Team:ETH Zurich/modeling/whole

From 2014.igem.org

(Difference between revisions)
m (Ideal case)
m
Line 268: Line 268:
<!--[[File:ETHZ_00TerminatorwithLeakiness.png|center|500px|thumb|No inputs and only basal leakiness]]-->
<!--[[File:ETHZ_00TerminatorwithLeakiness.png|center|500px|thumb|No inputs and only basal leakiness]]-->
-
<!--The figure above summarises the predicted effect of basal leakiness on the flipping of the terminator. The basal leakiness results in production of Bxb1 and ΦC31 which result in flipping of the terminator. In this case, since the cell produces LasI there is increased production of LasAHL. The LasAHL produced induces the production of ΦC31 which further causes flipping of all terminators flanked by the ΦC31 sites. Thus, by 200 minutes almost all ΦC31 sites are inactive and the cell will stay ON. -->
+
<!--The figure above summarizes the predicted effect of basal leakiness on the flipping of the terminator. The basal leakiness results in production of Bxb1 and ΦC31 which result in flipping of the terminator. In this case, since the cell produces LasI there is increased production of LasAHL. The LasAHL produced induces the production of ΦC31 which further causes flipping of all terminators flanked by the ΦC31 sites. Thus, by 200 minutes almost all ΦC31 sites are inactive and the cell will stay ON. -->
-
However, if we measure the fluorescence at around 400 mins, we observe a good and acceptable XOR behaviour. Therefore, one of the solutions we propose is to kill or freeze the cells in each row after 6.5 hours.  
+
However, if we measure the fluorescence at around 400 mins, the effect of leakiness becomes negligible: in the case with null inputs, the level of the output concentration, GFP, is negligible compared to the level of the GFP concentration produced when the cell receives only one type of AHL. At this point, our model behaves like an XOR gate. Therefore, one of the solutions we propose is to kill or freeze the cells in each row after 6.5 hours.  
<!-- Alternatively, we propose a modified construct, where production of LasI is regulated by a weaker promoter and is induced by a protein, whose production is coupled with production of GFP. -->
<!-- Alternatively, we propose a modified construct, where production of LasI is regulated by a weaker promoter and is induced by a protein, whose production is coupled with production of GFP. -->
-
Initially from our model we observed that the feedback was rapid and hence, the amplification was much higher. However, from literature <sup>[[Team:ETH_Zurich/project/references|[9]]]</sup> we see that the XOR module is relatively slow. We were able to correct this by modelling transcription and translation steps. The delay introduced seems more reliable although we do not have our own experimental data to validate the same. Further, we use a dilution factor (DF) which represents the density of the cells in the bead. By choosing and appropriate DF we can get a more delayed response.
+
Initially from our model we observed that the feedback was rapid and hence, the amplification was much higher. However, from literature <sup>[[Team:ETH_Zurich/project/references|[9]]]</sup> we see that the XOR module is relatively slow. We were able to correct this by modelling transcription and translation steps. The delay introduced seems more realistic although we do not have our own experimental data to validate the same. Further, we use a dilution factor (DF) which represents the density of the cells in the bead. By choosing and appropriate DF we can get a more delayed response.
$$DF = \frac{No. of cells * V_{E.coli}}{V_{Bead}}$$
$$DF = \frac{No. of cells * V_{E.coli}}{V_{Bead}}$$
Line 298: Line 298:
<br/>
<br/>
<br/>
<br/>
-
Here, we present the simulation results. The four possibilities of the XOR gate are presented in the following figure. The system was the one with a feedback corresponding to the metabolite pathway. The metabolite parameter taken was the one of xylose, which is supposed to be generic for all models
+
Here, we present the simulation results. The four possibilities of the XOR gate are presented in the following figure. The system was the one with a feedback corresponding to the metabolite pathway.
<br/>
<br/>
<br/>
<br/>

Revision as of 09:49, 17 October 2014

iGEM ETH Zurich 2014