http://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&feed=atom&action=historyTeam:BGU Israel/Modeling/Aspiration Shift - Revision history2024-03-29T12:06:42ZRevision history for this page on the wikiMediaWiki 1.16.5http://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=374096&oldid=prevPriels at 00:18, 18 October 20142014-10-18T00:18:32Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 style="border-bottom:dashed;border-color:#000000">Simulations Results & Conclusion</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 style="border-bottom:dashed;border-color:#000000">Simulations Results & Conclusion</h3></div></td></tr>
</table>Prielshttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=369186&oldid=prevAmitg at 23:36, 17 October 20142014-10-17T23:36:56Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Assignment of the parameters values we showed above shows that the system will be in a stable stationary point after the introduction of the treatment. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Assignment of the parameters values we showed above shows that the system will be in a stable stationary point after the introduction of the treatment. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p><strong>Regulated vs. Unregulated treatment</strong><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p><strong>Regulated vs. Unregulated treatment</strong><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> The modest expression mechanism has to meet two challenges. First to prevent too much synthesis of PGC-1α, that would make an increment over 80% in its concentration. The second challenge is the need to be very potent in cells with low PGC-1α activity, but to have minimum effect in cells with regular PGC-1α activity. The synthesis of the repressor supposes to meet the first challenge. As we can see in Figure <del class="diffchange diffchange-inline">9</del>, an unregulated mechanism without a repressor would lead to much more production of PGC-1α and could cross to a risk increment. To prove our mechanism produce around 80% of production we should test it in the lab, the model here just illustrate the potential. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> The modest expression mechanism has to meet two challenges. First to prevent too much synthesis of PGC-1α, that would make an increment over 80% in its concentration. The second challenge is the need to be very potent in cells with low PGC-1α activity, but to have minimum effect in cells with regular PGC-1α activity. The synthesis of the repressor supposes to meet the first challenge. As we can see in Figure <ins class="diffchange diffchange-inline">6</ins>, an unregulated mechanism without a repressor would lead to much more production of PGC-1α and could cross to a risk increment. To prove our mechanism produce around 80% of production we should test it in the lab, the model here just illustrate the potential. </p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>To face the second challenge we examined different values of natural rate of production of PGC-1α. We ran the model with different input rates and measured the increment in PGC-1α from its initial value to its final value on steady state (Figure <del class="diffchange diffchange-inline">10</del>).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>To face the second challenge we examined different values of natural rate of production of PGC-1α. We ran the model with different input rates and measured the increment in PGC-1α from its initial value to its final value on steady state (Figure <ins class="diffchange diffchange-inline">7</ins>).</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Figure 8 - The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Figure 8 - The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure <del class="diffchange diffchange-inline">11 </del>we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure <ins class="diffchange diffchange-inline">8 </ins>we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-1α, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-1α, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td></tr>
</table>Amitghttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=368817&oldid=prevAmitg at 23:33, 17 October 20142014-10-17T23:33:55Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">8 </del>- Parameters manipulation in Wolfram Mathematica</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">5 </ins>- Parameters manipulation in Wolfram Mathematica</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Another method for investigation the steady state behavior is the eigenvalues of the corresponding Jacobian matrix of the dynamic system. By defining our system variable as the vector (PGC1αmRNA, PGC1α, REPmRNA, REP), the Jacobian matrix is:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Another method for investigation the steady state behavior is the eigenvalues of the corresponding Jacobian matrix of the dynamic system. By defining our system variable as the vector (PGC1αmRNA, PGC1α, REPmRNA, REP), the Jacobian matrix is:</p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">5 </del>- The threshold located at 80% increment of PGC-1α. The PGC-1α level does not pass the threshold as a result of the regulated treatment, unlike the unregulated treatment</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">6 </ins>- The threshold located at 80% increment of PGC-1α. The PGC-1α level does not pass the threshold as a result of the regulated treatment, unlike the unregulated treatment</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The input level of PGC-1α, in a steady state before the introduction of the plasmids, can be simply determined like this:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The input level of PGC-1α, in a steady state before the introduction of the plasmids, can be simply determined like this:</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png"><img src="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png" style=" height:275px;border:solid;"/></a><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png"><img src="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png" style=" height:275px;border:solid;"/></a><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">6 </del>- For different initial levels of PGC-1α, the treatment increased it in different relative amounts</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">7 </ins>- For different initial levels of PGC-1α, the treatment increased it in different relative amounts</p></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><p>PGC-1α level stabilizes at the steady state of the system. If we give our regulated treatment to people with different natural production rate of PGC-1α from each other, the system stabilizes on different increment. This important feature provides the personalized medicine properties to our regulated treatment we designed.</p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>PGC-1α level stabilizes at the steady state of the system. If we give our regulated treatment to people with different natural production rate of PGC-1α from each other, the system stabilizes on different increment. This important feature provides the personalized medicine properties to our regulated treatment we designed.</p> </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">7 </del>- The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">8 </ins>- The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure 11 we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure 11 we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td></tr>
</table>Amitghttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=368569&oldid=prevAmitg at 23:31, 17 October 20142014-10-17T23:31:58Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/9/9c/BGU14MODEL2glucose_utilisation_vs_pgc1a.png"><img src="https://static.igem.org/mediawiki/2014/9/9c/BGU14MODEL2glucose_utilisation_vs_pgc1a.png" style="height:350px;border:solid"/></a><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/9/9c/BGU14MODEL2glucose_utilisation_vs_pgc1a.png"><img src="https://static.igem.org/mediawiki/2014/9/9c/BGU14MODEL2glucose_utilisation_vs_pgc1a.png" style="height:350px;border:solid"/></a><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure 1 <del class="diffchange diffchange-inline">–Comparison </del>between relative changes in PGC-1α overexpression (%)<br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure 1 <ins class="diffchange diffchange-inline">– Comparison </ins>between relative changes in PGC-1α overexpression (%)<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> and changes in insulin-stimulated glucose utilization (%)</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> and changes in insulin-stimulated glucose utilization (%)</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 68:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; 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><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/d/d9/BGU14MODEL2modelDiagram.png"><img src="https://static.igem.org/mediawiki/2014/d/d9/BGU14MODEL2modelDiagram.png" style="height:215px;border:solid"/></a><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/d/d9/BGU14MODEL2modelDiagram.png"><img src="https://static.igem.org/mediawiki/2014/d/d9/BGU14MODEL2modelDiagram.png" style="height:215px;border:solid"/></a><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure 2 <del class="diffchange diffchange-inline">–The </del>diagram of the model: The blue objects represent the variables and the yellow circles represent the interrelationship between the variables. The treatment comes in the form of the two plasmids, Dp and Dr, that we secrete into the body<br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure 2 <ins class="diffchange diffchange-inline">– The </ins>diagram of the model: The blue objects represent the variables and the yellow circles represent the interrelationship between the variables. The treatment comes in the form of the two plasmids, Dp and Dr, that we secrete into the body<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> A reaction of translation, for example, assumed to have a Michaelis-Menten behavior, when only the DNA transcription factor complex is able to make mRNA. On equation 1.1, the first part demonstrates the synthesis of the PGC-1α mRNA while the repressor acts as an inhibitor.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> A reaction of translation, for example, assumed to have a Michaelis-Menten behavior, when only the DNA transcription factor complex is able to make mRNA. On equation 1.1, the first part demonstrates the synthesis of the PGC-1α mRNA while the repressor acts as an inhibitor.</p></div></td></tr>
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<td colspan="2" class="diff-lineno">Line 91:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/72/BGU14MODEL2fig5.png"><img src="https://static.igem.org/mediawiki/2014/7/72/BGU14MODEL2fig5.png" style=" height:230px;"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/72/BGU14MODEL2fig5.png"><img src="https://static.igem.org/mediawiki/2014/7/72/BGU14MODEL2fig5.png" style=" height:230px;"/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline">Figure 4</del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p><strong>Doses of the treatment</strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p><strong>Doses of the treatment</strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/e/e1/BGU14MODEL2fig6.png"><img src="https://static.igem.org/mediawiki/2014/e/e1/BGU14MODEL2fig6.png" style=" height:62px;"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/e/e1/BGU14MODEL2fig6.png"><img src="https://static.igem.org/mediawiki/2014/e/e1/BGU14MODEL2fig6.png" style=" height:62px;"/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline">Figure 5</del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 118:</td>
<td colspan="2" class="diff-lineno">Line 118:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <a href="https://static.igem.org/mediawiki/2014/5/53/BGU14MODEL2fig8.png"><img src="https://static.igem.org/mediawiki/2014/5/53/BGU14MODEL2fig8.png" style=" height:280px; border:solid; "/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <a href="https://static.igem.org/mediawiki/2014/5/53/BGU14MODEL2fig8.png"><img src="https://static.igem.org/mediawiki/2014/5/53/BGU14MODEL2fig8.png" style=" height:280px; border:solid; "/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">6</del>,<del class="diffchange diffchange-inline">7</del>- The general description of the influence of the two plasmids on the system, while the two plasmids (DP and DR) are added at time=5. The elements of PGC-1α, the active PPARγ and the repressor are rising until a specific value and stay constant at steady state</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">3</ins>, <ins class="diffchange diffchange-inline">4 </ins>- The general description of the influence of the two plasmids on the system, while the two plasmids (DP and DR) are added at time=5. The elements of PGC-1α, the active PPARγ and the repressor are rising until a specific value and stay constant at steady state</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Using Wolfram Mathematica we studied the behavior of the dynamic system. The system showed similar behavior in various ranges of parameters values. A steady state is always achieved, stabilizes the levels of the variables in the system into values that depend in the given parameters.</p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Using Wolfram Mathematica we studied the behavior of the dynamic system. The system showed similar behavior in various ranges of parameters values. A steady state is always achieved, stabilizes the levels of the variables in the system into values that depend in the given parameters.</p> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/73/BGU14MODEL2mathematica1.png"><img src="https://static.igem.org/mediawiki/2014/7/73/BGU14MODEL2mathematica1.png" style=" height:225px; border:solid"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/73/BGU14MODEL2mathematica1.png"><img src="https://static.igem.org/mediawiki/2014/7/73/BGU14MODEL2mathematica1.png" style=" height:225px; border:solid"/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure 8- Parameters manipulation in Wolfram Mathematica</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure 8 - Parameters manipulation in Wolfram Mathematica</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; 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> <p>Another method for investigation the steady state behavior is the eigenvalues of the corresponding Jacobian matrix of the dynamic system. By defining our system variable as the vector (PGC1αmRNA, PGC1α, REPmRNA, REP), the Jacobian matrix is:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Another method for investigation the steady state behavior is the eigenvalues of the corresponding Jacobian matrix of the dynamic system. By defining our system variable as the vector (PGC1αmRNA, PGC1α, REPmRNA, REP), the Jacobian matrix is:</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/6/6e/BGU14MODEL2fig12.png"><img src="https://static.igem.org/mediawiki/2014/6/6e/BGU14MODEL2fig12.png" style=" height:96px;border:solid;"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/6/6e/BGU14MODEL2fig12.png"><img src="https://static.igem.org/mediawiki/2014/6/6e/BGU14MODEL2fig12.png" style=" height:96px;border:solid;"/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline">Figure 9 - The Jacobian of the system</del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; 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> <p>In every set of parameters chosen, we could calculate the eigenvalues of J and found the behavior of the system at steady state: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>In every set of parameters chosen, we could calculate the eigenvalues of J and found the behavior of the system at steady state: </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 147:</td>
<td colspan="2" class="diff-lineno">Line 147:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/9/91/BGU14MODEL2fig9.png"><img src="https://static.igem.org/mediawiki/2014/9/91/BGU14MODEL2fig9.png" style=" height:270px; border:solid"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/9/91/BGU14MODEL2fig9.png"><img src="https://static.igem.org/mediawiki/2014/9/91/BGU14MODEL2fig9.png" style=" height:270px; border:solid"/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">9</del>-The threshold located at 80% increment of PGC-1α. The PGC-1α level does not pass the threshold as a result of the regulated treatment, unlike the unregulated treatment</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">5 </ins>- The threshold located at 80% increment of PGC-1α. The PGC-1α level does not pass the threshold as a result of the regulated treatment, unlike the unregulated treatment</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The input level of PGC-1α, in a steady state before the introduction of the plasmids, can be simply determined like this:</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>The input level of PGC-1α, in a steady state before the introduction of the plasmids, can be simply determined like this:</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG"><img src="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG" style=" height:60px;border:solid;"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG"><img src="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG" style=" height:60px;border:solid;"/></a></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 155:</td>
<td colspan="2" class="diff-lineno">Line 155:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; 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> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png"><img src="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png" style=" height:275px;border:solid;"/></a><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png"><img src="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png" style=" height:275px;border:solid;"/></a><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">10</del>-For different initial levels of PGC-1α, the treatment increased it in different relative amounts</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">6 </ins>- For different initial levels of PGC-1α, the treatment increased it in different relative amounts</p></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><p>PGC-1α level stabilizes at the steady state of the system. If we give our regulated treatment to people with different natural production rate of PGC-1α from each other, the system stabilizes on different increment. This important feature provides the personalized medicine properties to our regulated treatment we designed.</p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>PGC-1α level stabilizes at the steady state of the system. If we give our regulated treatment to people with different natural production rate of PGC-1α from each other, the system stabilizes on different increment. This important feature provides the personalized medicine properties to our regulated treatment we designed.</p> </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 161:</td>
<td colspan="2" class="diff-lineno">Line 161:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png"><img src="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png" style=" height:400px; border:solid"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png"><img src="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png" style=" height:400px; border:solid"/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">11</del>-The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">7 </ins>- The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure 11 we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure 11 we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td></tr>
</table>Amitghttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=368326&oldid=prevAmitg at 23:30, 17 October 20142014-10-17T23:30:05Z<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">Figure 3</del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p style="font-size:14px">(*) will not change during treatment</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p style="font-size:14px">(*) will not change during treatment</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p><strong>Parameters of reactions</strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p><strong>Parameters of reactions</strong></p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">8</del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">9 - The Jacobian of the system</ins></p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>In every set of parameters chosen, we could calculate the eigenvalues of J and found the behavior of the system at steady state: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>In every set of parameters chosen, we could calculate the eigenvalues of J and found the behavior of the system at steady state: </div></td></tr>
</table>Amitghttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=351380&oldid=prevTomye at 20:36, 17 October 20142014-10-17T20:36:02Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure 11 we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure 11 we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-<del class="diffchange diffchange-inline">1</del>, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-<ins class="diffchange diffchange-inline">1α</ins>, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td></tr>
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</table>Tomyehttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=351075&oldid=prevTomye at 20:32, 17 October 20142014-10-17T20:32:49Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG"><img src="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG" style=" height:60px;border:solid;"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG"><img src="https://static.igem.org/mediawiki/2014/f/fe/BGU14MODEL2fig13.PNG" style=" height:60px;border:solid;"/></a></div></td></tr>
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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">Figure 10</del></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>To face the second challenge we examined different values of natural rate of production of PGC-1α. We ran the model with different input rates and measured the increment in PGC-1α from its initial value to its final value on steady state (Figure <del class="diffchange diffchange-inline">11</del>).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>To face the second challenge we examined different values of natural rate of production of PGC-1α. We ran the model with different input rates and measured the increment in PGC-1α from its initial value to its final value on steady state (Figure <ins class="diffchange diffchange-inline">10</ins>).</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png"><img src="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png" style=" height:275px;border:solid;"/></a><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png"><img src="https://static.igem.org/mediawiki/2014/7/77/BGU14MODEL2fig10.png" style=" height:275px;border:solid;"/></a><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">11-Figure 11</del>-For different initial levels of PGC-1α, the treatment increased it in different relative amounts</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">10</ins>-For different initial levels of PGC-1α, the treatment increased it in different relative amounts</p></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><p>PGC-1α level stabilizes at the steady state of the system. If we give our regulated treatment to people with different natural production rate of PGC-1α from each other, the system stabilizes on different increment. This important feature provides the personalized medicine properties to our regulated treatment we designed.</p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>PGC-1α level stabilizes at the steady state of the system. If we give our regulated treatment to people with different natural production rate of PGC-1α from each other, the system stabilizes on different increment. This important feature provides the personalized medicine properties to our regulated treatment we designed.</p> </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png"><img src="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png" style=" height:400px; border:solid"/></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" style="font-size:14px; font-weight:bold; line-height:normal"><a href="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png"><img src="https://static.igem.org/mediawiki/2014/1/11/BGU14MODEL2fig11.png" style=" height:400px; border:solid"/></a></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Figure <del class="diffchange diffchange-inline">12</del>-The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Figure <ins class="diffchange diffchange-inline">11</ins>-The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure <del class="diffchange diffchange-inline">12 </del>we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure <ins class="diffchange diffchange-inline">11 </ins>we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-1, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-1, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td></tr>
</table>Tomyehttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=350185&oldid=prevTomye at 20:23, 17 October 20142014-10-17T20:23:54Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Figure 12-The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Figure 12-The increment of PGC-1α decreases with the growth of the natural production rate</p> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see <del class="diffchange diffchange-inline">(Figure 6) </del>a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure <del class="diffchange diffchange-inline">7 </del>we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p>At low input of PGC-1α we can see a much more drastic raise in its concentration and a fixation on higher increment than high input values. On Figure <ins class="diffchange diffchange-inline">12 </ins>we can only see the final increment on the steady state. We clearly see a decline which shows that in cells with natural high levels of PGC-1α the influence of the plasmids will be insignificant. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="font-size:20px"><strong><u>Conclusion:</u></strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-1, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The model shows that our treatment is personalized and self-regulated. In other words, for those who have inefficient internal production rate, the increment of PGC-1, as a result of our treatment, will be the more significant than healthy and lean people. This concludes and confirms our method of design in order to achieve the main goal for this treatment. </p></div></td></tr>
</table>Tomyehttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=349928&oldid=prevTomye at 20:21, 17 October 20142014-10-17T20:21:00Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Assignment of the parameters values we showed above shows that the system will be in a stable stationary point after the introduction of the treatment. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Assignment of the parameters values we showed above shows that the system will be in a stable stationary point after the introduction of the treatment. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p><strong>Regulated vs. Unregulated treatment</strong><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p><strong>Regulated vs. Unregulated treatment</strong><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> The modest expression mechanism has to meet two challenges. First to prevent too much synthesis of PGC-1α, that would make an increment over 80% in its concentration. The second challenge is the need to be very potent in cells with low PGC-1α activity, but to have minimum effect in cells with regular PGC-1α activity. The synthesis of the repressor supposes to meet the first challenge. As we can see in Figure <del class="diffchange diffchange-inline">5</del>, an unregulated mechanism without a repressor would lead to much more production of PGC-1α and could cross to a risk increment. To prove our mechanism produce around 80% of production we should test it in the lab, the model here just illustrate the potential. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> The modest expression mechanism has to meet two challenges. First to prevent too much synthesis of PGC-1α, that would make an increment over 80% in its concentration. The second challenge is the need to be very potent in cells with low PGC-1α activity, but to have minimum effect in cells with regular PGC-1α activity. The synthesis of the repressor supposes to meet the first challenge. As we can see in Figure <ins class="diffchange diffchange-inline">9</ins>, an unregulated mechanism without a repressor would lead to much more production of PGC-1α and could cross to a risk increment. To prove our mechanism produce around 80% of production we should test it in the lab, the model here just illustrate the potential. </p></div></td></tr>
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</table>Tomyehttp://2014.igem.org/wiki/index.php?title=Team:BGU_Israel/Modeling/Aspiration_Shift&diff=337610&oldid=prevTomye at 17:47, 17 October 20142014-10-17T17:47:54Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 style="border-bottom:dashed;border-color:#000000">The Mathematical Model<a href="#" onclick="goToByScroll('test'); return false;" class="right"></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 style="border-bottom:dashed;border-color:#000000">The Mathematical Model<a href="#" onclick="goToByScroll('test'); return false;" class="right"></a></h3></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 described the dynamic circuits with differential equations, and used MATLAB SimBiology and Wolfram Mathemitica to analyze their numeric and analytical solution.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 style="border-bottom:dashed;border-color:#000000">Results & Conclusion<a href="#" onclick="goToByScroll('test2'); return false;" class="right"></a></h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3 style="border-bottom:dashed;border-color:#000000">Results & Conclusion<a href="#" onclick="goToByScroll('test2'); return false;" class="right"></a></h3></div></td></tr>
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<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 model describes the regulation advantages and the flexibility nature of the mechanism.</ins></div></td></tr>
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</table>Tomye