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

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     <div class="sec white" id="systemoverview"><h1>System Overview</h1>
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            <h1>System Overview</h1>
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            <div class="image_box" style="max-width: 500px;">
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                <a href="https://2016.igem.org/File:T--ETH_Zurich--GeneticCircuit">
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                    <img src="https://static.igem.org/mediawiki/2016/e/e5/T--ETH_Zurich--GeneticCircuit.svg">
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                <p><b>Figure 1:</b> System Overview</p>
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            <h2>Motivation</h2>
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            <p>
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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>
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        </div>
  
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                <h2>Motivation</h2>
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            <h3>Assumption</h3>
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                <p>
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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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                    In the absence of NO, NorR is produced constitutively and binds repressively to the PnorV promoter, preventing gene transcription.
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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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                    When NO is present in the medium, it binds cooperatively to the hexameric form of NorR,and activate the
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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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                    promoter.
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                 thus be simplified as follows:
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                <h3>Assumption</h3>
 
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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.
 
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                    Thus the reactions \begin{align*} NorR+NO&amp;\rightleftharpoons NorR_{NO}\\ \end{align*} and \begin{align*}
 
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                    PnorV_{NorR}+NO&amp;\rightleftharpoons NorR_{NO}\\ \end{align*} have the same reaction rate. Under those
 
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                    assumption, the system of equation can thus be simplified as follows:
 
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     <div class="sec light_grey" id="geneticcircuit">
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     <div class="sec light_grey" id="geneticcircuit"><h1>Genetic circuit</h1>
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            <h1>Genetic circuit</h1>
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                <a href="https://2016.igem.org/File:T--ETH_Zurich--SystemOverview.svg">
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                    <img src="https://static.igem.org/mediawiki/2016/7/78/T--ETH_Zurich--SystemOverview.svg">
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                </a>
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                <p><b>Figure 1:</b> System Overview</p>
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                 <h2>NO sensor</h2>
 
                 <h2>NO sensor</h2>
 
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                 <p>
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                 We assume a very fast dimerization of EsaR
 
                 We assume a very fast dimerization of EsaR
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Revision as of 16:27, 12 September 2016

PAVLOV'S COLI

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.

Assumption

We assume a very fast dimerization of EsaR