http://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&feed=atom&action=historyTeam:Michigan/Modeling - Revision history2024-03-28T23:31:43ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=160635&oldid=prevIfaulknr at 23:59, 21 October 20092009-10-21T23:59:02Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Production of antiholin, under constitutive promoter, is at a constant rate γA, which depends on the promoter that is used.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Production of antiholin, under constitutive promoter, is at a constant rate γA, which depends on the promoter that is used.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Dimerization:''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Dimerization:''</div></td></tr>
</table>Ifaulknrhttp://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=160600&oldid=prevIfaulknr at 23:57, 21 October 20092009-10-21T23:57:56Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Cell Growth/Death</font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Cell Growth/Death</font></B> ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Cell Lysis happens when holin creates pores in the cell membrane, allowing lysozyme to attack the cell wall.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Cell Lysis happens when holin creates pores in the cell membrane, allowing lysozyme to attack the cell wall.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Assume </del>rate of cell death <del class="diffchange diffchange-inline">∝</del>[holin](# cells), rate of cell growth in exponential phase</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Assuming </ins>rate of cell death <ins class="diffchange diffchange-inline">is proportional to </ins>[holin](# cells), rate of cell growth in exponential phase <ins class="diffchange diffchange-inline">is:</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation1.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation1.jpg]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation2.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation2.jpg]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">𝑓([𝑇]) is a function of toluene concentration</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Use Hill Equation to describe binding affinity of toluene to Pu promoter<del class="diffchange diffchange-inline">.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">f([T]) is a function of toluene concentration</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Use <ins class="diffchange diffchange-inline">the </ins>Hill Equation to describe binding affinity of toluene to <ins class="diffchange diffchange-inline">the </ins>Pu promoter<ins class="diffchange diffchange-inline">:</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation3.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation3.jpg]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Transcription of Lysozyme and Holin:</font></B>==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Transcription of Lysozyme and Holin:</font></B>==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Assume transcription rate is proportional to <del class="diffchange diffchange-inline"># </del>of free operator sites (which should be the same for both lysozyme and holin, since they are downstream of the same promoter)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Assume <ins class="diffchange diffchange-inline">the </ins>transcription rate is proportional to <ins class="diffchange diffchange-inline">the number </ins>of free operator sites (which should be the same for both lysozyme and holin, since they are downstream of the same promoter)<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation4.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation4.jpg]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Assume transcription rates for H and L are the same</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Assume transcription rates for H and L are the same<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Repression of Lysozyme and Holin Transcription </font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Repression of Lysozyme and Holin Transcription </font></B> ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Repressor binds with free operator site, preventing transcription of lysozyme and holin.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Repressor binds with free operator site, preventing transcription of lysozyme and holin.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Use a model invoking </del>law of mass action<del class="diffchange diffchange-inline">.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Invoking </ins>law of mass action<ins class="diffchange diffchange-inline">:</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation5.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation5.jpg]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Production of Repressor </font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Production of Repressor </font></B> ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Using the translation rate for R and taking into consideration the binding of R with fops<del class="diffchange diffchange-inline">,</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Using the translation rate for R and taking into consideration the binding of R with fops<ins class="diffchange diffchange-inline">:</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation6.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation6.jpg]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Production of Proteins </font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Production of Proteins </font></B> ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Production of antiholin, under constitutive promoter, is at a constant rate γA, which depends on the promoter that is used</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Production of antiholin, under constitutive promoter, is at a constant rate γA, which depends on the promoter that is used<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Dimerization:''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Dimerization:''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Since holin and antiholin form a complex</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Since holin and antiholin form a complex<ins class="diffchange diffchange-inline">--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation7.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation7.jpg]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Using </del>the translation rates and incorporating dimerization using the law of mass action<del class="diffchange diffchange-inline">,</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">--and using </ins>the translation rates and incorporating dimerization using the law of mass action<ins class="diffchange diffchange-inline">:</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation8.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation8.jpg]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Assumptions</font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Assumptions</font></B> ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Can </del>set γA equal to rate of production of holin in the case that all operating sites are free</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* We can </ins>set γA equal to rate of production of holin in the case that all operating sites are free<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** This is in order to balance antiholin and holin levels without repression</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** ''This can be tuned so that timing of cell death works out''</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** Set antiholin production rate to that of holin in the absence of repression</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** Put this through the transcription and translation equations to obtain production rate</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><ul></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li> This is in order to balance antiholin and holin levels without repression </li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li> ''This can be tuned so that timing of cell death works out'' </li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li> Set antiholin production rate to that of holin in the absence of repression </li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li> Put this through the transcription and translation equations to obtain production rate </li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></ul></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Assume </del>degradation rates of all mRNAs are the same</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* We assume </ins>degradation rates of all mRNAs are the same<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** Can use half life to calculate rate [[Image:Equation9.jpg]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><ul></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li>Can directly search for these rates in literature </li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li>Can use half life to calculate rate [[Image:Equation9.jpg]]</li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></ul></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For protein degradation rate:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For protein degradation rate:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>''Case 1: Proteins are stable:''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>''Case 1: Proteins are stable:''</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** Degradation rates equal reproduction rate of cell</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** This is due to dilution of proteins across daughter cells</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><ul></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* ''Case 2: Proteins are unstable''</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><li>Degradation rates equal reproduction rate of cell </li></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><li>This is due to dilution of proteins across daughter cells </li></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"></ul></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">''Case 2: Proteins are unstable''</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><ul></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li>If not other degradation rate information is provided, can possibly assume that the degradation rates are a few orders of magnitude above the reproduction rate of cell</li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><li>Will have to look into this further</li></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></ul></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Variables and Parameters</font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Variables and Parameters</font></B> ==</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 92:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Further Work</font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Further Work</font></B> ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We plan to run simulations of this model using MATLAB, focusing on the relationship between cell count and toluene concentration. Before this is done, we must find<del class="diffchange diffchange-inline">/</del>estimate values for the parameters listed above. Initial simulations will be tailored to fine-tuning parameters to satisfy the primary needs of the modeling: at high toluene concentrations, the cells will survive; at low toluene concentrations, the cells will die. After that, we will look at low-to-high and high-to-low transitions in toluene concentrations and look for equilibria that arise as a result. This will help us understand how responsive the system is to toluene levels (including initial concentrations).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We plan to run simulations of this model using MATLAB, focusing on the relationship between cell count and toluene concentration. Before this is done, we must find <ins class="diffchange diffchange-inline">or </ins>estimate values for the parameters listed above. Initial simulations will be tailored to fine-tuning parameters to satisfy the primary needs of the modeling: at high toluene concentrations, the cells will survive; at low toluene concentrations, the cells will die. After that, we will look at low-to-high and high-to-low transitions in toluene concentrations and look for equilibria that arise as a result. This will help us understand how responsive the system is to toluene levels (including initial concentrations).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Lastly, a future version of this model will couple the kill switch mechanism with the degradation mechanism. One of the major effects that this will have on the kill switch modeling is that toluene levels will be reduced by the degradation pathway. To understand coupling effect is one of the major goals down the road, as it will help us gain a deeper understanding of the overall dynamics of our proposed project <del class="diffchange diffchange-inline">(i.e. to see the "big picture")</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Lastly, a future version of this model will couple the kill switch mechanism with the degradation mechanism. One of the major effects that this will have on the kill switch modeling is that toluene levels will be reduced by the degradation pathway. To understand coupling effect is one of the major goals down the road, as it will help us gain a deeper understanding of the overall dynamics of our proposed project.</div></td></tr>
</table>Ifaulknrhttp://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=159493&oldid=prevIfaulknr at 23:24, 21 October 20092009-10-21T23:24:24Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Overview</font></B> : ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Overview</font></B> : ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The following mathematical model examines the dynamics of the <del class="diffchange diffchange-inline">suicide mechanism that employed tunable repression</del>. As outlined in the project description, the Pu promoter is placed in front of a repressor system that would inhibit the production of holin and lysozyme, while a constitutive promoter is placed in front of the gene for antiholin. In the presence of toluene, the Pu promoter would be activated, leading to repression of holin/lysozyme production and therefore cell survival. In the absence of toluene, the Pu promoter would not be activated, and as a result holin and lysozyme would be produced, leading to cell death.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The following mathematical model examines the dynamics of the <ins class="diffchange diffchange-inline">Suicide Mechanism with Tunable Repression (see Project Page)</ins>. As outlined in the project description, the Pu promoter is placed in front of a repressor system that would inhibit the production of holin and lysozyme, while a constitutive promoter is placed in front of the gene for antiholin. In the presence of toluene, the Pu promoter would be activated, leading to repression of holin/lysozyme production and therefore cell survival. In the absence of toluene, the Pu promoter would not be activated, and as a result holin and lysozyme would be produced, leading to cell death.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Cell Growth/Death</font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Cell Growth/Death</font></B> ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Cell Lysis happens when holin creates pores in membrane <del class="diffchange diffchange-inline">and </del>lysozyme <del class="diffchange diffchange-inline">enters</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Cell Lysis happens when holin creates pores in <ins class="diffchange diffchange-inline">the cell </ins>membrane<ins class="diffchange diffchange-inline">, allowing </ins>lysozyme <ins class="diffchange diffchange-inline">to attack the cell wall.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assume rate of cell death ∝[holin](# cells), rate of cell growth in exponential phase</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assume rate of cell death ∝[holin](# cells), rate of cell growth in exponential phase</div></td></tr>
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</table>Ifaulknrhttp://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=157343&oldid=prevSudarshan2009 at 22:20, 21 October 20092009-10-21T22:20:38Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Variables_and_Parameters.jpg|center]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Variables_and_Parameters.jpg|center]]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==<B><font size=3>Further Work</font></B> ==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">We plan to run simulations of this model using MATLAB, focusing on the relationship between cell count and toluene concentration. Before this is done, we must find/estimate values for the parameters listed above. Initial simulations will be tailored to fine-tuning parameters to satisfy the primary needs of the modeling: at high toluene concentrations, the cells will survive; at low toluene concentrations, the cells will die. After that, we will look at low-to-high and high-to-low transitions in toluene concentrations and look for equilibria that arise as a result. This will help us understand how responsive the system is to toluene levels (including initial concentrations).</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Lastly, a future version of this model will couple the kill switch mechanism with the degradation mechanism. One of the major effects that this will have on the kill switch modeling is that toluene levels will be reduced by the degradation pathway. To understand coupling effect is one of the major goals down the road, as it will help us gain a deeper understanding of the overall dynamics of our proposed project (i.e. to see the "big picture").</ins></div></td></tr>
</table>Sudarshan2009http://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=156954&oldid=prevSudarshan2009 at 22:06, 21 October 20092009-10-21T22:06:09Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Overview</font></B> : ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Overview</font></B> : ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The following mathematical model examines the dynamics of the suicide mechanism that employed tunable repression. As outlined in the project description, the Pu promoter is placed in front of a repressor system that would inhibit the production of holin and lysozyme, while a constitutive promoter is placed in front of the gene for antiholin. In the presence of toluene, the Pu promoter would be activated, leading to repression of holin/lysozyme production and therefore cell survival. In the absence of toluene, the Pu promoter would not be activated, and as a result holin and lysozyme would be produced, leading to cell death.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td></tr>
</table>Sudarshan2009http://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=156656&oldid=prevSudarshan2009 at 21:56, 21 October 20092009-10-21T21:56:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Variables and Parameters</font></B> ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Variables and Parameters</font></B> ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:<del class="diffchange diffchange-inline">VariablesParameters</del>.jpg|center]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:<ins class="diffchange diffchange-inline">Variables_and_Parameters</ins>.jpg|center]]</div></td></tr>
</table>Sudarshan2009http://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=156560&oldid=prevSudarshan2009 at 21:53, 21 October 20092009-10-21T21:53:29Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Overview</font></B> : ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<B><font size=3>Overview</font></B> : ==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td></tr>
</table>Sudarshan2009http://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=156531&oldid=prevAnnlesn at 21:52, 21 October 20092009-10-21T21:52:31Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assume transcription rates for H and L are the same</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assume transcription rates for H and L are the same</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>== Repression of Lysozyme and Holin Transcription ==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline"><B><font size=3></ins>Repression of Lysozyme and Holin Transcription <ins class="diffchange diffchange-inline"></font></B> </ins>==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Repressor binds with free operator site, preventing transcription of lysozyme and holin.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Repressor binds with free operator site, preventing transcription of lysozyme and holin.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Use a model invoking law of mass action.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Use a model invoking law of mass action.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assuming that fops and Rfops do not undergo spontaneous degradation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assuming that fops and Rfops do not undergo spontaneous degradation.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>== Production of Repressor ==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline"><B><font size=3></ins>Production of Repressor <ins class="diffchange diffchange-inline"></font></B> </ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Using the translation rate for R and taking into consideration the binding of R with fops,</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Using the translation rate for R and taking into consideration the binding of R with fops,</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 49:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation6.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation6.jpg]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>== Production of Proteins ==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline"><B><font size=3></ins>Production of Proteins <ins class="diffchange diffchange-inline"></font></B> </ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Production of antiholin, under constitutive promoter, is at a constant rate γA, which depends on the promoter that is used</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Production of antiholin, under constitutive promoter, is at a constant rate γA, which depends on the promoter that is used</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 62:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation8.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation8.jpg]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>== Assumptions ==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline"><B><font size=3></ins>Assumptions<ins class="diffchange diffchange-inline"></font></B> </ins>==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Can set γA equal to rate of production of holin in the case that all operating sites are free</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Can set γA equal to rate of production of holin in the case that all operating sites are free</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></ul></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></ul></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==Variables and Parameters==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline"><B><font size=3></ins>Variables and Parameters<ins class="diffchange diffchange-inline"></font></B> </ins>==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:VariablesParameters.jpg|center]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:VariablesParameters.jpg|center]]</div></td></tr>
</table>Annlesnhttp://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=154209&oldid=prevAnnlesn at 20:31, 21 October 20092009-10-21T20:31:32Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 20:31, 21 October 2009</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= <font color=royalblue size=6>The Toluene Terminator Model</font> =</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= <font color=royalblue size=6>The Toluene Terminator Model</font> =</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==<B><font size=3>Overview</font></B> : ==</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Kill_switch_topology_for_modeling.jpg|950px]]</div></td></tr>
</table>Annlesnhttp://2009.igem.org/wiki/index.php?title=Team:Michigan/Modeling&diff=154193&oldid=prevAnnlesn at 20:30, 21 October 20092009-10-21T20:30:59Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 20:30, 21 October 2009</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation3.jpg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Equation3.jpg]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==Transcription of Lysozyme and Holin:==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline"><B><font size=3></ins>Transcription of Lysozyme and Holin:<ins class="diffchange diffchange-inline"></font></B></ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assume transcription rate is proportional to # of free operator sites (which should be the same for both lysozyme and holin, since they are downstream of the same promoter)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Assume transcription rate is proportional to # of free operator sites (which should be the same for both lysozyme and holin, since they are downstream of the same promoter)</div></td></tr>
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</table>Annlesn