Team:ETH Zurich/modeling/qs

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== Model ==
== Model ==
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The Quorum sensing module is mainly involved in receiving signals from the sender cells. The sender cells secrete some signaling molecules (inducers) which diffuse out of their membrane, then diffuse in receiver cells membrane, and bind to the regulator molecules in the receiver cells, thus activating the transcription of certain genes. In order to characterize the quorum sensing module with a transfer function, we consider different initial inputs of external AHL, and see how much output is produced, as it was done in the [http://2014.igem.org/Team:ETH_Zurich/expresults#Quorum_Sensing quorum sensing experiments].
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The Quorum sensing module is mainly involved in receiving signals from the sender cells. The sender cells produce some signaling molecules (inducers) which diffuse out of their membrane, then diffuse in receiver cells membrane, and bind to the regulator molecules in the receiver cells, thus activating the transcription of certain genes. In order to characterize the quorum sensing module with a transfer function, we consider different initial inputs of external AHL, and see how much output is produced, as it was done in the [http://2014.igem.org/Team:ETH_Zurich/expresults#Quorum_Sensing quorum sensing experiments].
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As diffusion through the membrane is very fast<sup>[[Team:ETH_Zurich/project/references|[27]]]</sup>, according to Fick's law of diffusion, internal and external concentration of AHL can always be considered as equal. This can also be observed in the [http://2014.igem.org/Team:ETH_Zurich/modeling/diffmodel#Results diffusion model results]. When an initial external AHL concentration is given, AHL diffuses in the cells very quickly (less than 20 seconds)<sup>[[Team:ETH_Zurich/project/references|[27]]]</sup> until internal AHL concentration equals external concentration. Then as soon as some internal AHL is consumed in the cell, it is taken up again without affecting external concentration, because external volume is very high compared to internal volume. Therefore we can consider in this module that external AHL (which is equal to internal AHL) only degrades, with the rate of extracellular decay.
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As diffusion through the membrane is very fast<sup>[[Team:ETH_Zurich/project/references|[27]]]</sup>, according to Fick's law of diffusion, internal and external concentration of AHL can always be considered as equal. This can also be observed in the [http://2014.igem.org/Team:ETH_Zurich/modeling/diffmodel#Results diffusion model results]. When an initial external AHL concentration is given, AHL diffuses into the cells very quickly (less than 20 seconds)<sup>[[Team:ETH_Zurich/project/references|[27]]]</sup> until internal AHL concentration equals external concentration. Then as soon as some internal AHL is consumed in the cell, it is taken up again without affecting external concentration, because external volume is very high compared to internal volume. Therefore we can consider in this module that external AHL (which is equal to internal AHL) only degrades, with the rate of extracellular decay.
   
   
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The same holds true for the Las system.
The same holds true for the Las system.
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<strong>From the original set of reactions, we reduce the rate of production of mRNA<sub>Bxb1</sub> as a Hill function of RLux instead of Mass action kinetics in terms of P<sub>LuxON</sub>  and P<sub>LuxOFF</sub>. For more information please check the characterization section.</strong>
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<strong>From the original set of reactions, we reduce the rate of production of mRNA<sub>Bxb1</sub> to a Hill function of RLux instead of Mass action kinetics in terms of P<sub>LuxON</sub>  and P<sub>LuxOFF</sub>. For more information please check the characterization section.</strong>
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=== Simulations ===
=== Simulations ===
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We implemented this solution in our [http://2014.igem.org/Team:ETH_Zurich/modeling#Alternate_Design whole-cell model]. As no parameter is known, we assumed their values to be in the range of standard rates. It gave a possible valid result that could work in our system.
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We implemented this solution in our [http://2014.igem.org/Team:ETH_Zurich/modeling#Alternate_Design whole-cell model]. As no parameter were known, we assumed their values to be in the range of standard rates. It gave a possible valid result that could work in our system.
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Revision as of 09:13, 17 October 2014

iGEM ETH Zurich 2014