http://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&feed=atom&action=historyTeam:Oxford/how much can we degrade - Revision history2024-03-29T13:02:13ZRevision history for this page on the wikiMediaWiki 1.16.5http://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=404719&oldid=prevOlivervince at 09:55, 15 January 20152015-01-15T09:55:25Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>(what are Gompertz functions?)</a>. An example output growth curve of the model is shown here.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>(what are Gompertz functions?)</a>. An example output growth curve of the model is shown here.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The scaling of the growth rate of the Gompertz function comes directly from growth curves of the DM4 bacteria that we obtained in the lab. <del class="diffchange diffchange-inline"><u>See more about our work with growth curves here.</u> </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The scaling of the growth rate of the Gompertz function comes directly from growth curves of the DM4 bacteria that we obtained in the lab.</div></td></tr>
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</table>Olivervincehttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=398108&oldid=prevJHoffman at 03:33, 18 October 20142014-10-18T03:33:38Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">where </del>the <del class="diffchange diffchange-inline">red line is C=0M</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The numerical solution to this differential equation was confirmed by reducing </ins>the <ins class="diffchange diffchange-inline">n interval by a factor of 100, which gave the same result</ins>.</div></td></tr>
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</table>JHoffmanhttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=397035&oldid=prevJHoffman at 03:26, 18 October 20142014-10-18T03:26:33Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1blue2>Using buffers to reduce the pH change of our system</h1blue2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1blue2>Using buffers to reduce the pH change of our system</h1blue2></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have investigated the effect of using buffers in the aqueous part of our system.<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have investigated the effect of using buffers in the aqueous part of our system.<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As a first approximation, we model our system of bacteria turning over DCM, producing HCl, as a chemical system in which HCl immediately enters the 'bulk' (extracellular) solution; in this system we have a single buffer (HEPES) to reduce the drop in pH, maximising the amount of DCM the entire system can degrade before the pH drops below a toxic level. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As a first approximation, we model our system of bacteria turning over DCM, producing HCl, as a chemical system in which HCl immediately enters the 'bulk' (extracellular) solution; in this system we have a single buffer (HEPES) to reduce the drop in pH, maximising the amount of DCM the entire system can degrade before the pH drops below a toxic level. </div></td></tr>
</table>JHoffmanhttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=396986&oldid=prevJHoffman at 03:26, 18 October 20142014-10-18T03:26:16Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1blue2>Using buffers to reduce the pH change of our system</h1blue2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1blue2>Using buffers to reduce the pH change of our system</h1blue2></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have investigated the effect of using buffers in the aqueous part of our system.<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have investigated the effect of using buffers in the aqueous part of our system.<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As a first approximation, we model our system of bacteria turning over DCM, producing HCl, as a chemical system in which HCl immediately enters the 'bulk' (extracellular) solution; in this system we have a single buffer (HEPES) to reduce the drop in pH, maximising the amount of DCM the entire system can degrade before the pH drops below a toxic level. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As a first approximation, we model our system of bacteria turning over DCM, producing HCl, as a chemical system in which HCl immediately enters the 'bulk' (extracellular) solution; in this system we have a single buffer (HEPES) to reduce the drop in pH, maximising the amount of DCM the entire system can degrade before the pH drops below a toxic level. </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;"><br><br></del></div></td><td colspan="2"> </td></tr>
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</table>JHoffmanhttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=395192&oldid=prevJHoffman at 03:15, 18 October 20142014-10-18T03:15:34Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1blue2>Using buffers to reduce the pH change of our system</h1blue2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1blue2>Using buffers to reduce the pH change of our system</h1blue2></div></td></tr>
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<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 have investigated the effect of using buffers in the aqueous part of our system.<br></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;">As a first approximation, we model our system of bacteria turning over DCM, producing HCl, as a chemical system in which HCl immediately enters the 'bulk' (extracellular) solution; in this system we have a single buffer (HEPES) to reduce the drop in pH, maximising the amount of DCM the entire system can degrade before the pH drops below a toxic level. </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;"><br><br></ins></div></td></tr>
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<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;"></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;"><br><br></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;">As one of the products of our reaction is HCl, we have been able to calculate the pH change of the system. However, since a deviation of neutral pH is unfavourable for the bacteria we are working with, we have investigated the effect of using buffers in the aqueous part of our system.</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Derivation of the Van Slyke equation:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Derivation of the Van Slyke equation:</div></td></tr>
</table>JHoffmanhttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=387778&oldid=prevJHoffman at 02:18, 18 October 20142014-10-18T02:18:05Z<p></p>
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</table>JHoffmanhttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=371960&oldid=prevPhillo92 at 00:00, 18 October 20142014-10-18T00:00:19Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>d[Ndcm]/dt = rate of DCM molecule degradation (s-1)</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>d[Ndcm]/dt = rate of DCM molecule degradation (s-1)</li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li><del class="diffchange diffchange-inline">Kcat </del> = dcmA turnover rate (= 0.6 s-1 for DM4)</li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li><ins class="diffchange diffchange-inline">kcat </ins> = dcmA turnover rate (= 0.6 s-1 for DM4)</li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>[DCM] = DCM concentration (= 0.02M for our system)</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>[DCM] = DCM concentration (= 0.02M for our system)</li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>[DcmA] = Number of DcmA molecules per cell (87576) <a href="https://2014.igem.org/Team:Oxford/what_are_microcompartments?#hide4"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>[DcmA] = Number of DcmA molecules per cell (87576) <a href="https://2014.igem.org/Team:Oxford/what_are_microcompartments?#hide4"></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We used our model to predict the response of the system to a change in the kcat value of the DCM degradation enzyme, dcmA. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We used our model to predict the response of the system to a change in the kcat value of the DCM degradation enzyme, dcmA. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Increasing the value of <del class="diffchange diffchange-inline">Kcat </del>by a significant amount is unrealistic in the length of our project. However, in future work, the kcat could potentially be substantially improved. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Increasing the value of <ins class="diffchange diffchange-inline">kcat </ins>by a significant amount is unrealistic in the length of our project. However, in future work, the kcat could potentially be substantially improved. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the graph shown here, the total volume degraded doesn't change. This is because the amount of HCl that the system requires to reach a toxic pH level is constant, as we are not varying the volume of the aqueous layer. To increase the total amount of DCM degraded, we simply need to add more water or a pH buffer to the system.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the graph shown here, the total volume degraded doesn't change. This is because the amount of HCl that the system requires to reach a toxic pH level is constant, as we are not varying the volume of the aqueous layer. To increase the total amount of DCM degraded, we simply need to add more water or a pH buffer to the system.</div></td></tr>
</table>Phillo92http://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=362207&oldid=prevJHoffman at 22:30, 17 October 20142014-10-17T22:30:41Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><h1white>How does the amount of water added <del class="diffchange diffchange-inline">to the system </del>affect the output?</h1white></div></a></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><h1white>How does the amount of water added affect the output?</h1white></div></a></div></td></tr>
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</table>JHoffmanhttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=332882&oldid=prevJHoffman at 16:44, 17 October 20142014-10-17T16:44:28Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><a href="#showwetlab"><div class="orange_news_block1 showwetlab" style="background: #ADD8E6;border-radius:15px;color:black;float:left;height:40%;width:40<del class="diffchange diffchange-inline">%;padding-top:5</del>%;margin-left:3%;<del class="diffchange diffchange-inline">margin</del>-top:<del class="diffchange diffchange-inline">3px</del>;"><center></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><a href="#showwetlab"><div class="orange_news_block1 showwetlab" style="background: #ADD8E6;border-radius:15px;color:black;float:left;height:40%;width:40%;margin-left:3%;<ins class="diffchange diffchange-inline">padding</ins>-top:<ins class="diffchange diffchange-inline">10px</ins>;"><center></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1white><font style="font-size:15px;font-weight:500;">Wetlab</font></h1white></center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1white><font style="font-size:15px;font-weight:500;">Wetlab</font></h1white></center></div></td></tr>
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</table>JHoffmanhttp://2014.igem.org/wiki/index.php?title=Team:Oxford/how_much_can_we_degrade&diff=332818&oldid=prevJHoffman at 16:43, 17 October 20142014-10-17T16:43:32Z<p></p>
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