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

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<html>   
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<body>
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    <ul class="menu" id="outline">
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        <li class="outline_item"><a href="#systemoverview">System Overview</a></li>
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        <!--
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        -->
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        <li class="outline_item"><a href="#geneticcircuit">Genetic Circuit</a></li>
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    </ul>
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    <div class="sec white" id="systemoverview"><h1>System Overview</h1>
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        <div>
  
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<div class="sec blue"><h2>Wiki under construction</h2></div>
 
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<div class="column full_size judges-will-not-evaluate">
 
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<h3>★  ALERT! </h3>
 
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<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Awards#Special_Prizes"> design special prize</a>. </p>
 
  
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            <div class="sec white">
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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
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                    promoter.
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                </p>
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            </div>
  
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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            <div class="sec white">
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</div>
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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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                </p>
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            </div>
  
  
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        </div>
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    </div>
  
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<div class="column full_size">
 
  
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    <div class="sec light_grey" id="geneticcircuit"><h1>Genetic circuit</h1>
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        <div>
  
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<p>
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        <div class="sec light_grey">
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By talking about your design work on this page, there is one medal criterion that you can attempt to meet, and one award that you can apply for. If your team is going for a gold medal by building a functional prototype, you should tell us what you did on this page.
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                <h2>NO sensor</h2>
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</p>
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                <p>
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                    In the absence of AHL, EsaR is constitutively produced, dimerizes and bind as a dimer to the esaBox situated downstream the
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                    promoter, preventing transcription as a roadblock. When a higher than normal amount of AHL is present
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                    in the gut, it binds to the EsaR dimer, and free the promoter, allowing transcription. Later on, several
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                    EsaBox can be added, in order to tune the sensor sensitivity.
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                </p>
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            </div>
  
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            <div class="sec light_grey">
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                <h2>AHL sensor</h2>
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                <p>
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                    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>
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            </div>
  
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<p>This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.</p>
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            <div class="sec light_grey">
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                <h2>Lactate sensor</h2>
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                <p>
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                    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>
  
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<p>
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            <div class="sec light_grey">
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If you are working on art and design as your main project, please join the art and design track. If you are integrating art and design into the core of your main project, please apply for the award by completing this page.
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                <h2>AND GATE</h2>
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</p>
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                <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">
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                <h2>Switch Module</h2>
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                <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>
  
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<p>Teams who want to focus on art and design should be in the art and design special track. If you want to have a sub-project in this area, you should compete for this award.</p>
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            <div class="sec light_grey">
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</div>
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                <h2>Reporter Module</h2>
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                <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>
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            </div>
  
 +
            <p>
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                We assume a very fast dimerization of EsaR
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          </p>
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        </div>
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    </div>
 +
 +
    </body>
 
</html>
 
</html>
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{{:Template:ETH_Zurich/footer}}
 

Revision as of 14:55, 12 September 2016

PAVLOV'S COLI

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