Team:ETH Zurich/modeling/whole

From 2014.igem.org

(Difference between revisions)
(With Leakiness and Crosstalk)
(With Leakiness and Crosstalk)
Line 284: Line 284:
=== With Leakiness and Crosstalk ===  
=== With Leakiness and Crosstalk ===  
-
We modelled cross-talk by fitting Hill-functions to experimental data.  For each quorum sensing module, there are two levels of [https://2014.igem.org/Team:ETH_Zurich/expresults cross-talk]. At the first level, we could have any of the two AHLs binding to a given regulator thus activating the promoter while at the second level there is cross talk between regulators. Thus, for activation of a given promoter, we can have four Hill functions corresponding to the combinations of inducer and regulator interactions. Since, we are using two quorum sensing modules activating two different promoters, we have eight Hill functions.  
+
We modelled cross-talk by fitting Hill-functions to experimental data.  For each quorum sensing module, there are two levels of [https://2014.igem.org/Team:ETH_Zurich/expresults cross-talk]. At the first level, we could have any of the two AHLs binding to a given regulator thus activating the promoter while at the second level there is cross talk between regulators and their respective native promoters. Thus, for activation of a given promoter, we can have four Hill functions corresponding to the combinations of inducer and regulator interactions. Since, we are using two quorum sensing modules activating two different promoters, we have eight Hill functions.  
-
 
+
-
Since, all the measurements were in terms of fluorescence, the V<sub>max</sub> for each Hill function was also in terms of fluorescence. In order to observe the effect of cross-talk we normalized the V<sub>max</sub> of non native interactions (in Lux system, P<sub>Lux</sub> being activated by LasAHL-LuxR, LasAHL-LasR or LuxAHL-LasR complexes) with the V<sub>max</sub> of the native interaction (LuxR binding to LuxAHL and activating P<sub>Lux</sub>). The effect of di
+
 +
Since, all the measurements were in terms of fluorescence, the V<sub>max</sub> for each Hill function was also in terms of fluorescence. In order to observe the effect of cross-talk we normalized the V<sub>max</sub> of non native interactions (in Lux system, P<sub>Lux</sub> being activated by LasAHL-LuxR, LasAHL-LasR or LuxAHL-LasR complexes) with the V<sub>max</sub> of the native interaction (LuxR binding to LuxAHL and activating P<sub>Lux</sub>). These ratios acted as weights for the effect of a non-native interaction on the promoter.
 +
For an ideal whole cell model, it was necessary  to have no or minimum leakiness and cross-talk. However, in reality this was not the case. Although we were able to reduce leakiness significantly using riboregulators, we still had the issue of cross-talk. However,

Revision as of 21:47, 17 October 2014

iGEM ETH Zurich 2014