Difference between revisions of "Team:ETH Zurich/Design"

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                In the absence of NO, NorR is produced constitutively and binds repressively to the PnorV promoter, preventing gene transcription.
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                When NO is present in the medium, it binds cooperatively to the hexameric form of NorR,and activate the promoter.
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            <p> We considered here that the binding of NO to NorR and PnorV_{i} does not affect the other species binding. Thus
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                the reactions \begin{align*} NorR+NO&amp;\rightleftharpoons NorR_{NO}\\ \end{align*} and \begin{align*} PnorV_{NorR}+NO&amp;\rightleftharpoons
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                NorR_{NO}\\ \end{align*} have the same reaction rate. Under those assumption, the system of equation can
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                thus be simplified as follows:
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                <p><b>Figure 1:</b> System Overview</p>
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Revision as of 08:52, 13 September 2016

PAVLOV'S COLI

Abstract View

Figure 1: System Overview

Motivation

In the absence of NO, NorR is produced constitutively and binds repressively to the PnorV promoter, preventing gene transcription. When NO is present in the medium, it binds cooperatively to the hexameric form of NorR,and activate the promoter.

Assumption

We considered here that the binding of NO to NorR and PnorV_{i} does not affect the other species binding. Thus the reactions \begin{align*} NorR+NO&\rightleftharpoons NorR_{NO}\\ \end{align*} and \begin{align*} PnorV_{NorR}+NO&\rightleftharpoons NorR_{NO}\\ \end{align*} have the same reaction rate. Under those assumption, the system of equation can thus be simplified as follows:

System Overview

Figure 1: System Overview

Motivation

In the absence of NO, NorR is produced constitutively and binds repressively to the PnorV promoter, preventing gene transcription. When NO is present in the medium, it binds cooperatively to the hexameric form of NorR,and activate the promoter.

Assumption

We considered here that the binding of NO to NorR and PnorV_{i} does not affect the other species binding. Thus the reactions \begin{align*} NorR+NO&\rightleftharpoons NorR_{NO}\\ \end{align*} and \begin{align*} PnorV_{NorR}+NO&\rightleftharpoons NorR_{NO}\\ \end{align*} have the same reaction rate. Under those assumption, the system of equation can thus be simplified as follows:

Genetic circuit

Figure 1: System Overview

NO sensor

In the absence of AHL, EsaR is constitutively produced, dimerizes and bind as a dimer to the esaBox situated downstream the promoter, preventing transcription as a roadblock. When a higher than normal amount of AHL is present in the gut, it binds to the EsaR dimer, and free the promoter, allowing transcription. Later on, several EsaBox can be added, in order to tune the sensor sensitivity.

AHL sensor

In the absence of AHL, EsaR is constitutively produced, dimerizes and bind as a dimer to the esaBox situated downstream the promoter, preventing transcription as a roadblock. When a higher than normal amount of AHL is present in the gut, it binds to the EsaR dimer, and free the promoter, allowing transcription. Later on, several EsaBox can be added, in order to tune the sensor sensitivity.

Lactate sensor

In the absence of AHL, EsaR is constitutively produced, dimerizes and bind as a dimer to the esaBox situated downstream the promoter, preventing transcription as a roadblock. When a higher than normal amount of AHL is present in the gut, it binds to the EsaR dimer, and free the promoter, allowing transcription. Later on, several EsaBox can be added, in order to tune the sensor sensitivity.

AND GATE

In the absence of AHL, EsaR is constitutively produced, dimerizes and bind as a dimer to the esaBox situated downstream the promoter, preventing transcription as a roadblock. When a higher than normal amount of AHL is present in the gut, it binds to the EsaR dimer, and free the promoter, allowing transcription. Later on, several EsaBox can be added, in order to tune the sensor sensitivity.

Switch Module

In the absence of AHL, EsaR is constitutively produced, dimerizes and bind as a dimer to the esaBox situated downstream the promoter, preventing transcription as a roadblock. When a higher than normal amount of AHL is present in the gut, it binds to the EsaR dimer, and free the promoter, allowing transcription. Later on, several EsaBox can be added, in order to tune the sensor sensitivity.

Reporter Module

In the absence of AHL, EsaR is constitutively produced, dimerizes and bind as a dimer to the esaBox situated downstream the promoter, preventing transcription as a roadblock. When a higher than normal amount of AHL is present in the gut, it binds to the EsaR dimer, and free the promoter, allowing transcription. Later on, several EsaBox can be added, in order to tune the sensor sensitivity.

We assume a very fast dimerization of EsaR