http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&feed=atom&action=historyTeam:Marburg:Safety:Modelling - Revision history2024-03-29T13:28:47ZRevision history for this page on the wikiMediaWiki 1.16.5http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=390338&oldid=prevRomanM89 at 02:38, 18 October 20142014-10-18T02:38:59Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 02:38, 18 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 117:</td>
<td colspan="2" class="diff-lineno">Line 117:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/2/2b/Mr_modelling_scence_2.png" /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/2/2b/Mr_modelling_scence_2.png" /></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Figure 2:<b> Plotted on the left is the concentration of Holin (red) and Antiholin (blue) against time. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b>Figure 2:<<ins class="diffchange diffchange-inline">/</ins>b> Plotted on the left is the concentration of Holin (red) and Antiholin (blue) against time. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The right graph shows the difference in concentration between both. The cells die 32 min (green line) after the outbreak (red line).</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The right graph shows the difference in concentration between both. The cells die 32 min (green line) after the outbreak (red line).</span></div></html></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>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=390293&oldid=prevRomanM89 at 02:38, 18 October 20142014-10-18T02:38:34Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 02:38, 18 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 105:</td>
<td colspan="2" class="diff-lineno">Line 105:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/7/73/Scence_1.png"/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/7/73/Scence_1.png"/></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><span class="caption">Figure 1: mRNA concentration is plotted against time (left). Concentration of RpL5 plotted against time (right <del class="diffchange diffchange-inline">graph</del>). The time of outbreak is t=0 (red line). The cell is killed after 63 min at latest (green line).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><span class="caption"<ins class="diffchange diffchange-inline">><b</ins>>Figure 1:<ins class="diffchange diffchange-inline"></b> </ins>mRNA concentration is plotted against time <ins class="diffchange diffchange-inline"><b></ins>(left)<ins class="diffchange diffchange-inline"></b></ins>. Concentration of RpL5 plotted against time <ins class="diffchange diffchange-inline"><b></ins>(right)<ins class="diffchange diffchange-inline"></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>The time of outbreak is t=0 (red line). The cell is killed after 63 min at latest (green line).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></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 colspan="2" class="diff-lineno">Line 116:</td>
<td colspan="2" class="diff-lineno">Line 117:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/2/2b/Mr_modelling_scence_2.png" /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/2/2b/Mr_modelling_scence_2.png" /></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 2: Plotted on the left is the concentration of Holin (red) and Antiholin (blue) against time. The right graph shows the difference in concentration between both. The cells die 32 min (green line) after the outbreak (red line).</span></div></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Figure 2:<ins class="diffchange diffchange-inline"><b> </ins>Plotted on the left is the concentration of Holin (red) and Antiholin (blue) against time. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The right graph shows the difference in concentration between both. The cells die 32 min (green line) after the outbreak (red line).</span></div></html></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>As the organism leaves the laboratory environment, the level of antitoxin production start to sink, widening the gap between the level of toxin and antitoxin in the organism. The critical concentration of toxin in the cell, in the case of T4-Holin, is around 1000-3000 molecules. Since the number of free Holin molecules dictates cell death, we concentrate on the difference between toxin and antitoxin levels in the cell. Even if we take the worst case, where 3000 free T4- Holin molecules are needed, our model shows that the cell lysis will occur at latest 30 minutes after it leaves the laboratory environment.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As the organism leaves the laboratory environment, the level of antitoxin production start to sink, widening the gap between the level of toxin and antitoxin in the organism. The critical concentration of toxin in the cell, in the case of T4-Holin, is around 1000-3000 molecules. Since the number of free Holin molecules dictates cell death, we concentrate on the difference between toxin and antitoxin levels in the cell. Even if we take the worst case, where 3000 free T4- Holin molecules are needed, our model shows that the cell lysis will occur at latest 30 minutes after it leaves the laboratory environment.</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 123:</td>
<td colspan="2" class="diff-lineno">Line 125:</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><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 3: Concentration of RpL5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Figure 3: Concentration of RpL5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.<ins class="diffchange diffchange-inline"></b></ins></span></div></html></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><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/e/ed/Mr_modelling_scence_4.png" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/e/ed/Mr_modelling_scence_4.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 4: On the left concentration of Holin (red) and Antiholin (blue) is plotted against time. On the right graph the </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Figure 4:<ins class="diffchange diffchange-inline"></b> </ins>On the left concentration of Holin (red) and Antiholin (blue) is plotted against time. On the right graph the </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>difference between both is shown. With the mutation occurring 50 min after the outbreak (red line) the cells are dead 31 min later (green line).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>difference between both is shown. With the mutation occurring 50 min after the outbreak (red line) the cells are dead 31 min later (green line).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 137:</td>
<td colspan="2" class="diff-lineno">Line 139:</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><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/a/ae/Mr_graph5.png" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/a/ae/Mr_graph5.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.<ins class="diffchange diffchange-inline"></b></ins></span></div></html></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>Outside of the laboratory environment the TetR production stops, and its concentration starts to sink, as shown in Figure 5. As its </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Outside of the laboratory environment the TetR production stops, and its concentration starts to sink, as shown in Figure 5. As its </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 151:</td>
<td colspan="2" class="diff-lineno">Line 153:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/9/93/Mr_modelling_scence_6.png" width="50%" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/9/93/Mr_modelling_scence_6.png" width="50%" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 6: Time till the cells die plotted against translation or transcription rate showing the values (green line) used in the calculation of the above scenarios.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Figure 6: Time till the cells die plotted against translation or transcription rate showing the values (green line) used in the calculation of the above scenarios.<ins class="diffchange diffchange-inline"></b></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></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>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=278558&oldid=prevRomanM89 at 16:06, 16 October 20142014-10-16T16:06:18Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 16:06, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 65:</td>
<td colspan="2" class="diff-lineno">Line 65:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''a) Production of Antiholin'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''a) Production of Antiholin'''</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><html><img src="https://static.igem.org/mediawiki/2014/3/30/Mr_modelling_eq_1.png /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/3/30/Mr_modelling_eq_1.png<ins class="diffchange diffchange-inline">" </ins>/></html></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><html><img src="https://static.igem.org/mediawiki/2014/c/c8/Mr_modelling_eq_2.png" /></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/c/c8/Mr_modelling_eq_2.png" /></html></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 93:</td>
<td colspan="2" class="diff-lineno">Line 93:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/6/6d/Mr_modelling_eq_11.png" /></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/6/6d/Mr_modelling_eq_11.png" /></html></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>We assumed the transcription rate of both promoters to be ''α<sub>0</sub>''=10 nM/min representing a strong promoter. The translation rate is set to ''β''=2.3 min<sup>-1</sup> to represent the average burst size of 10 proteins/mRNA for the assumed half-life time of five minutes resulting in the degradation rate ''δ<sub>mx</sub>''=log(2)/5 min<sup>-1</sup>. The proteins except for TetR are assumed to be stable and only diluted by cell division every 30 min resulting in the degradation rate ''δ<sub>P</sub>''=log(2)/30 min<sup>-1</sup>. The additional degradation of TetR due to the lva-tag is assumed to be ''δ<sub>P</sub>''=0.018 min<sup>-1</sup>.<del class="diffchange diffchange-inline"><sup>http://www</del>.<del class="diffchange diffchange-inline">ncbi.nlm.nih.gov/pubmed/9603842</sup></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We assumed the transcription rate of both promoters to be ''α<sub>0</sub>''=10 nM/min representing a strong promoter. The translation rate is set to ''β''=2.3 min<sup>-1</sup> to represent the average burst size of 10 proteins/mRNA for the assumed half-life time of five minutes resulting in the degradation rate ''δ<sub>mx</sub>''=log(2)/5 min<sup>-1</sup>. The proteins except for TetR are assumed to be stable and only diluted by cell division every 30 min resulting in the degradation rate ''δ<sub>P</sub>''=log(2)/30 min<sup>-1</sup>. The additional degradation of TetR due to the lva-tag is assumed to be ''δ<sub>P</sub>''=0.018 min<sup>-1</sup> <ins class="diffchange diffchange-inline">(Andersen et al</ins>.<ins class="diffchange diffchange-inline">, 1998)</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>'''Challenging different SURFkiller scenarios <i>in silico</i>'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Challenging different SURFkiller scenarios <i>in silico</i>'''</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 159:</td>
<td colspan="2" class="diff-lineno">Line 159:</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><html><hr /></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><hr /></html></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;">Andersen, J. B., Sternberg, C., Poulsen, L. K., Bjorn, S. P., Givskov, M., & Molin, S. (1998). New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Applied and Environmental Microbiology, 64(6), 2240–6. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306&tool=pmcentrez&rendertype=abstract</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>Lauber, M.A., Running, W.E., and Reilly, J.P. (2009) B. subtilis ribosomal proteins: structural homology and post-translational modifications. J Proteome Res 8: 4193–206 http://www.ncbi.nlm.nih.gov/pubmed/19653700. Accessed October 6, 2014.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Lauber, M.A., Running, W.E., and Reilly, J.P. (2009) B. subtilis ribosomal proteins: structural homology and post-translational modifications. J Proteome Res 8: 4193–206 http://www.ncbi.nlm.nih.gov/pubmed/19653700. Accessed October 6, 2014.</div></td></tr>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=278390&oldid=prevRomanM89 at 16:02, 16 October 20142014-10-16T16:02:07Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 16:02, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 65:</td>
<td colspan="2" class="diff-lineno">Line 65:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''a) Production of Antiholin'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''a) Production of Antiholin'''</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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">8</del>/<del class="diffchange diffchange-inline">85</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_1</del>.png<del class="diffchange diffchange-inline">" </del>/></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">3</ins>/<ins class="diffchange diffchange-inline">30</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_1</ins>.png /></html></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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">2</del>/<del class="diffchange diffchange-inline">2a</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_2</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">c</ins>/<ins class="diffchange diffchange-inline">c8</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_2</ins>.png" /></html></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) Production of Holin'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''b) Production of Holin'''</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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">2</del>/<del class="diffchange diffchange-inline">2b</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_3</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">5</ins>/<ins class="diffchange diffchange-inline">55</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_3</ins>.png" /></html></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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">0</del>/<del class="diffchange diffchange-inline">07</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_4</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">d</ins>/<ins class="diffchange diffchange-inline">d9</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_4</ins>.png" /></html></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>'''c) Production of TetR''' </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''c) Production of TetR''' </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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">8</del>/<del class="diffchange diffchange-inline">88</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_5</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">6</ins>/<ins class="diffchange diffchange-inline">60</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_5</ins>.png" /></html></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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">6</del>/<del class="diffchange diffchange-inline">6a</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_6</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">d</ins>/<ins class="diffchange diffchange-inline">d5</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_6</ins>.png" /></html></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>'''d) Production of the ribosome-hibernation factor YvyD''' </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''d) Production of the ribosome-hibernation factor YvyD''' </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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">0</del>/<del class="diffchange diffchange-inline">07</del>/<del class="diffchange diffchange-inline">Mr_equation_level1</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">9</ins>/<ins class="diffchange diffchange-inline">94</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_8</ins>.png" /></html></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><html><img src="https://static.igem.org/mediawiki/2014/9/<del class="diffchange diffchange-inline">9a</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_8</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/9/<ins class="diffchange diffchange-inline">9e</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_9</ins>.png" /></html></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>'''e) Production of the ribosomal protein RpL5'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''e) Production of the ribosomal protein RpL5'''</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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">c</del>/<del class="diffchange diffchange-inline">c7</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_9</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">5</ins>/<ins class="diffchange diffchange-inline">57</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_10</ins>.png" /></html></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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">f</del>/<del class="diffchange diffchange-inline">f9</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_10</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">6</ins>/<ins class="diffchange diffchange-inline">6d</ins>/<ins class="diffchange diffchange-inline">Mr_modelling_eq_11</ins>.png" /></html></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>We assumed the transcription rate of both promoters to be ''α<sub>0</sub>''=10 nM/min representing a strong promoter. The translation rate is set to ''β''=2.3 min<sup>-1</sup> to represent the average burst size of 10 proteins/mRNA for the assumed half-life time of five minutes resulting in the degradation rate ''δ<sub>mx</sub>''=log(2)/5 min<sup>-1</sup>. The proteins except for TetR are assumed to be stable and only diluted by cell division every 30 min resulting in the degradation rate ''δ<sub>P</sub>''=log(2)/30 min<sup>-1</sup>. The additional degradation of TetR due to the lva-tag is assumed to be ''δ<sub>P</sub>''=0.018 min<sup>-1</sup>.<sup>http://www.ncbi.nlm.nih.gov/pubmed/9603842</sup></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We assumed the transcription rate of both promoters to be ''α<sub>0</sub>''=10 nM/min representing a strong promoter. The translation rate is set to ''β''=2.3 min<sup>-1</sup> to represent the average burst size of 10 proteins/mRNA for the assumed half-life time of five minutes resulting in the degradation rate ''δ<sub>mx</sub>''=log(2)/5 min<sup>-1</sup>. The proteins except for TetR are assumed to be stable and only diluted by cell division every 30 min resulting in the degradation rate ''δ<sub>P</sub>''=log(2)/30 min<sup>-1</sup>. The additional degradation of TetR due to the lva-tag is assumed to be ''δ<sub>P</sub>''=0.018 min<sup>-1</sup>.<sup>http://www.ncbi.nlm.nih.gov/pubmed/9603842</sup></div></td></tr>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=276405&oldid=prevRomanM89 at 15:07, 16 October 20142014-10-16T15:07:31Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:07, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:Marburg/Template:StartContinue}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:Marburg/Template:StartContinue}}</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>In order to predict the behaviour of our SURFkiller, we created a model of our system. For this we used MATLAB software environment. The aim was to simulate cellular protein synthesis in different situations, and based on this information predict the robustness of the SURFkiller. Modelling was based on the following parameters<del class="diffchange diffchange-inline">:</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to predict the behaviour of our SURFkiller, we created a model of our system. For this we used MATLAB software environment. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The aim was to simulate cellular protein synthesis in different situations, and based on this information predict the robustness of the SURFkiller. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Modelling was based on the following <ins class="diffchange diffchange-inline">equations using the </ins>parameters <ins class="diffchange diffchange-inline">explained in Table 1.</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><html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table></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;"> <caption></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;"> Table 1: Parameters used in the equations modelling the SURFkiller.</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;"> </caption></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><colgroup></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><colgroup></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><col width="35%" /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><col width="35%" /></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 47:</td>
<td colspan="2" class="diff-lineno">Line 52:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <td class="t1">&Kappa;<sub>x</sub></td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <td class="t1">&Kappa;<sub>x</sub></td></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <td class="t2">Dissociation (Equilibrium) constant</td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <td class="t2">Dissociation (Equilibrium) constant</td></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;"> </tr></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;"> <tr></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;"> <td class="t1">n<sub>x</sub></td></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;"> <td class="t2">Hill coefficient</td></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </tr></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </tr></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <tr></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <tr></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 82:</td>
<td colspan="2" class="diff-lineno">Line 83:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''d) Production of the ribosome-hibernation factor YvyD''' </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''d) Production of the ribosome-hibernation factor YvyD''' </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><html><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">3</del>/<del class="diffchange diffchange-inline">3b</del>/<del class="diffchange diffchange-inline">Mr_killswitch_eq_7</del>.png" /></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">0</ins>/<ins class="diffchange diffchange-inline">07</ins>/<ins class="diffchange diffchange-inline">Mr_equation_level1</ins>.png" /></html></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><html><img src="https://static.igem.org/mediawiki/2014/9/9a/Mr_killswitch_eq_8.png" /></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/9/9a/Mr_killswitch_eq_8.png" /></html></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 91:</td>
<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><html><img src="https://static.igem.org/mediawiki/2014/f/f9/Mr_killswitch_eq_10.png" /></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><img src="https://static.igem.org/mediawiki/2014/f/f9/Mr_killswitch_eq_10.png" /></html></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;">We assumed the transcription rate of both promoters to be ''α<sub>0</sub>''=10 nM/min representing a strong promoter. The translation rate is set to ''β''=2.3 min<sup>-1</sup> to represent the average burst size of 10 proteins/mRNA for the assumed half-life time of five minutes resulting in the degradation rate ''δ<sub>mx</sub>''=log(2)/5 min<sup>-1</sup>. The proteins except for TetR are assumed to be stable and only diluted by cell division every 30 min resulting in the degradation rate ''δ<sub>P</sub>''=log(2)/30 min<sup>-1</sup>. The additional degradation of TetR due to the lva-tag is assumed to be ''δ<sub>P</sub>''=0.018 min<sup>-1</sup>.<sup>http://www.ncbi.nlm.nih.gov/pubmed/9603842</sup></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>'''Challenging different SURFkiller scenarios <i>in silico</i>'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Challenging different SURFkiller scenarios <i>in silico</i>'''</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 105:</td>
<td colspan="2" class="diff-lineno">Line 108:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></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>At the time point <del class="diffchange diffchange-inline">T</del>=200 min, the mRNA concentration sharply drops, production of the RpL5 protein stops and its concentration in the cells starts to decrease. If we assume that a cell needs around 2000 functional ribosomes in order to survive the cell death occurs at latest when the level of the RpL5 protein drops below 2000 nM. A concentration of 2000 nM in the volume of a cell, which is about 1 fL, equals about 2000 molecules. From our simulation we can see that the current number of ribosomes is below the critical number of 2000 at latest 60 minutes after the cell leaves the laboratory environment even if we assume that every RpL5 molecule leads to the formation of a functional ribosome.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>At the time point <ins class="diffchange diffchange-inline">t</ins>=200 min, the mRNA concentration sharply drops, production of the RpL5 protein stops and its concentration in the cells starts to decrease. If we assume that a cell needs around 2000 functional ribosomes in order to survive the cell death occurs at latest when the level of the RpL5 protein drops below 2000 nM. A concentration of 2000 nM in the volume of a cell, which is about 1 fL, equals about 2000 molecules. From our simulation we can see that the current number of ribosomes is below the critical number of 2000 at latest 60 minutes after the cell leaves the laboratory environment even if we assume that every RpL5 molecule leads to the formation of a functional ribosome.</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>'''Case 2: Mutations compromising modular functions of the SURFkiller'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Case 2: Mutations compromising modular functions of the SURFkiller'''</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 136:</td>
<td colspan="2" class="diff-lineno">Line 139:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></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>Outside of the laboratory environment the TetR <del class="diffchange diffchange-inline">protein synthesis </del>stops, and its concentration starts to sink, as shown <del class="diffchange diffchange-inline">with the red line </del>in <del class="diffchange diffchange-inline">the graph above</del>. As its concentration sinks <del class="diffchange diffchange-inline">below the threshold level (around 20 molecules), </del>it is unable to repress the constitutive promoter and the ''yvyD'' <del class="diffchange diffchange-inline">gene gets expressed starting synthesis of </del>the <del class="diffchange diffchange-inline">protein</del>, shown in <del class="diffchange diffchange-inline">blue</del>. As the YvyD <del class="diffchange diffchange-inline">levels rise</del>, more and more ribosomes dimerize, resulting in cell death. The short period of YvyD production at the beginning is due to the fact that the <del class="diffchange diffchange-inline">amount of TetR protein starts below 20 molecules at the very </del>beginning of the simulation. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Outside of the laboratory environment the TetR <ins class="diffchange diffchange-inline">production </ins>stops, and its concentration starts to sink, as shown in <ins class="diffchange diffchange-inline">Figure 5</ins>. As its </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>concentration sinks it is unable to repress the constitutive promoter and the''yvyD'' <ins class="diffchange diffchange-inline">transcription slowly starts resulting in </ins>the </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">production of YvyD</ins>, shown in <ins class="diffchange diffchange-inline">red</ins>. As the YvyD <ins class="diffchange diffchange-inline">level rises</ins>, more and more ribosomes dimerize, resulting in cell death. The short period </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>of YvyD production at the beginning is due to the fact that <ins class="diffchange diffchange-inline">in </ins>the beginning of the simulation <ins class="diffchange diffchange-inline">the concentration to TetR is assumed to </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">be zero</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>'''Sensitivity of the simulation on the parameters used'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Sensitivity of the simulation on the parameters used'''</div></td></tr>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=269181&oldid=prevRomanM89 at 10:37, 16 October 20142014-10-16T10:37:13Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 10:37, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 98:</td>
<td colspan="2" class="diff-lineno">Line 98:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Scenario 1: A SURFkiller-equipped GMO leaves the laboratory''' </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Scenario 1: A SURFkiller-equipped GMO leaves the laboratory''' </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>The organism leaves the laboratory environment. Concentration of the IPTG anti-repressor quickly drops to minimal levels, as a consequence of the degradation and diffusion through the cell membrane. In this case the critical variable is the concentration of the <del class="diffchange diffchange-inline">L5 </del>essential ribosomal protein. The results are shown in graphs below.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The organism leaves the laboratory environment. Concentration of the IPTG anti-repressor quickly drops to minimal levels, as a consequence of the degradation and diffusion through the cell membrane. In this case the critical variable is the concentration of the <ins class="diffchange diffchange-inline">RpL5 </ins>essential ribosomal protein. The results are shown in graphs below.</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><html><div class="figure" style="width:90%;"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/7/73/Scence_1.png"/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/7/73/Scence_1.png"/></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><span class="caption">Figure 1: mRNA concentration is plotted against time (left). Concentration of <del class="diffchange diffchange-inline">L5 </del>plotted against time (right graph). The time of outbreak is t=0 (red line). The cell is killed after 63 min at latest (green line).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><span class="caption">Figure 1: mRNA concentration is plotted against time (left). Concentration of <ins class="diffchange diffchange-inline">RpL5 </ins>plotted against time (right graph). The time of outbreak is t=0 (red line). The cell is killed after 63 min at latest (green line).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></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>At the time point T=200 min, the mRNA concentration sharply drops, production of the <del class="diffchange diffchange-inline">L5 </del>protein stops and its concentration in the cells starts to decrease. If we assume that a cell needs around 2000 functional ribosomes in order to survive the cell death occurs at latest when the level of the <del class="diffchange diffchange-inline">L5 </del>protein drops below 2000 nM. A concentration of 2000 nM in the volume of a cell, which is about 1 fL, equals about 2000 molecules. From our simulation we can see that the current number of ribosomes is below the critical number of 2000 at latest 60 minutes after the cell leaves the laboratory environment even if we assume that every <del class="diffchange diffchange-inline">L5 </del>molecule leads to the formation of a functional ribosome.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>At the time point T=200 min, the mRNA concentration sharply drops, production of the <ins class="diffchange diffchange-inline">RpL5 </ins>protein stops and its concentration in the cells starts to decrease. If we assume that a cell needs around 2000 functional ribosomes in order to survive the cell death occurs at latest when the level of the <ins class="diffchange diffchange-inline">RpL5 </ins>protein drops below 2000 nM. A concentration of 2000 nM in the volume of a cell, which is about 1 fL, equals about 2000 molecules. From our simulation we can see that the current number of ribosomes is below the critical number of 2000 at latest 60 minutes after the cell leaves the laboratory environment even if we assume that every <ins class="diffchange diffchange-inline">RpL5 </ins>molecule leads to the formation of a functional ribosome.</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>'''Case 2: Mutations compromising modular functions of the SURFkiller'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Case 2: Mutations compromising modular functions of the SURFkiller'''</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>The efficiency of a killswitch can be compromised with mutation that may occur in one of the promoters used in the system. SURFkiller is designed to remain robust even in these situations, incorporating a secondary toxin-antitoxin system (Holin-Antiholin) that balances the promoter function in our system. In this case we simulated a situation where one of the LacI promoters gets constitutive. The essential <del class="diffchange diffchange-inline">L5 </del>protein is always produced in this case, and does not lead to cell death. However, since the toxin is also under control of the same promoter it also gets produced.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The efficiency of a killswitch can be compromised with mutation that may occur in one of the promoters used in the system. SURFkiller is designed to remain robust even in these situations, incorporating a secondary toxin-antitoxin system (Holin-Antiholin) that balances the promoter function in our system. In this case we simulated a situation where one of the LacI promoters gets constitutive. The essential <ins class="diffchange diffchange-inline">RpL5 </ins>protein is always produced in this case, and does not lead to cell death. However, since the toxin is also under control of the same promoter it also gets produced.</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><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/2/2b/Mr_modelling_scence_2.png" /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/2/2b/Mr_modelling_scence_2.png" /></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 117:</td>
<td colspan="2" class="diff-lineno">Line 117:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As the organism leaves the laboratory environment, the level of antitoxin production start to sink, widening the gap between the level of toxin and antitoxin in the organism. The critical concentration of toxin in the cell, in the case of T4-Holin, is around 1000-3000 molecules. Since the number of free Holin molecules dictates cell death, we concentrate on the difference between toxin and antitoxin levels in the cell. Even if we take the worst case, where 3000 free T4- Holin molecules are needed, our model shows that the cell lysis will occur at latest 30 minutes after it leaves the laboratory environment.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As the organism leaves the laboratory environment, the level of antitoxin production start to sink, widening the gap between the level of toxin and antitoxin in the organism. The critical concentration of toxin in the cell, in the case of T4-Holin, is around 1000-3000 molecules. Since the number of free Holin molecules dictates cell death, we concentrate on the difference between toxin and antitoxin levels in the cell. Even if we take the worst case, where 3000 free T4- Holin molecules are needed, our model shows that the cell lysis will occur at latest 30 minutes after it leaves the laboratory environment.</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>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of <del class="diffchange diffchange-inline">L5</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of <ins class="diffchange diffchange-inline">RpL5</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><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 3: Concentration of <del class="diffchange diffchange-inline">L5 </del>plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Figure 3: Concentration of <ins class="diffchange diffchange-inline">RpL5 </ins>plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></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><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/e/ed/Mr_modelling_scence_4.png" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/e/ed/Mr_modelling_scence_4.png" /><span class="caption"></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 127:</td>
<td colspan="2" class="diff-lineno">Line 127:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></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>The mutation occurs at the T=250 min in the simulation depicted in graphs above, and we can see how the concentration of both the <del class="diffchange diffchange-inline">L5 </del>protein and the T4-Holin rebounds after the initial drop caused by the bacteria leaving the laboratory. The Antiholin production is not affected by this mutation, as it is located on another module in the system. Regardless of the mutation, Holin-induced cell lysis still occurs at latest 30 minutes after the mutation. Otherwise, cell dies from the lack of the <del class="diffchange diffchange-inline">L5 </del>protein, as in the first case.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The mutation occurs at the T=250 min in the simulation depicted in graphs above, and we can see how the concentration of both the <ins class="diffchange diffchange-inline">RpL5 </ins>protein and the T4-Holin rebounds after the initial drop caused by the bacteria leaving the laboratory. The Antiholin production is not affected by this mutation, as it is located on another module in the system. Regardless of the mutation, Holin-induced cell lysis still occurs at latest 30 minutes after the mutation. Otherwise, cell dies from the lack of the <ins class="diffchange diffchange-inline">RpL5 </ins>protein, as in the first case.</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>'''Scenario 3: <del class="diffchange diffchange-inline">Rpl5 </del>is lost from SURFkiller'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Scenario 3: <ins class="diffchange diffchange-inline">RpL5 </ins>is lost from SURFkiller'''</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>For our third scenario we decided to test the unlikely case where the <del class="diffchange diffchange-inline">L5 </del>encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the <del class="diffchange diffchange-inline">L5 </del>protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>For our third scenario we decided to test the unlikely case where the <ins class="diffchange diffchange-inline">RpL5 </ins>encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the <ins class="diffchange diffchange-inline">RpL5 </ins>protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </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><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/a/ae/Mr_graph5.png" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:40%;"><img src="https://static.igem.org/mediawiki/2014/a/ae/Mr_graph5.png" /><span class="caption"></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 149:</td>
<td colspan="2" class="diff-lineno">Line 149:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As we can see from the graphs above, if we vary the standard translation rate of 2.3 min <sup>-1</sup> there is comparatively small change in the time needed for the cell death to occur. If the translation rate is below 0.6 the cells cannot survive even under laboratory conditions because the steady state number of ribosomes is below 2000. Similar is applicable to variations in transcription rate. If the assumed transcription rate of 10 nM/min doubles, the expected survival time of the cell is around 25 minutes longer.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As we can see from the graphs above, if we vary the standard translation rate of 2.3 min <sup>-1</sup> there is comparatively small change in the time needed for the cell death to occur. If the translation rate is below 0.6 the cells cannot survive even under laboratory conditions because the steady state number of ribosomes is below 2000. Similar is applicable to variations in transcription rate. If the assumed transcription rate of 10 nM/min doubles, the expected survival time of the cell is around 25 minutes longer.</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>The modelling of our SURFkiller showed that the system indeed works and leads to a quick decrease of <del class="diffchange diffchange-inline">L5 </del>upon the deprivation of IPTG. Also the further layers of security against mutations that might occur have been shown to be working. What we learned though is that it might be better to use several copies of ''yvyD'' to increase the steady state protein concentration, so that the ribosome number decreases by dimerization quickly below an essential number for survival. Our analysis of the sensitivity of the system suggest that we established a robust circuit design concerning the translation rate, which means that changes of this rate lead only to a small change in time until the cells die. However the transcription rate should be increased for example by using a stronger promoter in order to make the system even more robust.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The modelling of our SURFkiller showed that the system indeed works and leads to a quick decrease of <ins class="diffchange diffchange-inline">RpL5 </ins>upon the deprivation of IPTG. Also the further layers of security against mutations that might occur have been shown to be working. What we learned though is that it might be better to use several copies of ''yvyD'' to increase the steady state protein concentration, so that the ribosome number decreases by dimerization quickly below an essential number for survival. Our analysis of the sensitivity of the system suggest that we established a robust circuit design concerning the translation rate, which means that changes of this rate lead only to a small change in time until the cells die. However the transcription rate should be increased for example by using a stronger promoter in order to make the system even more robust.</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><html><hr /></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><hr /></html></div></td></tr>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=268984&oldid=prevRomanM89 at 10:25, 16 October 20142014-10-16T10:25:10Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 10:25, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 119:</td>
<td colspan="2" class="diff-lineno">Line 119:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</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><html><div class="figure" style="width:<del class="diffchange diffchange-inline">45</del>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:<ins class="diffchange diffchange-inline">40</ins>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></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 colspan="2" class="diff-lineno">Line 133:</td>
<td colspan="2" class="diff-lineno">Line 133:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For our third scenario we decided to test the unlikely case where the L5 encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the L5 protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For our third scenario we decided to test the unlikely case where the L5 encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the L5 protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </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><html><div class="figure" style="width:<del class="diffchange diffchange-inline">45</del>%;"><img src="https://static.igem.org/mediawiki/2014/<del class="diffchange diffchange-inline">5</del>/<del class="diffchange diffchange-inline">5f</del>/<del class="diffchange diffchange-inline">Mr_modelling_scence_5</del>.png" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:<ins class="diffchange diffchange-inline">40</ins>%;"><img src="https://static.igem.org/mediawiki/2014/<ins class="diffchange diffchange-inline">a</ins>/<ins class="diffchange diffchange-inline">ae</ins>/<ins class="diffchange diffchange-inline">Mr_graph5</ins>.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></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>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=268884&oldid=prevRomanM89 at 10:18, 16 October 20142014-10-16T10:18:07Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 10:18, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 119:</td>
<td colspan="2" class="diff-lineno">Line 119:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</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><html><div class="figure" style="width:<del class="diffchange diffchange-inline">60</del>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:<ins class="diffchange diffchange-inline">45</ins>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></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 colspan="2" class="diff-lineno">Line 133:</td>
<td colspan="2" class="diff-lineno">Line 133:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For our third scenario we decided to test the unlikely case where the L5 encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the L5 protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For our third scenario we decided to test the unlikely case where the L5 encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the L5 protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </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><html><div class="figure" style="width:<del class="diffchange diffchange-inline">60</del>%;"><img src="https://static.igem.org/mediawiki/2014/5/5f/Mr_modelling_scence_5.png" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:<ins class="diffchange diffchange-inline">45</ins>%;"><img src="https://static.igem.org/mediawiki/2014/5/5f/Mr_modelling_scence_5.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></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>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=268865&oldid=prevRomanM89 at 10:17, 16 October 20142014-10-16T10:17:15Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 10:17, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 119:</td>
<td colspan="2" class="diff-lineno">Line 119:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</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><html><div class="figure" style="width:<del class="diffchange diffchange-inline">75</del>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:<ins class="diffchange diffchange-inline">60</ins>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></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><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/e/ed/Mr_modelling_scence_4.png<del class="diffchange diffchange-inline">" width="50%</del>" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"><img src="https://static.igem.org/mediawiki/2014/e/ed/Mr_modelling_scence_4.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 4: On the left concentration of Holin (red) and Antiholin (blue) is plotted against time. On the right graph the </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 4: On the left concentration of Holin (red) and Antiholin (blue) is plotted against time. On the right graph the </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>difference between both is shown. With the mutation occurring 50 min after the outbreak (red line) the cells are dead 31 min later (green line).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>difference between both is shown. With the mutation occurring 50 min after the outbreak (red line) the cells are dead 31 min later (green line).</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 133:</td>
<td colspan="2" class="diff-lineno">Line 133:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For our third scenario we decided to test the unlikely case where the L5 encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the L5 protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For our third scenario we decided to test the unlikely case where the L5 encoding gene is removed from the operon controlled by the Lac-promoter, for instance by the means of homologous recombination. It is then possible that the levels of the L5 protein will be high enough in the cell while the difference between Holin and Antiholin is kept low, even if it escapes the laboratory. The third security layer of our SURFkiller is designed for this case, and activated if all other security measures get compromised. </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><html><div class="figure" style="width:<del class="diffchange diffchange-inline">90</del>%;"><img src="https://static.igem.org/mediawiki/2014/5/5f/Mr_modelling_scence_5.png<del class="diffchange diffchange-inline">" width="50%</del>" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:<ins class="diffchange diffchange-inline">60</ins>%;"><img src="https://static.igem.org/mediawiki/2014/5/5f/Mr_modelling_scence_5.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Concentration of TetR (red) and YvyD (blue) plotted against time.</span></div></html></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>
</table>RomanM89http://2014.igem.org/wiki/index.php?title=Team:Marburg:Safety:Modelling&diff=268835&oldid=prevRomanM89 at 10:16, 16 October 20142014-10-16T10:16:22Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 10:16, 16 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 119:</td>
<td colspan="2" class="diff-lineno">Line 119:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A variation of this scenario could be when a mutation occurs after the bacteria leave the laboratory but before they die due to the lack of L5.</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><html><div class="figure" style="width:<del class="diffchange diffchange-inline">90</del>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html><div class="figure" style="width:<ins class="diffchange diffchange-inline">75</ins>%;"><img src="https://static.igem.org/mediawiki/2014/2/21/Mr_modelling_scence_3.png" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Concentration of L5 plotted against time showing that a mutation occurs before the concentration drops below a safe level.</span></div></html></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 colspan="2" class="diff-lineno">Line 144:</td>
<td colspan="2" class="diff-lineno">Line 144:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><div class="figure" style="width:90%;"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/9/93/Mr_modelling_scence_6.png" width="50%" /><span class="caption"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2014/9/93/Mr_modelling_scence_6.png" width="50%" /><span class="caption"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 6:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Figure 6: <ins class="diffchange diffchange-inline">Time till the cells die plotted against translation or transcription rate showing the values (green line) used in the calculation of the above scenarios.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></span></div></html></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>
</table>RomanM89