Team:ETH Zurich/modeling/whole

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From our experimental data, we observed some basal leakiness for P<sub>Lux</sub> and P<sub>Las</sub> even after using riboregulators. From the model we see that, this small basal leakiness is amplified downstream. The basal leakiness results in production of integrases which further act on the XOR module and cause the switching of the terminator. Thus, there is GFP and LasI produced, and the LasI produced further catalyses the production of more LasAHL. Thus, we observe some GFP even without inputs.  
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From our experimental data, we observed some basal leakiness for P<sub>Lux</sub> and P<sub>Las</sub> even after using riboregulators. From the model we see that, this small basal leakiness is amplified downstream. The basal leakiness results in production of integrases which further act on the XOR module and cause the switching of the terminator. Thus, there is GFP and LasI produced, and the LasI produced further catalyses the production of more LasAHL. Thus, we observe some GFP even without inputs.
<!--[[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]]-->
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<!--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 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. -->
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However, if we measure the fluorescence at around 300 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 3 hours.  
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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.  
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<!-- 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. -->
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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.
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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.
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$$DF = \frac{No. of cells * V_{E.coli}}{V_{Bead}}$$
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<html><article id="Alternate"></html>
<html><article id="Alternate"></html>
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== Alternate Design ==
== Alternate Design ==

Revision as of 04:31, 17 October 2014

iGEM ETH Zurich 2014