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| | <div id="MathBook" class="content"> | | <div id="MathBook" class="content"> |
| | <div class="tabcontents"> | | <div class="tabcontents"> |
| - | <p>Our <b>Math Book</b> is meant to be the mathematical modelling equivelent 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> | + | <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> |
| - | <p>We modelled 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">silencing RNA</a> and <a href="https://2014.igem.org/Team:Waterloo/Math_Book/Conjugation">Conjugation</a>.</p>
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| | <h3>We hope you enjoy learning more about our model on the subpages!</h3> | | <h3>We hope you enjoy learning more about our model on the subpages!</h3> |
| | + | <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> |
| | <p> </p> | | <p> </p> |
| | <ul class="tabs"> | | <ul class="tabs"> |
| - | <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/CRISPRi">CRISPR</a></li> | + | <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/CRISPRi">CRISPRi</a></li> |
| - | <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/sRNA">sRNA</a></li> | + | <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/sRNA">RNAi</a></li> |
| | <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/Conjugation">Conjugation</a></li> | | <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/Conjugation">Conjugation</a></li> |
| | + | <li><a href="https://2014.igem.org/Team:Waterloo/Math_Book/References">Bibliography</a></li> |
| | </ul> | | </ul> |
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| - | <!------------------- sRNA SECTION --------------------------------->
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| - | <div class="anchor" id="view1">
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| - | <h2>sRNA</h2>
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| - | <p>Bacterial small RNAs (sRNA) are non-coding RNA molecules produced by bacteria. The role of sRNA in bacterial physiology is extremely diverse; they can either bind to protein targets, and modify the function of the bound protein, or bind to mRNA targets and regulate gene expression. Antisense sRNAs can be categorised as cis-encoded sRNAs, where there is an overlap between the antisense sRNA and the target gene, and trans-encoded sRNAs, where the antisense sRNA gene is separate from the target gene.</p>
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| - | <h3> Relevant Biology </h3>
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| - | The model is based on sRNAs that bind to the chaperone protein, Hfq. Hfq binds to sRNA, forming a complex. This complex then binds to mRNA and promotes degradation of both the mRNA and sRNA in a stoichiometric manner. Mechanistically, the Hfq-mRNA-sRNA complex is broken down by a <b>degradosome</b>, a complex of proteins where the protein RNAse E is the centerpiece~\cite{aiba2007mechanism}. The important thing to note here is that the order is <b>compulsory</b>.</p>
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| - | <p>We can also assume that binding of mRNA to sRNA doesn't happen on its own, which Professor Scott and myself talked about. Some papers seem to suggest that it does, others note the requirement for Hfq.</p>
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| - | <p>In some cases Hfq is actually part of the degradosome, for example in SgrS regulation, and sometimes its not, in the case of RyhB. Both SrgS and RyhB are names for specific sRNA that regulate different metabolic pathways; RyhB is responsible for regulating iron metabolism in <em>E. coli</em>, SrgS is responsible for handling glucose-phosphate stress (a rapid increase in glucose-6-phosphate, a precursor to glycolysis). This changes the mechanism quite a bit, however, for the purposes of this model, I'm going to assume that our sRNA suppression style is more akin to RyhB - although we really should look into this.</p>
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| - | <p>Our previous models haven't considered the fact that sRNA gets degraded with the mRNA by the degradosome simultaneously. This new formulation is that assumptions' reckoning.</p>
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| - | <h3> Model Formation </h3>
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| - | <p>The model of chemical network is shown below. Before writing this out as a system of equations, I want to describe what's happening first. We are tracking the concentrations of seven species: <code>s, m, M, h, H, H<sub>s</sub> and H<sub>ms</sub></code>, representing the sRNA, the mRNA, the target protein, Hfq mRNA, Hfq, Hfq-sRNA complex, and Hfq-sRNA-mRNA complex respectively.</p>
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| - | <h3></h3>
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| - | </div>
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| - |
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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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| - | <h3>ABM</h3>
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| - | <img src="https://static.igem.org/mediawiki/2014/e/e2/Waterloo_Wiki_ABM_sufficient_0h.png" alt="ABM 0h">
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| - | <img src="https://static.igem.org/mediawiki/2014/0/09/Waterloo_wiki_ABM_sufficient_6h.png" alt="ABM 6h">
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| - | <img src="https://static.igem.org/mediawiki/2014/f/f0/Waterloo_wiki_ABM_sufficient_12h.png" alt="ABM 12h">
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| - | <img src="https://static.igem.org/mediawiki/2014/0/0e/Waterloo_wiki_ABM_sufficient_18h.png" alt="ABM 18h">
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| - | <img src="https://static.igem.org/mediawiki/2014/4/4a/Waterloo_wiki_ABM_sufficient_24h.png" alt="ABM 24h">
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| - | <img src="https://static.igem.org/mediawiki/2014/2/21/Waterloo_wiki_ABM_sufficient_plot_n10.png" alt="ABM Plot n=10">
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| - | <img src="https://static.igem.org/mediawiki/2014/9/95/Waterloo_wiki_ABM_sufficient_plot_n100.png" alt="ABM Plot n=100">
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| - | </div>
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| | </div> | | </div> |
| | </div> | | </div> |
| | </html> | | </html> |
| - | {{Template:Team:Waterloo/Modeling/Citations}}
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| | {{Template:Team:Waterloo/Footbar}} | | {{Template:Team:Waterloo/Footbar}} |
| | {{Template:Team:Waterloo/JS/baseWiki}} | | {{Template:Team:Waterloo/JS/baseWiki}} |
| | {{Template:Team:Waterloo/JS/CiteTag}} | | {{Template:Team:Waterloo/JS/CiteTag}} |
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.
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