, cell 3</td>
+
<td>LuxR degradation rate</td>
-
<td>row 13, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Manefield2002">Manefield <i>et al.</i>, 2002</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 14, cell 1</td>
+
<td>&rho;<sub>R</sub></td>
-
<td>row 14, cell 2</td>
+
<td>0.5 &mu;M<sup>-3</sup>min<sup>-1</sup></td>
-
<td>row 14, cell 3</td>
+
<td>LuxR/AHL dimerization</td>
-
<td>row 14, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 15, cell 1</td>
+
<td>d<sub>R</sub></td>
-
<td>row 15, cell 2</td>
+
<td>0.0231 min<sup>-1</sup></td>
-
<td>row 15, cell 3</td>
+
<td>Dimer LuxR/AHL degradation rate</td>
-
<td>row 15, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 16, cell 1</td>
+
<td>K<sub>R</sub></td>
-
<td>row 16, cell 2</td>
+
<td>0.013 nM</td>
-
<td>row 16, cell 3</td>
+
<td>LuxR/AHL activation coefficient</td>
-
<td>row 16, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated</a> from experimental data (scaled)</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 17, cell 1</td>
+
<td>n</td>
-
<td>row 17, cell 2</td>
+
<td>1</td>
-
<td>row 17, cell 3</td>
+
<td>Hill coefficient</td>
-
<td>row 17, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 18, cell 1</td>
+
<td>&alpha;<sub>GFP</sub></td>
-
<td>row 18, cell 2</td>
+
<td> 2 &mu;M min<sup>-1</sup></td>
-
<td>row 18, cell 3</td>
+
<td>GFP synthesis rate</td>
-
<td>row 18, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Basu2005">Basu <i>et al.</i>, 2005</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 19, cell 1</td>
+
<td>d<sub>GFP</sub></td>
-
<td>row 19, cell 2</td>
+
<td>4.4432 x 10<sup>-4</sup> min<sup>-1</sup> </td>
-
<td>row 19, cell 3</td>
+
<td>GFP degradation rate</td>
-
<td>row 19, cell 4</td>
+
<td> <a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Corish1999">Corish and Tyler-Smith, 1999 </td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 20, cell 1</td>
+
<td>&alpha;<sub>GusA</sub></td>
-
<td>row 20, cell 2</td>
+
<td>1 &mu;M min<sup>-1</sup></td>
-
<td>row 20, cell 3</td>
+
<td>GusA synthesis rate</td>
-
<td>row 20, cell 4</td>
+
<td>estimated</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 21, cell 1</td>
+
<td>d<sub>GusA</sub></td>
-
<td>row 21, cell 2</td>
+
<td>9.6270<sup>-5</sup> s<sup>-1</sup></td>
-
<td>row 21, cell 3</td>
+
<td>GusA degradation (half-life 55<sup>o</sup>C 2 hr)</td>
-
<td>row 21, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Jefferson1995">Jefferson, 1995</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 22, cell 1</td>
+
<td>K<sub>R1</sub></td>
-
<td>row 22, cell 2</td>
+
<td>4.45 nM</td>
-
<td>row 22, cell 3</td>
+
<td>AHL activation coefficient </td>
-
<td>row 22, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 23, cell 1</td>
+
<td>n<sub>1</sub></td>
-
<td>row 23, cell 2</td>
+
<td>1.7</td>
-
<td>row 23, cell 3</td>
+
<td>Hill coefficient</td>
-
<td>row 23, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 24, cell 1</td>
+
<td>k<sub>leaky</sub></td>
-
<td>row 24, cell 2</td>
+
<td> 0.0375 </td>
-
<td>row 24, cell 3</td>
+
<td>GusA basal expression</td>
-
<td>row 24, cell 4</td>
+
<td>estimated</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 25, cell 1</td>
+
<td>&alpha;<sub>AES</sub></td>
-
<td>row 25, cell 2</td>
+
<td>1 &mu;M min<sup>-1</sup></td>
-
<td>row 25, cell 3</td>
+
<td>AES synthesis rate</td>
-
<td>row 25, cell 4</td>
+
<td>estimated</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 26, cell 1</td>
+
<td>d<sub>AES</sub></td>
-
<td>row 26, cell 2</td>
+
<td>9.6270<sup>-5</sup> s<sup>-1</sup></td>
-
<td>row 26, cell 3</td>
+
<td>AES degradation (half-life 55<sup>o</sup>C 2 hr)</td>
-
<td>row 26, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter#Jefferson1995">Jefferson, 1995</td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 27, cell 1</td>
+
<td>K<sub>R2</sub></td>
-
<td>row 27, cell 2</td>
+
<td>12555 nM</td>
-
<td>row 27, cell 3</td>
+
<td>AHL activation coefficient </td>
-
<td>row 27, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 28, cell 1</td>
+
<td>n<sub>2</sub></td>
-
<td>row 28, cell 2</td>
+
<td>0.8</td>
-
<td>row 28, cell 3</td>
+
<td>Hill coefficient</td>
-
<td>row 28, cell 4</td>
+
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td>
</tr>
</tr>
<tr>
<tr>
-
<td>row 29, cell 1</td>
+
<td>k<sub>GFP</sub></td>
-
<td>row 29, cell 2</td>
+
<td> 0.0375 </td>
-
<td>row 29, cell 3</td>
+
<td>Hydrolases basal expression</td>
-
<td>row 29, cell 4</td>
+
<td>estimated</td>
-
</tr>
+
-
<tr>
+
-
<td>row 29, cell 1</td>
+
-
<td>row 29, cell 2</td>
+
-
<td>row 29, cell 3</td>
+
-
<td>row 29, cell 4</td>
+
</tr>
</tr>
 +
</table>
</table>
-
</hmtl>
+
</html>
 +
 
 +
<h1>References</h1>
 +
 
 +
<html><a id="Basu2005" class="frog"></a></html>
 +
<br>
 +
 
 +
<p>Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R.; <i>Nature</i>; 2005 Apr; 434: 1130-1134. <br>
 +
<i>A synthetic multicellular system for programmed pattern formation</i>.
 +
[http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html Nature]</p>
 +
<br>
 +
 
 +
<html><a id="Corish1999" class="frog"></a></html>
 +
<p>Corish P, Tyler-Smith C; <i>Protein Engineering</i>. 199; 12(12): 1053-1040. <br>
 +
<i>Attenuation of green fluorescent protein half-life in mammalian cells.</i>
 +
[http://peds.oxfordjournals.org/content/12/12/1035.full peds]</p>
 +
<br>
 +
 
 +
<html><a id="Farias2007" class="frog"></a></html>
 +
<p> Farias T, Mandrich L, Rossi M, Manco G; Protein Pept Lett. 2007; 14(2):165-9.
 +
<i>Biochemical and thermostability features of acetyl esterase Aes from Escherichia coli.</i>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/17305603 PubMed] </p>
 +
<br>
 +
 
 +
<html><a id="Fatin2004" class="frog"></a></html>
 +
<p>Fatin-Rouge N., Starchev K., Buffle J.; <i>Biophysical Journal</i>. 2004 May; 86:2710–2719.<br>
 +
<i>Size Effects on Diffusion Processes within Agarose Gels</i>
 +
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304142/ PMC]</p>
 +
<br>
 +
 
 +
<html><a id="Garcia2004" class="frog"></a></html>
 +
<p> Garcia-Ojalvo J., Elowitz M.B., Strogatz S.H.; <i>PNAS</i>; 2004 Jul; 101(30): 10955–10960. <br>
 +
<i>Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing. </i>
 +
[http://www.pnas.org/content/101/30/10955.long PNAS]</p>
 +
<br>
 +
 
 +
<html><a id="Horswill2007" class="frog"></a></html>
 +
<p>Horswill A.R., Stoodley P., Stewart P.S., Parsek M.R.; <i> Anal Bioanal Chem</i>.; 2007 Jan; 387(2): 371–380.<br>
 +
<i>The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities. </i>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797063/ PMC] </p>
 +
<br>
 +
 
 +
<html><a id="Jefferson1995" class="frog"></a></html>
 +
<p> Jefferson RA; US 5432081 A. 1995 Jul.
 +
<i>Host cells transformed with the ''E. coli'' glucoronide permease gene</i> </p>
 +
<br>
 +
 
 +
<html><a id="Manefield2002" class="frog"></a></html>
 +
<p>Manefield M., Rasmussen T.B., Henzter M., Andersen J.B., Steinberg P., Kjelleberg S., Givskov M.; <i>Microbiology </i>. 2002 Apr; 148(4):1119-1127<br>
 +
<i>Halogenated furanones inhibit quorum sensing through accelerated LuxR turnover</i>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/11932456 PubMed]</p>
 +
<br>
 +
 
 +
<html><a id="Stewart2003" class="frog"></a></html>
 +
<p>Stewart P.S.;<i> Journal of Bacteriology</i>; 2003 Mar.; 185(5): 1485-1491. <br>
 +
<i>Diffusion in Biofilms.</i>
 +
[http://jb.asm.org/content/185/5/1485.full JB]</p>
 +
 
 +
<br clear="all"/>
 +
 
 +
<br clear="all"/>
 +
{{:Team:ETH_Zurich/templates/footer}}

Latest revision as of 00:27, 29 October 2013

Header2.png
80px-Eth igem logo.png

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]



Retrieved from "http://2013.igem.org/Team:ETH_Zurich/Parameter"