http://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Arsenic_reporter/June10&feed=atom&action=historyTeam:Cornell/Notebook/Arsenic reporter/June10 - Revision history2024-03-29T00:16:04ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Arsenic_reporter/June10&diff=42107&oldid=prevM.Simpson: Blanked the page2012-07-19T19:49:58Z<p>Blanked the page</p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">{{:Team:Cornell/TOC|right}}</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;">The goal of the arsenate reporter is to detect soluble arsenic-containing compounds and produce an electrical current. In this subproject, we put control of the mtrB gene under an arsenate-inducible promoter, allowing Shewanella to activate the [[Team:Cornell/Project/Mtr pathway|Mtr pathway]], producing an electrical current.</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;">[[Team:Cornell/Notebook/Arsenic_reporter|Back to arsenic reporter week view]]</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">=June 10th-16th=</del></div></td><td colspan="2"> </td></tr>
</table>M.Simpsonhttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Arsenic_reporter/June10&diff=24096&oldid=prevCpaduano at 21:50, 3 July 20122012-07-03T21:50:27Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:Cornell/Notebook/Arsenic_reporter|Back to arsenic reporter week view]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:Cornell/Notebook/Arsenic_reporter|Back to arsenic reporter week view]]</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">==</del>=June 10th-16th<del class="diffchange diffchange-inline">==</del>=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=June 10th-16th=</div></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Arsenic_reporter/June10&diff=24072&oldid=prevCpaduano at 21:41, 3 July 20122012-07-03T21:41:21Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Cornell/TOC|right}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Cornell/TOC|right}}</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The <del class="diffchange diffchange-inline">purpose </del>of <del class="diffchange diffchange-inline">this subproject </del>is to <del class="diffchange diffchange-inline">make the nah operon biobrick compatible for the use of future iGEM teams. The nah operon codes for a pathway that converts naphthalene into salicylate</del>. In <del class="diffchange diffchange-inline">our system</del>, <del class="diffchange diffchange-inline">this will allow naphthalene to be detected by </del>the <del class="diffchange diffchange-inline">salicylate reporter. There are three standard cut sites internal </del>to the <del class="diffchange diffchange-inline">operon which we are removing - PstI</del>, <del class="diffchange diffchange-inline">and two NotI sites. This biobrick compatible piece could be useful to future teams in projects that involve bioremediation or detection of naphthalene</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The <ins class="diffchange diffchange-inline">goal </ins>of <ins class="diffchange diffchange-inline">the arsenate reporter </ins>is to <ins class="diffchange diffchange-inline">detect soluble arsenic-containing compounds and produce an electrical current</ins>. In <ins class="diffchange diffchange-inline">this subproject</ins>, <ins class="diffchange diffchange-inline">we put control of </ins>the <ins class="diffchange diffchange-inline">mtrB gene under an arsenate-inducible promoter, allowing Shewanella </ins>to <ins class="diffchange diffchange-inline">activate </ins>the <ins class="diffchange diffchange-inline">[[Team:Cornell/Project/Mtr pathway|Mtr pathway]]</ins>, <ins class="diffchange diffchange-inline">producing an electrical current</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:Cornell/Notebook/Arsenic_reporter|Back to arsenic reporter week view]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:Cornell/Notebook/Arsenic_reporter|Back to arsenic reporter week view]]</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>===June 10th-16th===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===June 10th-16th===</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;">====June 13th, Wednesday====</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;">*Set up [[PCR]] for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites concurrently with Gibson Assembly. Also set up a PCR for the entire nah operon. Due to length of the fragments, a longer extension time was chosen.</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;">*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon using Phusion polymerase, an alternate method of mutation using Phusion will be pursued.</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;">**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</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;"></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;">====June 14th, Thursday====</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;">*PCR only amplified nah1, nah3, and nah4 - longer fragments (nah2, the full nah operon, and pBMT-1) were not identified on the PCR product gel. Set up another [[PCR]] with shorter extension time.</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;"></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;">====June 15th, Friday====</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;">*PCR of four out of five products visible on gel. Set up PCR of pBMT-1, final fragment required for Gibson Assembly of the nah operon.</del></div></td><td colspan="2"> </td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Arsenic_reporter/June10&diff=24013&oldid=prevCpaduano at 21:11, 3 July 20122012-07-03T21:11:32Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Cornell/TOC|right}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Cornell/TOC|right}}</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;">The purpose of this subproject is to make the nah operon biobrick compatible for the use of future iGEM teams. The nah operon codes for a pathway that converts naphthalene into salicylate. In our system, this will allow naphthalene to be detected by the salicylate reporter. There are three standard cut sites internal to the operon which we are removing - PstI, and two NotI sites. This biobrick compatible piece could be useful to future teams in projects that involve bioremediation or detection of naphthalene.</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;">[[Team:Cornell/Notebook/Arsenic_reporter|Back to arsenic reporter week view]]</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;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===June 10th-16th===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===June 10th-16th===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====June 13th, Wednesday====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====June 13th, Wednesday====</div></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Arsenic_reporter/June10&diff=24009&oldid=prevCpaduano at 21:09, 3 July 20122012-07-03T21:09:45Z<p></p>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">{{:Team:Cornell/TOC|right}}</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===June 10th-16th===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===June 10th-16th===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====June 13th, Wednesday====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====June 13th, Wednesday====</div></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Arsenic_reporter/June10&diff=24008&oldid=prevCpaduano: Created page with "===June 10th-16th=== ====June 13th, Wednesday==== *Set up PCR for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites ..."2012-07-03T21:09:23Z<p>Created page with "===June 10th-16th=== ====June 13th, Wednesday==== *Set up <a href="/wiki/index.php?title=PCR&action=edit&redlink=1" class="new" title="PCR (page does not exist)">PCR</a> for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites ..."</p>
<p><b>New page</b></p><div>===June 10th-16th===<br />
====June 13th, Wednesday====<br />
*Set up [[PCR]] for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites concurrently with Gibson Assembly. Also set up a PCR for the entire nah operon. Due to length of the fragments, a longer extension time was chosen.<br />
*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon using Phusion polymerase, an alternate method of mutation using Phusion will be pursued.<br />
**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''<br />
<br />
====June 14th, Thursday====<br />
*PCR only amplified nah1, nah3, and nah4 - longer fragments (nah2, the full nah operon, and pBMT-1) were not identified on the PCR product gel. Set up another [[PCR]] with shorter extension time.<br />
<br />
====June 15th, Friday====<br />
*PCR of four out of five products visible on gel. Set up PCR of pBMT-1, final fragment required for Gibson Assembly of the nah operon.</div>Cpaduano