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− | {{ETH_Zurich}} | + | {{ETH_Zurich}} {{:Template:ETH_Zurich/math}} |
− | <html> | + | <html> |
+ | <body> | ||
+ | <ul class="menu" id="outline"> | ||
+ | <li class="outline_item"><a href="#systemoverview">System Overview</a></li> | ||
+ | <!-- | ||
+ | --> | ||
+ | <li class="outline_item"><a href="#geneticcircuit">Genetic Circuit</a></li> | ||
+ | <!-- | ||
+ | --> | ||
+ | </ul> | ||
+ | |||
+ | <div class="sec white" id="systemoverview"><h1>System Overview</h1> | ||
+ | <div> | ||
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− | |||
− | |||
− | |||
+ | <div class="sec white"> | ||
+ | <h2>Motivation</h2> | ||
+ | <p> | ||
+ | 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. | ||
+ | </p> | ||
+ | </div> | ||
− | < | + | <div class="sec white"> |
− | </div> | + | <h3>Assumption</h3> |
+ | <p> 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: | ||
+ | </p> | ||
+ | </div> | ||
+ | </div> | ||
+ | </div> | ||
− | |||
+ | <div class="sec light_grey" id="geneticcircuit"><h1>Genetic circuit</h1> | ||
+ | <div> | ||
− | <p> | + | <div class="sec light_grey"> |
− | + | <h2>NO sensor</h2> | |
− | </p> | + | <p> |
+ | 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. | ||
+ | </p> | ||
+ | </div> | ||
+ | <div class="sec light_grey"> | ||
+ | <h2>AHL sensor</h2> | ||
+ | <p> | ||
+ | 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. | ||
+ | </p> | ||
+ | </div> | ||
− | <p> | + | <div class="sec light_grey"> |
+ | <h2>Lactate sensor</h2> | ||
+ | <p> | ||
+ | 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. | ||
+ | </p> | ||
+ | </div> | ||
− | <p> | + | <div class="sec light_grey"> |
− | + | <h2>AND GATE</h2> | |
− | </p> | + | <p> |
+ | 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. | ||
+ | </p> | ||
+ | </div> | ||
+ | <div class="sec light_grey"> | ||
+ | <h2>Switch Module</h2> | ||
+ | <p> | ||
+ | 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. | ||
+ | </p> | ||
+ | </div> | ||
− | <p> | + | <div class="sec light_grey"> |
− | </div> | + | <h2>Reporter Module</h2> |
+ | <p> | ||
+ | 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. | ||
+ | </p> | ||
+ | </div> | ||
+ | <div class="sec light_grey"> | ||
+ | <h4>Assumption</h4> | ||
+ | </div> | ||
+ | <p> | ||
+ | We assume a very fast dimerization of EsaR | ||
+ | </p> | ||
+ | </div> | ||
+ | </div> | ||
+ | |||
+ | </body> | ||
</html> | </html> | ||
− |
Revision as of 14:55, 12 September 2016
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
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