http://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&feed=atom&action=historyTeam:SJTU-BioX-Shanghai/Project/project2.3 - Revision history2024-03-29T09:30:17ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=298401&oldid=prevStephen.W: /* Membrane Accelerator - PAH degradation & DBT desulfurization */2012-10-27T03:55:51Z<p><span class="autocomment">Membrane Accelerator - PAH degradation & DBT desulfurization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__NOTOC__</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__NOTOC__</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=Membrane Accelerator<br><br> - PAH <del class="diffchange diffchange-inline">degradation </del>& DBT <del class="diffchange diffchange-inline">desulfurization</del>=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=Membrane Accelerator<br><br> - PAH <ins class="diffchange diffchange-inline">Degradation </ins>& DBT <ins class="diffchange diffchange-inline">Desulfurization</ins>=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Template:12SJTU_part_summary_head}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Template:12SJTU_part_summary_head}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''State of the art'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''State of the art'''</div></td></tr>
</table>Stephen.Whttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=297486&oldid=prevZhiantinglan: /* Membrane Accelerator - PAH degradation & DBT desulfurization */2012-10-27T03:26:28Z<p><span class="autocomment">Membrane Accelerator - PAH degradation & DBT desulfurization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Achievements'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Achievements'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">We proposed </del>a <del class="diffchange diffchange-inline">novel </del>concept to apply scaffold system in facilitating biodegradation pathway</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">''</ins>a <ins class="diffchange diffchange-inline">brand-new </ins>concept<ins class="diffchange diffchange-inline">'' proposed </ins>to apply scaffold system in facilitating biodegradation pathway</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">We selected two </del>well-studied biodegradation pathways, which could potentially benefit environment restoration</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">''2 </ins>well-studied biodegradation pathways<ins class="diffchange diffchange-inline">'' selected</ins>, which could potentially benefit environment restoration</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Template:12SJTU_part_summary_foot}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Template:12SJTU_part_summary_foot}}</div></td></tr>
</table>Zhiantinglanhttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=285262&oldid=prevAleAlejandro: /* Membrane Accelerator - PAH degradation & DBT desulfurization */2012-10-26T15:04:00Z<p><span class="autocomment">Membrane Accelerator - PAH degradation & DBT desulfurization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''State of the art'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''State of the art'''</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>Natural biodegradation is a very slow process but indispensible in environment restoration. Previous synthetic scaffold system has been used to accelerate biosynthetic pathway. <del class="diffchange diffchange-inline">This year, iGEM team SJTU-BioX-Shanghai is </del>trying for the first time to recruit scaffold system to accelerate biodegradation pathway. It offered a new direction in the application of synthetic scaffold system.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Natural biodegradation is a very slow process but indispensible in environment restoration. Previous synthetic scaffold system has been used to accelerate biosynthetic pathway. <ins class="diffchange diffchange-inline">We are </ins>trying for the first time to recruit scaffold system to accelerate biodegradation pathway. It offered a new direction in the application of synthetic scaffold system.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Aims'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Aims'''</div></td></tr>
</table>AleAlejandrohttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=285234&oldid=prevAleAlejandro: /* Desulfurization Pathway */2012-10-26T15:01:40Z<p><span class="autocomment">Desulfurization Pathway</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:12SJTU desulpathway1.png|thumb|<del class="diffchange diffchange-inline">700px</del>|center|''Fig3: ''The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulpathway1.png|thumb|<ins class="diffchange diffchange-inline">500px</ins>|center|''Fig3: ''The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Design of Experiment===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Design of Experiment===</div></td></tr>
</table>AleAlejandrohttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=284474&oldid=prevAleAlejandro: /* Desulfurization Pathway */2012-10-26T13:56:33Z<p><span class="autocomment">Desulfurization Pathway</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Desulfurization Pathway===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Desulfurization Pathway===</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>Four enzymes are involved in the 4S desulfurization pathway. Dibenzothiophene monooxygenase (DszC) is responsible for converting DBT to DBT-sulfoxide and finally to DBT-sulfone (DBTO<sub>2<<del class="diffchange diffchange-inline">\</del>sub>). DBT-sulfone monooxygenase (DszA) then carries out the next step in the pathway, producing 2-hydroxybiphenyl-2-sulfinic acid (HBPS). HBPS is then converted to the final product by HBPS desulfinase (DszB), producing 2-HBP. The sulfur is released from the hydrocarbon in the form of sulfite. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Four enzymes are involved in the 4S desulfurization pathway. Dibenzothiophene monooxygenase (DszC) is responsible for converting DBT to DBT-sulfoxide and finally to DBT-sulfone (DBTO<sub>2<<ins class="diffchange diffchange-inline">/</ins>sub>). DBT-sulfone monooxygenase (DszA) then carries out the next step in the pathway, producing 2-hydroxybiphenyl-2-sulfinic acid (HBPS). HBPS is then converted to the final product by HBPS desulfinase (DszB), producing 2-HBP. The sulfur is released from the hydrocarbon in the form of sulfite. </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>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td></tr>
</table>AleAlejandrohttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=284362&oldid=prevAleAlejandro: /* Desulfurization Pathway */2012-10-26T13:44:28Z<p><span class="autocomment">Desulfurization Pathway</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Desulfurization Pathway===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Desulfurization Pathway===</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>Four enzymes are involved in the 4S desulfurization pathway. Dibenzothiophene monooxygenase (DszC) is responsible for converting DBT to DBT-sulfoxide and finally to DBT-sulfone (<del class="diffchange diffchange-inline">DBTO2</del>). DBT-sulfone monooxygenase (DszA) then carries out the next step in the pathway, producing 2-hydroxybiphenyl-2-sulfinic acid (HBPS). HBPS is then converted to the final product by HBPS desulfinase (DszB), producing 2-HBP. The sulfur is released from the hydrocarbon in the form of sulfite. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Four enzymes are involved in the 4S desulfurization pathway. Dibenzothiophene monooxygenase (DszC) is responsible for converting DBT to DBT-sulfoxide and finally to DBT-sulfone (<ins class="diffchange diffchange-inline">DBTO<sub>2<\sub></ins>). DBT-sulfone monooxygenase (DszA) then carries out the next step in the pathway, producing 2-hydroxybiphenyl-2-sulfinic acid (HBPS). HBPS is then converted to the final product by HBPS desulfinase (DszB), producing 2-HBP. The sulfur is released from the hydrocarbon in the form of sulfite. </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>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td></tr>
</table>AleAlejandrohttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=284347&oldid=prevAleAlejandro: /* Desulfurization Pathway */2012-10-26T13:41:38Z<p><span class="autocomment">Desulfurization Pathway</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:12SJTU <del class="diffchange diffchange-inline">desulpathway</del>.png|thumb|700px|center|''Fig3: ''The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU <ins class="diffchange diffchange-inline">desulpathway1</ins>.png|thumb|700px|center|''Fig3: ''The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Design of Experiment===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Design of Experiment===</div></td></tr>
</table>AleAlejandrohttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=284050&oldid=prevAleAlejandro: /* Design of Experiment */2012-10-26T12:59:43Z<p><span class="autocomment">Design of Experiment</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are trying to organize DszA, DszB, DszC and DszD according to the pattern shown in ''Fig4''. Due to decreased distance between those enzymes and optimized organization, the proceeding speed of Biodesulfurization pathway should increase sharply.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are trying to organize DszA, DszB, DszC and DszD according to the pattern shown in ''Fig4''. Due to decreased distance between those enzymes and optimized organization, the proceeding speed of Biodesulfurization pathway should increase sharply.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:12SJTU desulconstruction.png|thumb|700px|center|''Fig5: ''Sketch map of Desulfurizing ''Membrane Accelerator''.<br>''Fig5A'' shows the three dimensional sketch of the device<del class="diffchange diffchange-inline">. <br></del>''Fig5B'' offers a bottom view of the device.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulconstruction.png|thumb|700px|center|''Fig5: ''Sketch map of Desulfurizing ''Membrane Accelerator''.<br>''Fig5A'' shows the three dimensional sketch of the device<ins class="diffchange diffchange-inline">; </ins>''Fig5B'' offers a bottom view of the device.]]</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>==Reference==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reference==</div></td></tr>
</table>AleAlejandrohttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=284043&oldid=prevAleAlejandro: /* Membrane Accelerator - PAH degradation & DBT desulfurization */2012-10-26T12:59:03Z<p><span class="autocomment">Membrane Accelerator - PAH degradation & DBT desulfurization</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 12:59, 26 October 2012</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We recruited naphthalene degradation pathway in ''Pseudomonas'' species, which has been well characterized. Six crucial enzymes are involved in naphthalene degradation pathway.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We recruited naphthalene degradation pathway in ''Pseudomonas'' species, which has been well characterized. Six crucial enzymes are involved in naphthalene degradation pathway.</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>[[File:12SJTU_PAHbiodegradation.png|thumb|500px|center|''Fig1:''Demonstration of naphthalene degradation pathway in ''Pseudomonas'' species]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU_PAHbiodegradation.png|thumb|500px|center|''Fig1: ''Demonstration of naphthalene degradation pathway in ''Pseudomonas'' species]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the first catabolic step, an oxygen molecule is introduced at the 1,2-position of the aromatic nucleus to produce cis-1,2-dihydroxy-1,2-dihydronaphthalene by naphthalene dihydrodiol dioxygenase(NahA). cis-1,2-Dihydroxy-1,2-dihydronaphthalene is then dehydrogenated to 1,2-dihydroxynaphthalene by cis-naphthalene dihydrodiol dehydrogenase(NahB). 1,2-Dihydroxynaphthalene is cleaved by 1,2-dihydroxynaphthalene dioxygenase(NahC), and the resulting ring-cleavage product spontaneously cyclizes to form 2-hydroxy-2H-chromene-2-carboxylic acid. Enzymatic reactions by an isomerase(NahD) and a hydratase-aldolase(NahE) result in the production of salicylaldehyde, which is then transformed to salicylate by salicyladehyde dehydrogenase(NahF).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the first catabolic step, an oxygen molecule is introduced at the 1,2-position of the aromatic nucleus to produce cis-1,2-dihydroxy-1,2-dihydronaphthalene by naphthalene dihydrodiol dioxygenase(NahA). cis-1,2-Dihydroxy-1,2-dihydronaphthalene is then dehydrogenated to 1,2-dihydroxynaphthalene by cis-naphthalene dihydrodiol dehydrogenase(NahB). 1,2-Dihydroxynaphthalene is cleaved by 1,2-dihydroxynaphthalene dioxygenase(NahC), and the resulting ring-cleavage product spontaneously cyclizes to form 2-hydroxy-2H-chromene-2-carboxylic acid. Enzymatic reactions by an isomerase(NahD) and a hydratase-aldolase(NahE) result in the production of salicylaldehyde, which is then transformed to salicylate by salicyladehyde dehydrogenase(NahF).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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<td colspan="2" class="diff-lineno">Line 62:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To test whether Membrane Accelerator could accelerate naphthalene biodegradation pathway, we are trying to link six crucial enzymes (NahA, B, C, D and E) to orderly organized membrane anchors and expressed them in ''E.coli''. ''E.coli'' expressing the same type and amount of cytoplasmic enzymes is set as control group.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To test whether Membrane Accelerator could accelerate naphthalene biodegradation pathway, we are trying to link six crucial enzymes (NahA, B, C, D and E) to orderly organized membrane anchors and expressed them in ''E.coli''. ''E.coli'' expressing the same type and amount of cytoplasmic enzymes is set as control group.</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>[[File:12SJTU_PAHconstruction.png|thumb|600px|center|''Fig2:''Demonstration of Membrane Accelerator designed for speeding naphthalene biodegradation process]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU_PAHconstruction.png|thumb|600px|center|''Fig2: ''Demonstration of Membrane Accelerator designed for speeding naphthalene biodegradation process]]</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>==Biodesulfurization of Dibenzothiophene (DBT) ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Biodesulfurization of Dibenzothiophene (DBT) ==</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</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>[[File:12SJTU desulpathway.png|thumb|700px|center|''Fig3:''The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulpathway.png|thumb|700px|center|''Fig3: ''The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</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>=== Design of Experiment===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Design of Experiment===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As shown above, DszD plays a special role in this Biodesulfurization pathway: offering FMNH<sub>2</sub> for DszC and DszA. Ideal organization of the four enzymes should be DszC, DszA and DszB aligning together, with DszD paired with DszC and DszA respectively(''Fig.4''). In this way, metabolic flux in desulfurization pathway could be facilitated and accelerated. All intermediates could be passed to downstream enzymes efficiently. Furthermore, paired DszD could offer sufficient amount of FMNH<sub>2</sub> for DszC and DszA in time.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As shown above, DszD plays a special role in this Biodesulfurization pathway: offering FMNH<sub>2</sub> for DszC and DszA. Ideal organization of the four enzymes should be DszC, DszA and DszB aligning together, with DszD paired with DszC and DszA respectively(''Fig.4''). In this way, metabolic flux in desulfurization pathway could be facilitated and accelerated. All intermediates could be passed to downstream enzymes efficiently. Furthermore, paired DszD could offer sufficient amount of FMNH<sub>2</sub> for DszC and DszA in time.</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>[[File:12SJTU desulidealconstruction.png|thumb|600px|center|''Fig4:''Ideal organization of DszA, DszB, DszC and DszD in desulfurization pathway. In each assembly two DszD should be paired with DszC and DszA respectively to offer FMNH<sub>2</sub> timely]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulidealconstruction.png|thumb|600px|center|''Fig4: ''Ideal organization of DszA, DszB, DszC and DszD in desulfurization pathway. In each assembly two DszD should be paired with DszC and DszA respectively to offer FMNH<sub>2</sub> timely]]</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>This ideal organization of enzymes is hard to achieve with traditional linear synthetic scaffolds. However, Membrane Scaffold is two dimensional, so we can organize corresponding enzymes in desired two dimensional pattern. This again shows the superiority of Membrane Scaffold.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This ideal organization of enzymes is hard to achieve with traditional linear synthetic scaffolds. However, Membrane Scaffold is two dimensional, so we can organize corresponding enzymes in desired two dimensional pattern. This again shows the superiority of Membrane Scaffold.</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 91:</td>
<td colspan="2" class="diff-lineno">Line 91:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are trying to organize DszA, DszB, DszC and DszD according to the pattern shown in ''Fig4''. Due to decreased distance between those enzymes and optimized organization, the proceeding speed of Biodesulfurization pathway should increase sharply.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are trying to organize DszA, DszB, DszC and DszD according to the pattern shown in ''Fig4''. Due to decreased distance between those enzymes and optimized organization, the proceeding speed of Biodesulfurization pathway should increase sharply.</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>[[File:12SJTU desulconstruction.png|thumb|700px|center|''Fig5:''Sketch map of Desulfurizing ''Membrane Accelerator'']]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulconstruction.png|thumb|700px|center|''Fig5: ''Sketch map of Desulfurizing ''Membrane Accelerator''<ins class="diffchange diffchange-inline">.<br>''Fig5A'' shows the three dimensional sketch of the device. <br>''Fig5B'' offers a bottom view of the device.</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>==Reference==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reference==</div></td></tr>
</table>AleAlejandrohttp://2012.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Project/project2.3&diff=284016&oldid=prevAleAlejandro: /* Membrane Accelerator - PAH degradation & DBT desulfurization */2012-10-26T12:54:24Z<p><span class="autocomment">Membrane Accelerator - PAH degradation & DBT desulfurization</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 12:54, 26 October 2012</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 56:</td>
<td colspan="2" class="diff-lineno">Line 56:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We recruited naphthalene degradation pathway in ''Pseudomonas'' species, which has been well characterized. Six crucial enzymes are involved in naphthalene degradation pathway.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We recruited naphthalene degradation pathway in ''Pseudomonas'' species, which has been well characterized. Six crucial enzymes are involved in naphthalene degradation pathway.</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>[[File:12SJTU_PAHbiodegradation.png|thumb|500px|center|Demonstration of naphthalene degradation pathway in ''Pseudomonas'' species]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU_PAHbiodegradation.png|thumb|500px|center|<ins class="diffchange diffchange-inline">''Fig1:''</ins>Demonstration of naphthalene degradation pathway in ''Pseudomonas'' species]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the first catabolic step, an oxygen molecule is introduced at the 1,2-position of the aromatic nucleus to produce cis-1,2-dihydroxy-1,2-dihydronaphthalene by naphthalene dihydrodiol dioxygenase(NahA). cis-1,2-Dihydroxy-1,2-dihydronaphthalene is then dehydrogenated to 1,2-dihydroxynaphthalene by cis-naphthalene dihydrodiol dehydrogenase(NahB). 1,2-Dihydroxynaphthalene is cleaved by 1,2-dihydroxynaphthalene dioxygenase(NahC), and the resulting ring-cleavage product spontaneously cyclizes to form 2-hydroxy-2H-chromene-2-carboxylic acid. Enzymatic reactions by an isomerase(NahD) and a hydratase-aldolase(NahE) result in the production of salicylaldehyde, which is then transformed to salicylate by salicyladehyde dehydrogenase(NahF).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the first catabolic step, an oxygen molecule is introduced at the 1,2-position of the aromatic nucleus to produce cis-1,2-dihydroxy-1,2-dihydronaphthalene by naphthalene dihydrodiol dioxygenase(NahA). cis-1,2-Dihydroxy-1,2-dihydronaphthalene is then dehydrogenated to 1,2-dihydroxynaphthalene by cis-naphthalene dihydrodiol dehydrogenase(NahB). 1,2-Dihydroxynaphthalene is cleaved by 1,2-dihydroxynaphthalene dioxygenase(NahC), and the resulting ring-cleavage product spontaneously cyclizes to form 2-hydroxy-2H-chromene-2-carboxylic acid. Enzymatic reactions by an isomerase(NahD) and a hydratase-aldolase(NahE) result in the production of salicylaldehyde, which is then transformed to salicylate by salicyladehyde dehydrogenase(NahF).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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<td colspan="2" class="diff-lineno">Line 62:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To test whether Membrane Accelerator could accelerate naphthalene biodegradation pathway, we are trying to link six crucial enzymes (NahA, B, C, D and E) to orderly organized membrane anchors and expressed them in ''E.coli''. ''E.coli'' expressing the same type and amount of cytoplasmic enzymes is set as control group.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To test whether Membrane Accelerator could accelerate naphthalene biodegradation pathway, we are trying to link six crucial enzymes (NahA, B, C, D and E) to orderly organized membrane anchors and expressed them in ''E.coli''. ''E.coli'' expressing the same type and amount of cytoplasmic enzymes is set as control group.</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>[[File:12SJTU_PAHconstruction.png|thumb|600px|center|Demonstration of Membrane Accelerator designed for speeding naphthalene biodegradation process]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU_PAHconstruction.png|thumb|600px|center|<ins class="diffchange diffchange-inline">''Fig2:''</ins>Demonstration of Membrane Accelerator designed for speeding naphthalene biodegradation process]]</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>==Biodesulfurization of Dibenzothiophene (DBT) ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Biodesulfurization of Dibenzothiophene (DBT) ==</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 80:</td>
<td colspan="2" class="diff-lineno">Line 80:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the first three steps of the this Desulfurization pathway require FMNH<sub>2</sub> as a reductant. In order to regain this power an Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the reaction to proceed. For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization Wiki of team Calgary]</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>[[File:12SJTU desulpathway.png|thumb|700px|center|The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulpathway.png|thumb|700px|center|<ins class="diffchange diffchange-inline">''Fig3:''</ins>The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD.]]</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>=== Design of Experiment===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Design of Experiment===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>As shown above, DszD plays a special role in this Biodesulfurization pathway: offering FMNH<sub>2</sub> for DszC and DszA. Ideal organization of the four enzymes should be DszC, DszA and DszB aligning together, with DszD paired with DszC and DszA respectively(''Fig.''). In this way, metabolic flux in desulfurization pathway could be facilitated and accelerated. All intermediates could be passed to downstream enzymes efficiently. Furthermore, paired DszD could offer sufficient amount of FMNH<sub>2</sub> for DszC and DszA in time.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>As shown above, DszD plays a special role in this Biodesulfurization pathway: offering FMNH<sub>2</sub> for DszC and DszA. Ideal organization of the four enzymes should be DszC, DszA and DszB aligning together, with DszD paired with DszC and DszA respectively(''Fig.<ins class="diffchange diffchange-inline">4</ins>''). In this way, metabolic flux in desulfurization pathway could be facilitated and accelerated. All intermediates could be passed to downstream enzymes efficiently. Furthermore, paired DszD could offer sufficient amount of FMNH<sub>2</sub> for DszC and DszA in time.</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>[[File:12SJTU desulidealconstruction.png|thumb|600px|center|Ideal organization of DszA, DszB, DszC and DszD in desulfurization pathway. In each assembly two DszD should be paired with DszC and DszA respectively to offer FMNH<sub>2</sub> timely]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulidealconstruction.png|thumb|600px|center|<ins class="diffchange diffchange-inline">''Fig4:''</ins>Ideal organization of DszA, DszB, DszC and DszD in desulfurization pathway. In each assembly two DszD should be paired with DszC and DszA respectively to offer FMNH<sub>2</sub> timely]]</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>This ideal organization of enzymes is hard to achieve with traditional linear synthetic scaffolds. However, Membrane Scaffold is two dimensional, so we can organize corresponding enzymes in desired two dimensional pattern. This again shows the superiority of Membrane Scaffold.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This ideal organization of enzymes is hard to achieve with traditional linear synthetic scaffolds. However, Membrane Scaffold is two dimensional, so we can organize corresponding enzymes in desired two dimensional pattern. This again shows the superiority of Membrane Scaffold.</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 are trying to organize DszA, DszB, DszC and DszD according to the pattern shown in ''<del class="diffchange diffchange-inline">Fig</del>''. Due to decreased distance between those enzymes and optimized organization, the proceeding speed of Biodesulfurization pathway should increase sharply.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We are trying to organize DszA, DszB, DszC and DszD according to the pattern shown in ''<ins class="diffchange diffchange-inline">Fig4</ins>''. Due to decreased distance between those enzymes and optimized organization, the proceeding speed of Biodesulfurization pathway should increase sharply.</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>[[File:12SJTU desulconstruction.png|thumb|700px|center|Sketch map of Desulfurizing ''Membrane Accelerator'']]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:12SJTU desulconstruction.png|thumb|700px|center|<ins class="diffchange diffchange-inline">''Fig5:''</ins>Sketch map of Desulfurizing ''Membrane Accelerator'']]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reference==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reference==</div></td></tr>
</table>AleAlejandro