http://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&feed=atom&action=historyTeam:Cornell/Notebook/Nah operon/June10 - Revision history2024-03-29T15:39:07ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&diff=24113&oldid=prevCpaduano: /* June 14th, Thursday */2012-07-03T21:56:42Z<p><span class="autocomment">June 14th, Thursday</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==June 14th, Thursday==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==June 14th, Thursday==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*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 [[Team:Cornell/Notebook/<del class="diffchange diffchange-inline">PCR</del>|PCR]] with shorter extension time.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*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 [[Team:Cornell/Notebook/<ins class="diffchange diffchange-inline">Phusion_PCR</ins>|PCR]] with shorter extension 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: #eee; color:black; font-size: smaller;"><div>==June 15th, Friday==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==June 15th, Friday==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&diff=24112&oldid=prevCpaduano: /* June 13th, Wednesday */2012-07-03T21:56:33Z<p><span class="autocomment">June 13th, Wednesday</span></p>
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<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>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*Set up [[Team:Cornell/Notebook/<del class="diffchange diffchange-inline">PCR</del>|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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*Set up [[Team:Cornell/Notebook/<ins class="diffchange diffchange-inline">Phusion_PCR</ins>|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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using three sequential site-directed mutageneses will be pursued.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using three sequential site-directed mutageneses will be pursued.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</div></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&diff=24102&oldid=prevCpaduano at 21:51, 3 July 20122012-07-03T21:51:46Z<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/Nah_operon|Back to nah operon week view]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:Cornell/Notebook/Nah_operon|Back to nah operon 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: #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>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">==</del>==June 13th, Wednesday<del class="diffchange diffchange-inline">==</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==June 13th, Wednesday==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Set up [[Team:Cornell/Notebook/PCR|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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Set up [[Team:Cornell/Notebook/PCR|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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using three sequential site-directed mutageneses will be pursued.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using three sequential site-directed mutageneses will be pursued.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</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">==</del>==June 14th, Thursday<del class="diffchange diffchange-inline">==</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==June 14th, Thursday==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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 [[Team:Cornell/Notebook/PCR|PCR]] with shorter extension time.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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 [[Team:Cornell/Notebook/PCR|PCR]] with shorter extension 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><del class="diffchange diffchange-inline">==</del>==June 15th, Friday<del class="diffchange diffchange-inline">==</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==June 15th, Friday==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&diff=24062&oldid=prevCpaduano: /* June 10th-16th */2012-07-03T21:33:21Z<p><span class="autocomment">June 10th-16th</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 21:33, 3 July 2012</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====June 14th, Thursday====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====June 14th, Thursday====</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*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 [[<ins class="diffchange diffchange-inline">Team:Cornell/Notebook/PCR|</ins>PCR]] with shorter extension 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: #eee; color:black; font-size: smaller;"><div>====June 15th, Friday====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====June 15th, Friday====</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&diff=24061&oldid=prevCpaduano: /* June 10th-16th */2012-07-03T21:33:01Z<p><span class="autocomment">June 10th-16th</span></p>
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<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>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*Set up [[<ins class="diffchange diffchange-inline">Team:Cornell/Notebook/PCR|</ins>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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using three sequential site-directed mutageneses will be pursued.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using three sequential site-directed mutageneses will be pursued.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</div></td></tr>
</table>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&diff=24041&oldid=prevCpaduano: /* June 13th, Wednesday */2012-07-03T21:21:09Z<p><span class="autocomment">June 13th, Wednesday</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 21:21, 3 July 2012</td>
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<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>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*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.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon <del class="diffchange diffchange-inline">using Phusion polymerase</del>, an alternate method of mutation using <del class="diffchange diffchange-inline">Phusion </del>will be pursued.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using <ins class="diffchange diffchange-inline">three sequential site-directed mutageneses </ins>will be pursued.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''</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>Cpaduanohttp://2012.igem.org/wiki/index.php?title=Team:Cornell/Notebook/Nah_operon/June10&diff=24018&oldid=prevCpaduano: Created page with "{{:Team:Cornell/Navbar}} {{:Team:Cornell/TOC|right}} The purpose of this subproject is to make the nah operon biobrick compatible for the use of future iGEM teams. The nah operon..."2012-07-03T21:12:42Z<p>Created page with "{{:Team:Cornell/Navbar}} {{:Team:Cornell/TOC|right}} The purpose of this subproject is to make the nah operon biobrick compatible for the use of future iGEM teams. The nah operon..."</p>
<p><b>New page</b></p><div>{{:Team:Cornell/Navbar}}<br />
{{:Team:Cornell/TOC|right}}<br />
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.<br />
[[Team:Cornell/Notebook/Nah_operon|Back to nah operon week view]]<br />
<br />
===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