http://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&feed=atom&action=historyTeam:NTNU Trondheim/Experiments and Results - Revision history2024-03-28T23:58:37ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=224340&oldid=prevOyas: /* Colicin (BBa_K822002) */2012-09-26T23:37:05Z<p><span class="autocomment">Colicin (BBa_K822002)</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|style="vertical-align: top;"|[[File:Colisin2.png|thumb|center|450px|OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|style="vertical-align: top;"|[[File:Colisin2.png|thumb|center|450px|OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[File:Colisin_1.png|thumb|center|450px|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|style="vertical-align: top;"</ins>|[[File:Colisin_1.png|thumb|center|450px|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</div></td></tr>
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</table>Oyashttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=224312&oldid=prevOyas: /* Colicin (BBa_K822002) */2012-09-26T23:36:31Z<p><span class="autocomment">Colicin (BBa_K822002)</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We performed two experiments; one experiment with two parallel cell cultures, where one was containing colicin and the other buffer (1), and one experiment with two parallels of cells with colicin lysate added, and one with lysate of non-colicin-producing cells added (2). The latter experiment was performed to prove that no other proteins expressed by the cells inhibited growth in other cells. The results of the experiments are given below:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We performed two experiments; one experiment with two parallel cell cultures, where one was containing colicin and the other buffer (1), and one experiment with two parallels of cells with colicin lysate added, and one with lysate of non-colicin-producing cells added (2). The latter experiment was performed to prove that no other proteins expressed by the cells inhibited growth in other cells. The results of the experiments are given below:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Colisin2.png|thumb|center|<del class="diffchange diffchange-inline">400px|</del>|OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">{| style="margin: 1em auto 1em auto; width: auto;"</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">|style="vertical-align: top;"|</ins>[[File:Colisin2.png|thumb|center|<ins class="diffchange diffchange-inline">450px</ins>|OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)]]</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">|</ins>[[File:Colisin_1.png|thumb|center|<ins class="diffchange diffchange-inline">450px</ins>|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Colisin_1.png|thumb|center|<del class="diffchange diffchange-inline">400px|</del>|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|}</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added.</div></td></tr>
</table>Oyashttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=224129&oldid=prevGunvor: /* Colicin (BBa_K822002) */2012-09-26T23:33:27Z<p><span class="autocomment">Colicin (BBa_K822002)</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We performed two experiments; one experiment with two parallel cell cultures, where one was containing colicin and the other buffer (1), and one experiment with two parallels of cells with colicin lysate added, and one with lysate of non-colicin-producing cells added (2). The latter experiment was performed to prove that no other proteins expressed by the cells inhibited growth in other cells. The results of the experiments are given below:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We performed two experiments; one experiment with two parallel cell cultures, where one was containing colicin and the other buffer (1), and one experiment with two parallels of cells with colicin lysate added, and one with lysate of non-colicin-producing cells added (2). The latter experiment was performed to prove that no other proteins expressed by the cells inhibited growth in other cells. The results of the experiments are given below:</div></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;">[[File:Colisin2.png|thumb|center|500px||OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)]]</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>[[File:Colisin_1.png|thumb|center|<del class="diffchange diffchange-inline">500px</del>||OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Colisin_1.png|thumb|center|<ins class="diffchange diffchange-inline">400px</ins>||OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</div></td></tr>
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</table>Gunvorhttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=224085&oldid=prevGunvor: /* Colicin (BBa_K822002) */2012-09-26T23:32:38Z<p><span class="autocomment">Colicin (BBa_K822002)</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We performed two experiments; one experiment with two parallel cell cultures, where one was containing colicin and the other buffer (1), and one experiment with two parallels of cells with colicin lysate added, and one with lysate of non-colicin-producing cells added (2). The latter experiment was performed to prove that no other proteins expressed by the cells inhibited growth in other cells. The results of the experiments are given below:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We performed two experiments; one experiment with two parallel cell cultures, where one was containing colicin and the other buffer (1), and one experiment with two parallels of cells with colicin lysate added, and one with lysate of non-colicin-producing cells added (2). The latter experiment was performed to prove that no other proteins expressed by the cells inhibited growth in other cells. The results of the experiments are given below:</div></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;">{|</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;">|[[File:Colisin2.png|thumb|center|500px||OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)]]</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 class="diffchange diffchange-inline">{</del>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[File:Colisin2.png</ins>|<ins class="diffchange diffchange-inline">thumb</ins>|<ins class="diffchange diffchange-inline">center|500px||OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)]]</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[File:Colisin_1.png|thumb|center|500px||OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</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">|}</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Colisin_1.png|thumb|center|500px||OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added.</div></td></tr>
</table>Gunvorhttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=224004&oldid=prevGunvor: /* Colicin (BBa_K822002) */2012-09-26T23:31:06Z<p><span class="autocomment">Colicin (BBa_K822002)</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|</div></td><td class='diff-marker'> </td><td style="background: #eee; 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>|[[File:Colisin2.png|500px<del class="diffchange diffchange-inline">]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[File:Colisin2.png<ins class="diffchange diffchange-inline">|thumb|center</ins>|500px||OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)<ins class="diffchange diffchange-inline">]]</ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)</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>|[[File:Colisin_1.png|500px<del class="diffchange diffchange-inline">]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[File:Colisin_1.png<ins class="diffchange diffchange-inline">|thumb|center</ins>|500px||OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)<ins class="diffchange diffchange-inline">]]</ins></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></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>|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)</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>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added. <del class="diffchange diffchange-inline"> </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==YFP generator (<partinfo>BBa_K822003</partinfo>)==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==YFP generator (<partinfo>BBa_K822003</partinfo>)==</div></td></tr>
</table>Gunvorhttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=223881&oldid=prevGunvor at 23:28, 26 September 20122012-09-26T23:28:55Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|OD measured over time in cell cultures with added colicin lysate (red dots) and buffer (blue dots)</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[File:<del class="diffchange diffchange-inline">Colicin_1</del>.png|500px]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[File:<ins class="diffchange diffchange-inline">Colisin_1</ins>.png|500px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)</div></td></tr>
</table>Gunvorhttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=223819&oldid=prevGunvor at 23:27, 26 September 20122012-09-26T23:27:29Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|[[File:<del class="diffchange diffchange-inline">Colicin1</del>.png|500px]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|[[File:<ins class="diffchange diffchange-inline">Colicin_1</ins>.png|500px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|OD measured over time in two parallel cell cultures with added colicin lysate (red and purple dots) and lysate of non-colicin-producing cells (blue dots)</div></td></tr>
</table>Gunvorhttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=223066&oldid=prevOyas at 23:13, 26 September 20122012-09-26T23:13:05Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|GTTTCTTCCTGCAGCGGCCGCTACTAGTAtgcgatggtccctccctgaa</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|GTTTCTTCCTGCAGCGGCCGCTACTAGTAtgcgatggtccctccctgaa</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To test if the our colicin brick worked, we cloned it together with a constitutive promoter + RBS <partinfo>BBa_K081005</partinfo>. Then, we grew overnight cultures with the Promoter+RBS+Colicin construct, and also with a negative control. The negative control were different in different experiments, but were always cells containing a non-expressing plasmid with ampicillin resistance, since the plasmid colicin was tested in, also had ampicillin resistance. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To test if the our colicin brick worked, we cloned it together with a constitutive promoter + RBS <partinfo>BBa_K081005</partinfo>. Then, we grew overnight cultures with the Promoter+RBS+Colicin construct, and also with a negative control. The negative control were different in different experiments, but were always cells containing a non-expressing plasmid with ampicillin resistance, since the plasmid colicin was tested in, also had ampicillin resistance. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Both experiments show that the cells without added colicin lysate has a significantly higher growth rate than the cells where colicin lysate was added. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==YFP generator (<partinfo>BBa_K822003</partinfo>)==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==YFP generator (<partinfo>BBa_K822003</partinfo>)==</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The primers used to amplify the sequence are given below:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The primers used to amplify the sequence are given below:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|class="table table-bordered table-hover" style="margin: 1em auto 1em auto; width: auto;"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|class="table table-bordered table-hover" style="margin: 1em auto 1em auto; width: auto;"</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We did not have sufficient time to test the Plld EcR biobrick, but it was sent to sequencing in the official shipping plasmid, pSB1C3, and the sequencing result had a 100 % match with the theoretical sequence of the amplified Plld + RBS sequence in pSB1C3.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We did not have sufficient time to test the Plld EcR biobrick, but it was sent to sequencing in the official shipping plasmid, pSB1C3, and the sequencing result had a 100 % match with the theoretical sequence of the amplified Plld + RBS sequence in pSB1C3.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==ldhA promoter + RBS from ''C.glutamicum'' (<partinfo>BBa_K822001</partinfo>)==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==ldhA promoter + RBS from ''C.glutamicum'' (<partinfo>BBa_K822001</partinfo>)==</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We also amplified the ldhA promoter from ''Corynebacterium glutamicum''. This has similar properties as the lld promoter from ''E.coli'', so this promoter was also a candidate to being used as the lactate inducable promoter in our project.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We also amplified the ldhA promoter from ''Corynebacterium glutamicum''. This has similar properties as the lld promoter from ''E.coli'', so this promoter was also a candidate to being used as the lactate inducable promoter in our project.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ldhA promoter was amplified using the genome of ''C.glutamicum'' ATC 13032 as template, and the primers below:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ldhA promoter was amplified using the genome of ''C.glutamicum'' ATC 13032 as template, and the primers below:</div></td></tr>
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</table>Oyashttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=223003&oldid=prevOyas: /* BioBrick parts */2012-09-26T23:11:28Z<p><span class="autocomment">BioBrick parts</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__TOC__</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__TOC__</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==<del class="diffchange diffchange-inline">BioBrick parts</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline">Introduction</ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To make a genetic circuit releasing colicin as a response to a low oxygen level and a high lactate level, we needed several biobricks. For a detailed list of all biobricks present in our construct, see the [https://2012.igem.org/Team:NTNU_Trondheim/Parts parts page].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To make a genetic circuit releasing colicin as a response to a low oxygen level and a high lactate level, we needed several biobricks. For a detailed list of all biobricks present in our construct, see the [https://2012.igem.org/Team:NTNU_Trondheim/Parts parts page].</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>Oyashttp://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Experiments_and_Results&diff=222980&oldid=prevOyas at 23:10, 26 September 20122012-09-26T23:10:59Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__TOC__</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__TOC__</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">BioBrick parts</ins>==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==<del class="diffchange diffchange-inline">Experiments and results</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: #eee; color:black; font-size: smaller;"><div>To make a genetic circuit releasing colicin as a response to a low oxygen level and a high lactate level, we needed several biobricks. For a detailed list of all biobricks present in our construct, see the [https://2012.igem.org/Team:NTNU_Trondheim/Parts parts page].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To make a genetic circuit releasing colicin as a response to a low oxygen level and a high lactate level, we needed several biobricks. For a detailed list of all biobricks present in our construct, see the [https://2012.igem.org/Team:NTNU_Trondheim/Parts parts page].</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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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This page will focus on the biobricks we have made, how we made them, and how we have characterized them to show that they work.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This page will focus on the biobricks we have made, how we made them, and how we have characterized them to show that they work.</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> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==Colicin (<partinfo>BBa_K822002</partinfo>)==</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>==Colicin (<partinfo>BBa_K822002</partinfo>)<del class="diffchange diffchange-inline">=</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Colicin is the protein we have chosen as toxin in our bacterial anti-cancer-kamikaze device. We amplified the brick using <partinfo>BBa_K150009</partinfo> as template. The brick contains protein coding sequences both for Colicin E1 and for colicin immunity protein. The following primers were used:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Colicin is the protein we have chosen as toxin in our bacterial anti-cancer-kamikaze device. We amplified the brick using <partinfo>BBa_K150009</partinfo> as template. The brick contains protein coding sequences both for Colicin E1 and for colicin immunity protein. The following primers were used:</div></td></tr>
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<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>==YFP generator (<partinfo>BBa_K822003</partinfo>)<del class="diffchange diffchange-inline">=</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==YFP generator (<partinfo>BBa_K822003</partinfo>)==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We made the YFP generator to verify that the YFP coding sequence worked, in order to use it in experiments verifying that the Vgb promoter worked. The YFP generator was cloned together from a constitutive promoter + RBS (<partinfo>BBa_K081005</partinfo>), YFP (<partinfo>BBa_E0030</partinfo>) and a double terminator (<partinfo>BBa_B0015</partinfo>).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We made the YFP generator to verify that the YFP coding sequence worked, in order to use it in experiments verifying that the Vgb promoter worked. The YFP generator was cloned together from a constitutive promoter + RBS (<partinfo>BBa_K081005</partinfo>), YFP (<partinfo>BBa_E0030</partinfo>) and a double terminator (<partinfo>BBa_B0015</partinfo>).</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Even though we were not able to prove that the Vgb promoter works, we proved that the YFP generator works, as the fluorescence divided by OD is much higher for cells containing this biobrick, than for example for cells containing plasmids with only YFP.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Even though we were not able to prove that the Vgb promoter works, we proved that the YFP generator works, as the fluorescence divided by OD is much higher for cells containing this biobrick, than for example for cells containing plasmids with only YFP.</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>==Regulative LacI generator (<partinfo>BBa_K822004</partinfo>)<del class="diffchange diffchange-inline">=</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==Regulative LacI generator (<partinfo>BBa_K822004</partinfo>)==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We made this brick in an effort to improve an already existing biobrick. The brick we wanted to improve was <partinfo>BBa_K292006</partinfo>. The NTNU iGEM team 2011 tried to use this brick in their stress sensor, but did not get it to work. They also tried to test-cut it and investigate the fragments using gel electrophoresis, however the resulting fragments were not as expected. This is why we thought of this biobrick as a suitable candidate for improvement. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We made this brick in an effort to improve an already existing biobrick. The brick we wanted to improve was <partinfo>BBa_K292006</partinfo>. The NTNU iGEM team 2011 tried to use this brick in their stress sensor, but did not get it to work. They also tried to test-cut it and investigate the fragments using gel electrophoresis, however the resulting fragments were not as expected. This is why we thought of this biobrick as a suitable candidate for improvement. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; 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 class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">=</del>==lld promoter + RBS from ''E.coli'' (<partinfo>BBa_K822000</partinfo>)<del class="diffchange diffchange-inline">=</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==lld promoter + RBS from ''E.coli'' (<partinfo>BBa_K822000</partinfo>)==</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>The two criteria we wanted fulfilled to initiate lysis and subsequent release of colicin were a low oxygen level and a high lactate level. A promoter activated by low oxygen level was already present in the registry (microaerobic Vgb promoter, <partinfo>BBa_K561001</partinfo>), but we found no suitable lactate-induced promoter. Therefore, we decided to convert the promotor regulating the lldPRD operon in ''E.coli'' into a biobrick, and to use this biobrick in our project [[http://www.ncbi.nlm.nih.gov/pubmed/18263722 1]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The two criteria we wanted fulfilled to initiate lysis and subsequent release of colicin were a low oxygen level and a high lactate level. A promoter activated by low oxygen level was already present in the registry (microaerobic Vgb promoter, <partinfo>BBa_K561001</partinfo>), but we found no suitable lactate-induced promoter. Therefore, we decided to convert the promotor regulating the lldPRD operon in ''E.coli'' into a biobrick, and to use this biobrick in our project [[http://www.ncbi.nlm.nih.gov/pubmed/18263722 1]].</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 108:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></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;"></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>==ldhA promoter + RBS from ''C.glutamicum'' (<partinfo>BBa_K822001</partinfo>)<del class="diffchange diffchange-inline">=</del>==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==ldhA promoter + RBS from ''C.glutamicum'' (<partinfo>BBa_K822001</partinfo>)==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We also amplified the ldhA promoter from ''Corynebacterium glutamicum''. This has similar properties as the lld promoter from ''E.coli'', so this promoter was also a candidate to being used as the lactate inducable promoter in our project.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We also amplified the ldhA promoter from ''Corynebacterium glutamicum''. This has similar properties as the lld promoter from ''E.coli'', so this promoter was also a candidate to being used as the lactate inducable promoter in our project.</div></td></tr>
</table>Oyas