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Team:Waterloo/Math Book
From 2014.igem.org
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| - | <li><a href="#view0">CRISPR</a></li> | + | <li list-style-type="none"><a href="#view0">CRISPR</a></li> |
<li><a href="#view1">sRNA</a></li> | <li><a href="#view1">sRNA</a></li> | ||
<li><a href="#view2">Conjugation</a></li> | <li><a href="#view2">Conjugation</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>. | 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>. | ||
| + | |||
| + | <!------------------- CRISPR SECTION ---------------------------------> | ||
<div class="anchor" id="view0"> | <div class="anchor" id="view0"> | ||
<h2>CRISPR</h2> | <h2>CRISPR</h2> | ||
<p>We decided to create a model of the CRISPR system for two main reasons:</p> | <p>We decided to create a model of the CRISPR system for two main reasons:</p> | ||
<ul> | <ul> | ||
| - | + | <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> | |
| - | + | <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> | |
</ul> | </ul> | ||
<h3> Model Formation </h3> | <h3> Model Formation </h3> | ||
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<h3> Sensitivity Analysis </h3> | <h3> Sensitivity Analysis </h3> | ||
</div> | </div> | ||
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| + | <!------------------- CONJUGATION SECTION ---------------------------------> | ||
<div class="anchor" id="view1"> | <div class="anchor" id="view1"> | ||
<h2>sRNA</h2> | <h2>sRNA</h2> | ||
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</div> | </div> | ||
| + | |||
| + | <!------------------- CONJUGATION SECTION ---------------------------------> | ||
<div class="anchor" id="view2"> | <div class="anchor" id="view2"> | ||
<h2>Conjugation</h2> | <h2>Conjugation</h2> | ||
Revision as of 04:10, 17 October 2014
Math Book
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 this github page.
CRISPR
We decided to create a model of the CRISPR system for two main reasons:
- Identifying the parts of the network that could be targeted by our lab team to improve repression efficiency
- To approximate time-series mecA repression data for use in modelling the overall vulnerability of a S. aureus population
Model Formation
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 . The bound complex prevents transcription elongation by RNA polymerase, repressing YFP mRNA expression . The chemical network is shown below:
Using standard mass-action kinetics, the network simplifies into the following set of differential equations:
