Team:ETH Zurich/modeling/qs

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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> 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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'''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 [http://2014.igem.org/Team:ETH_Zurich/expresults characterization section].'''
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[[File:ETHZ_LuxParameterFitting.png|center|500 px|thumb|Lux QS Module fitted to experimental data from riboregulated Lux system.]]
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[[File:ETHZ_LuxParameterFitting.png|center|500 px|thumb|'''Figure 1''' Lux QS Module fitted to experimental data from riboregulated Lux system.]]
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respectively.
respectively.
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[[File:ETHZ_LasParameterFitting.png|center|500 px|thumb|Las QS Module fitted to experimental data from riboregulated Las system.]]
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[[File:ETHZ_LasParameterFitting.png|center|500 px|thumb|'''Figure 2''' Las QS Module fitted to experimental data from riboregulated Las system.]]
=== Range of validity of the assumptions ===
=== Range of validity of the assumptions ===
These assumptions hold true for all input LuxAHL and LasAHL concentrations.
These assumptions hold true for all input LuxAHL and LasAHL concentrations.
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== Retrieving degradation rates==
== Retrieving degradation rates==
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[[File:ETH_Zurich_dGFP_Dynamic.png|500px|center|thumb| Dynamic response of the promoter Plux to a dose entry at time t=0.]]
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[[File:ETH_Zurich_dGFP_Dynamic.png|500px|center|thumb| '''Figure 3''' Dynamic response of the promoter Plux to a dose entry at time t=0.]]
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Given this offset and the maximal expression, the signal over noise ratio can be derived. This ratio, which can then be compared amongst all curves, characterizes the impact of leakiness on the behavior of a system. Our final construct (Promoters with a [http://2014.igem.org/Team:ETH_Zurich/expresults riboregulating system]) have the following parameters.
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Given this offset and the maximal expression, the signal over noise ratio can be derived. This ratio, which can then be compared amongst all curves, characterizes the impact of leakiness on the behavior of a system. The leakier a construct in its native form is, the more impact the riboregulator will have, and the more likely it is for the riboregulator to increase the signal over noise ratio. Our final constructs (Promoters with a [http://2014.igem.org/Team:ETH_Zurich/expresults riboregulating system]) have the following parameters:
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%%Insert table%%
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{| class="wikitable"
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|-
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! '''Promoter used'''
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! '''Signal over noise ratio'''
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|-
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|P<sub>Lux</sub> without riboregulating system
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|23
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|-
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|P<sub>Lux</sub> with riboregulating system
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|79
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|-
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|P<sub>Las</sub> without riboregulating system
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|84
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|-
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|P<sub>Las</sub> with riboregulating system
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|55
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|}
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[[File:ETH Zurich Crosstalk.png|1500px|center|thumb|Each quorum sensing system is based on three components: a signaling molecule, a regulatory protein and a promoter. These elements are here ordered into three layers. Cross-talk evaluation can be done by comparing all combinations of those three elements. After collecting the [http://2014.igem.org/Team:ETH_Zurich/expresults experimental data] of all possible pathways, we modeled their influence.]]
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[[File:ETH Zurich Crosstalk.png|1500px|center|thumb|'''Figure 4''' Each quorum sensing system is based on three components: a signaling molecule, a regulatory protein and a promoter. These elements are here ordered into three layers. Cross-talk evaluation can be done by comparing all combinations of those three elements. After collecting the [http://2014.igem.org/Team:ETH_Zurich/expresults experimental data] of all possible pathways, we modeled their influence.]]
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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 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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We implemented this solution in our [[Team:ETH_Zurich/modeling/whole#Alternate_Design|whole-cell model]]. As no parameters were known, we assumed their values to be in the range of standard rates. The results indicate that the system could work, the next step would be to test this prediction experimentally.
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{{:Team:ETH Zurich/tpl/foot}}
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Latest revision as of 11:26, 20 July 2015

iGEM ETH Zurich 2014