# Team:ETH Zurich/modeling/qs

(Difference between revisions)
 Revision as of 15:50, 17 October 2014 (view source)Eledieu (Talk | contribs)m (→Leakiness)← Older edit Latest revision as of 11:26, 20 July 2015 (view source)Rmeli (Talk | contribs) m (→Data) (11 intermediate revisions not shown) Line 116: Line 116: The same holds true for the Las system. The same holds true for the Las system. - From the original set of reactions, we reduce the rate of production of mRNABxb1 to a Hill function of RLux instead of Mass action kinetics in terms of PLuxON  and PLuxOFF. For more information please check the characterization section. + '''From the original set of reactions, we reduce the rate of production of mRNABxb1 to a Hill function of RLux instead of Mass action kinetics in terms of PLuxON  and PLuxOFF. For more information please check the [http://2014.igem.org/Team:ETH_Zurich/expresults characterization section].''' Line 164: Line 164: - [[File:ETHZ_LuxParameterFitting.png|center|500 px|thumb|Lux QS Module fitted to experimental data from riboregulated Lux system.]] + [[File:ETHZ_LuxParameterFitting.png|center|500 px|thumb|'''Figure 1''' Lux QS Module fitted to experimental data from riboregulated Lux system.]] Line 176: Line 176: respectively. respectively. - [[File:ETHZ_LasParameterFitting.png|center|500 px|thumb|Las QS Module fitted to experimental data from riboregulated Las system.]] + [[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== Line 189: Line 189: - [[File:ETH_Zurich_dGFP_Dynamic.png|500px|center|thumb| Dynamic response of the promoter Plux to a dose entry at time t=0.]] + [[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.]] Line 241: Line 241: - 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 is a construct in its native form, the more impact the riboregulator will have, the more likely it is for the riboregulator to increase the signal over noise ratio/ Our final construct (Promoters with a [http://2014.igem.org/Team:ETH_Zurich/expresults riboregulating system]) have the following parameters. + 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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- [[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.]] + [[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.]]

Line 424: Line 424: === Simulations === === Simulations === - 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. + 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.
{{:Team:ETH Zurich/tpl/foot}} {{:Team:ETH Zurich/tpl/foot}}

## Latest revision as of 11:26, 20 July 2015

iGEM ETH Zurich 2014