Team:Waterloo/Math Book

From 2014.igem.org

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  <p>Our <b>Math Book</b> is meant to be the mathematical modeling equivalent of a lab book, where we store everything another team might need to recreate our models. You can access code related to the models can be accessed from <a href="https://github.com/alexanian/uwaterloo-igem-2014">this GitHub page</a>.</p>
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<h3>We hope you enjoy learning more about our model on the subpages!</h3>
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<p>We created mathematical models of the three main aspects of the Staphylocide system: <a href="https://2014.igem.org/Team:Waterloo/Math_Book/CRISPRi">CRISPR Interference</a>, <a href="https://2014.igem.org/Team:Waterloo/Math_Book/sRNA">RNA Interference</a> and <a href="https://2014.igem.org/Team:Waterloo/Math_Book/Conjugation">Conjugation</a> and have created sub-pages for each of them that detail all the steps in our analysis.</p>
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<p>&nbsp;</p>
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     <li list-style-type="none"><a href="#view0">CRISPR</a></li>
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     <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/CRISPRi">CRISPRi</a></li>
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     <li><a href="#view1">sRNA</a></li>
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    <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/sRNA">RNAi</a></li>
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     <li><a href="#view2">Conjugation</a></li>
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     <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/Conjugation">Conjugation</a></li>
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     <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/References">Bibliography</a></li>
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  This page gathers the detailed process information for the mathematical models created by the team this year. Code related to the models can be accessed from <a href="https://github.com/alexanian/uwaterloo-igem-2014">this github page</a>.
 
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<!------------------- CRISPR SECTION --------------------------------->
 
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      <h2>CRISPR</h2>
 
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      <p>We decided to create a model of the CRISPR system for two main reasons:</p>
 
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      <li style="list-style-type: circle;">Identifying the parts of the network that could be targeted by our lab team to improve repression efficiency</li>
 
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      <li style="list-style-type: circle;">To approximate time-series <em>mecA</em> repression data for use in modelling the overall vulnerability of a <em>S. aureus</em> population</li>
 
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      <h3> Model Formation </h3>
 
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<p>After a literature review we were able to construct the CRISPR interference system network. The targeted single guide RNA (sgRNA) associates with nuclease-deficient Cas9 protein (dCas9) to form a complex that binds with the DNA complementary to the sgRNA target <cite ref="Qi2013"></cite>. The bound complex prevents transcription elongation by RNA polymerase, repressing YFP mRNA expression <cite ref="Bikard2013"></cite>. The chemical network is shown below:</p>
 
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<img src="https://static.igem.org/mediawiki/2014/c/c9/CRISPRNetwork.png" alt="CRISPR Network Diagram" />
 
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<p>Using standard mass-action kinetics, the network simplifies into the following set of differential equations:</p>
 
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          <h4> Modelling Incomplete Repression </h4>
 
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      <h3> Parameters </h3>
 
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          <h4> Production of dCas9 from dCas9 mRNA </h4>
 
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          <h4> Degradation rate of dCas9 </h4>
 
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          <h4> mRNA production from the <em>sarA</em> promoter </h4>
 
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      <h3> Initial Model Results </h3>
 
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      <h3> Updating mRNA Production Rates </h3>
 
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      <h3> Sensitivity Analysis </h3>
 
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<!------------------- CONJUGATION SECTION --------------------------------->
 
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      <h2>sRNA</h2>
 
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      <h3> Relevant Biology </h3>
 
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      <h3> Model Formation </h3>
 
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      <h3></h3>
 
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    </div>
 
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<!------------------- CONJUGATION SECTION --------------------------------->
 
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    <div class="anchor" id="view2">
 
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      <h2>Conjugation</h2>
 
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    </div>
 
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Latest revision as of 23:07, 21 November 2014

Math Book

Our Math Book is meant to be the mathematical modeling equivalent of a lab book, where we store everything another team might need to recreate our models. You can access code related to the models can be accessed from this GitHub page.

We hope you enjoy learning more about our model on the subpages!

We created mathematical models of the three main aspects of the Staphylocide system: CRISPR Interference, RNA Interference and Conjugation and have created sub-pages for each of them that detail all the steps in our analysis.

 

Retrieved from "http://2014.igem.org/Team:Waterloo/Math_Book"