Team:ETH Zurich/Parameter

From 2013.igem.org

(Difference between revisions)
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<td>k<sub>GFP</sub></td>
<td>k<sub>GFP</sub></td>
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<td> 0.025 </td>
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<td> 0.0375 </td>
<td>GFP basal expression</td>
<td>GFP basal expression</td>
<td>estimated</td>
<td>estimated</td>
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-
<td>k<sub>GusA</sub></td>
+
<td>k<sub>leaky</sub></td>
-
<td> 0.025 </td>
+
<td> 0.0375 </td>
<td>GusA basal expression</td>
<td>GusA basal expression</td>
<td>estimated</td>
<td>estimated</td>
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<td>Hill coefficient</td>
<td>Hill coefficient</td>
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td>
<td><a href="https://2013.igem.org/Team:ETH_Zurich/Experiments_5">estimated from experimental data</a></td>
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-
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<td>k<sub>AES</sub></td>
 
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<td> 0.025 </td>
 
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<td>AES basal expression</td>
 
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<td>estimated</td>
 
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</tr>

Revision as of 21:33, 28 October 2013

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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 0.0375 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
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
η2 0.8 Hill coefficient estimated from experimental data

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. Nature


Corish P, Tyler-Smith C; Protein Engineering. 199; 12(12): 1053-1040.
Attenuation of green fluorescent protein half-life in mammalian cells. 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. PubMed


Fatin-Rouge N., Starchev K., Buffle J.; Biophysical Journal. 2004 May; 86:2710–2719.
Size Effects on Diffusion Processes within Agarose Gels 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. 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. 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 PubMed


Stewart P.S.; Journal of Bacteriology; 2003 Mar.; 185(5): 1485-1491.
Diffusion in Biofilms. JB



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