http://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&feed=atom&action=historyTeam:KU Leuven/Project/Glucosemodel/MeS/Modelling-FBA - Revision history2024-03-28T13:09:58ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=360444&oldid=prevFrederikM at 03:24, 29 October 20132013-10-29T03:24:13Z<p></p>
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</table>FrederikMhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=359384&oldid=prevTomasvp at 02:47, 29 October 20132013-10-29T02:47:11Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a <b>trade off</b> between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. <b>These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I></b> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak.<br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E. coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a <b>trade off</b> between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. <b>These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I></b> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak.<br/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These results not only show correlation between wetlab and modelling data but also suggest that cellular level modelling can result in colony wide effects (as observed in the delayed growth). </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These results not only show correlation between wetlab and modelling data but also suggest that cellular level modelling can result in colony wide effects (as observed in the delayed growth). </div></td></tr>
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</table>Tomasvphttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=357720&oldid=prevSanderW at 01:48, 29 October 20132013-10-29T01:48:17Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Flux Balance Analysis</h3> </a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Flux Balance Analysis</h3> </a></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Kinetic Parameters</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h3>Kinetic Parameters</h3></div></td></tr>
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</table>SanderWhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=357435&oldid=prevPieter at 01:38, 29 October 20132013-10-29T01:38:18Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a <b>trade off</b> between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. <b>These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I></b> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, <del class="diffchange diffchange-inline">in sofar that </del>when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak.<br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a <b>trade off</b> between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. <b>These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I></b> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak.<br/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These results not only show correlation between wetlab and modelling data but also suggest that cellular level modelling can result in colony wide effects (as observed in the delayed growth). </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These results not only show correlation between wetlab and modelling data but also suggest that cellular level modelling can result in colony wide effects (as observed in the delayed growth). </div></td></tr>
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</table>Pieterhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=357355&oldid=prevPieter at 01:35, 29 October 20132013-10-29T01:35:44Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a <b>trade off<<del class="diffchange diffchange-inline">b</del>/> between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. <b>These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I></b> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, in sofar that when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak.<br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a <b>trade off</<ins class="diffchange diffchange-inline">b</ins>> between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. <b>These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I></b> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, in sofar that when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak.<br/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These results not only show correlation between wetlab and modelling data but also suggest that cellular level modelling can result in colony wide effects (as observed in the delayed growth). </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These results not only show correlation between wetlab and modelling data but also suggest that cellular level modelling can result in colony wide effects (as observed in the delayed growth). </div></td></tr>
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</table>Pieterhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=356102&oldid=prevVeerledewever at 00:50, 29 October 20132013-10-29T00:50:43Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.<del class="diffchange diffchange-inline">Coli</del></i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a trade off between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, in sofar that when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.<ins class="diffchange diffchange-inline">coli</ins></i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a <ins class="diffchange diffchange-inline"><b></ins>trade off<ins class="diffchange diffchange-inline"><b/> </ins>between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. <ins class="diffchange diffchange-inline"><b></ins>These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I<ins class="diffchange diffchange-inline">></b</ins>> in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, in sofar that when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak.<ins class="diffchange diffchange-inline"><br/></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">These results not only show correlation between wetlab and modelling data but also suggest that cellular level modelling can result in colony wide effects (as observed in the delayed growth). </ins> </div></td></tr>
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</table>Veerledeweverhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=355730&oldid=prevVeerledewever at 00:38, 29 October 20132013-10-29T00:38:42Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.Coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a trade off between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p align = "justify">FBA analysis predicted LB medium conditions to be beneficial for both <i>E.Coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover, a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a trade off between the two. This linear correlation is present not only for LB medium conditions but also for minimal medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions. These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I> <ins class="diffchange diffchange-inline">in the choice between methyl salicylate production and growth rate. Finally, also our GC-MS analysis fits with this modelling, in sofar that when salicylate was added to the medium, we not only observed a reduced growth rate but also a distinct MeS production peak</ins>. </div></td></tr>
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</table>Veerledeweverhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=355460&oldid=prevVeerledewever at 00:29, 29 October 20132013-10-29T00:29:02Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p align = "justify">LB medium conditions <del class="diffchange diffchange-inline">are predicted by FBA analysis </del>to be beneficial for both <i>E.Coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a trade off between the two. This linear correlation is present for <del class="diffchange diffchange-inline">the minimal and </del>LB medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p align = "justify"><ins class="diffchange diffchange-inline">FBA analysis predicted </ins>LB medium conditions to be beneficial for both <i>E.Coli</i> growth and the flux towards chorismate, an important precursor for methylsalicylate. Moreover<ins class="diffchange diffchange-inline">, </ins>a linear correlation between maximal predicted MeS flux and maximal growth rate exists, showing a trade off between the two. This linear correlation is present <ins class="diffchange diffchange-inline">not only </ins>for LB <ins class="diffchange diffchange-inline">medium conditions but also for minimal </ins>medium conditions and is qualitatively similar, showing a steeper correlation for LB medium conditions<ins class="diffchange diffchange-inline">. These trade-offs are not only present <I>in silico</I> but we also found them <I>in vivo</I></ins>. </div></td></tr>
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</table>Veerledeweverhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=355196&oldid=prevVeerledewever at 00:18, 29 October 20132013-10-29T00:18:37Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/d/d5/BBa_K1060003.jpg"/><br/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/d/d5/BBa_K1060003.jpg"/><br/></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><p align = "justify">This figure shows how higher concentrations of added salicylate result in a longer lag phase. <del class="diffchange diffchange-inline">If we assume that the production </del>of <del class="diffchange diffchange-inline">SAM (</del>S-adenosylmethionine), a <del class="diffchange diffchange-inline">common </del>co-substrate of the methyltransferase reaction from salicylate <del class="diffchange diffchange-inline">to methylsalicylate, is important for cell metabolism, providing </del>higher <del class="diffchange diffchange-inline">levels of salicylate would increase SAM </del>consumption<del class="diffchange diffchange-inline">. However, high </del>levels <del class="diffchange diffchange-inline">of salicylate may lead to higher levels of SAM. These </del>in turn <del class="diffchange diffchange-inline">can </del>be associated with higher homocysteine levels, a side-product that stays behind when the methylgroup has been transferred to <del class="diffchange diffchange-inline">the substrate</del>. Increased homocysteine levels are toxic for <i>E. coli</i> strains (Tuite <i>et al.</i> which may explain the ceiling we observe when adding salicylate, hoping for higher MeS fluxes.</p><br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p align = "justify">This figure shows how higher concentrations of added salicylate <ins class="diffchange diffchange-inline">(0.1 mM) </ins>result in a longer lag phase. <ins class="diffchange diffchange-inline">Higher levels of salicylate may lead to higher levels </ins>of S-adenosylmethionine <ins class="diffchange diffchange-inline">(SAM</ins>) <ins class="diffchange diffchange-inline">consumption</ins>, a co-substrate of the methyltransferase reaction <ins class="diffchange diffchange-inline">producing methylsalicylate </ins>from salicylate<ins class="diffchange diffchange-inline">. These </ins>higher consumption levels <ins class="diffchange diffchange-inline">can </ins>in turn be associated with higher homocysteine levels, a side-product that stays behind when the methylgroup has been transferred to <ins class="diffchange diffchange-inline">salicylate</ins>. Increased homocysteine levels are toxic for <i>E. coli</i> strains (Tuite <i>et al.</i> which may explain the ceiling we observe when adding salicylate, hoping for higher MeS fluxes.</p><br/></div></td></tr>
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</table>Veerledeweverhttp://2013.igem.org/wiki/index.php?title=Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA&diff=355119&oldid=prevVeerledewever at 00:14, 29 October 20132013-10-29T00:14:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align = "justify">As can be seen in the graph, there is a linear correlation between maximal flux towards MeS and maximal <i>E. coli</i> growth. This linear correlation is qualitatively similar both under minimal growth conditions as in LB medium conditions and shows that we are dealing with a trade off between bacterial growth and MeS production.<br/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align = "justify">As can be seen in the graph, there is a linear correlation between maximal flux towards MeS and maximal <i>E. coli</i> growth. This linear correlation is qualitatively similar both under minimal growth conditions as in LB medium conditions and shows that we are dealing with a trade off between bacterial growth and MeS production.<br/></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>If a higher flux to MeS is preferred over a lower <i>E. coli</i> growth mass a value at the left side of the graph should be considered, whereas a value to the right would give a higher <i>E. coli</i> production rate and a lower flux towards MeS. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>If a higher flux to MeS is preferred over a lower <i>E. coli</i> growth mass a value at the left side of the graph should be considered, whereas a value to the right would give a higher <i>E. coli</i> production rate and a lower flux towards MeS. This trade-off is reminiscent of our <ins class="diffchange diffchange-inline">wet-lab </ins>growth curve results for the MeS brick.</<ins class="diffchange diffchange-inline">p</ins>><<ins class="diffchange diffchange-inline">br</ins>/></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This trade-off is reminiscent of our <del class="diffchange diffchange-inline"><a href="https://static.igem.org/mediawiki/2013/d/d5/BBa_K1060003.jpg"></del>growth curve results<del class="diffchange diffchange-inline"></a> </del>for the MeS brick. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><<del class="diffchange diffchange-inline">img src="https://static.igem.org/mediawiki/2013/d/d5/BBa_K1060003.jpg"</del>/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">is consistent when taking into account the results from the wetlab since we observed lower growth curves for higher concentrations of added salicylate. If we assume that the production of SAM (S-adenosylmethionine), a common co-substrate of the methyltransferase reaction from salicylate to methylsalicylate, is important for cell metabolism, providing higher levels of salicylate would increase SAM consumption. However, high levels of salicylate may lead to higher levels of SAM which are in turn associated with higher homocysteine levels (a side-product that stays behind when the methylgroup has been transferred to the substrate). Increased homocysteine levels are toxic for <i>E. coli</del></<del class="diffchange diffchange-inline">i</del>> <del class="diffchange diffchange-inline">strains (Tuite <i>et al.</i> which may explain the ceiling we observe when adding salicylate, hoping for higher MeS fluxes.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td 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;"><img src="https://static.igem.org/mediawiki/2013/d/d5/BBa_K1060003.jpg"/><br/></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 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;"><p align = "justify">This figure shows how higher concentrations of added salicylate result in a longer lag phase. If we assume that the production of SAM (S-adenosylmethionine), a common co-substrate of the methyltransferase reaction from salicylate to methylsalicylate, is important for cell metabolism, providing higher levels of salicylate would increase SAM consumption. However, high levels of salicylate may lead to higher levels of SAM. These in turn can be associated with higher homocysteine levels, a side-product that stays behind when the methylgroup has been transferred to the substrate. Increased homocysteine levels are toxic for <i>E. coli</i> strains (Tuite <i>et al.</i> which may explain the ceiling we observe when adding salicylate, hoping for higher MeS fluxes.</p><br/></ins></div></td></tr>
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