http://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&feed=atom&action=historyTeam:SDU-Denmark/Project - Revision history2024-03-29T09:21:08ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=161154&oldid=prevMbarnkob: /* Results */2009-10-22T00:14:14Z<p><span class="autocomment">Results</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Problems===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Problems===</div></td></tr>
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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;">Throughout most of the summer, we've had problems getting our ligations product sizes to match. What ever we tried nothing seemed to work, since it was always the wrong size. Then a few weeks ago, it was discovered, that the [[Team:SDU-Denmark/Parts/backbone_troubles|problem]] was with our backbone (1K from plate 1, 2009 spring distribution), not our work. 1K was suppose to be <partinfo>pSB1A3</partinfo>, but instead it was <partinfo>pSB1A2</partinfo>.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Sadly we didn't discover this till the very last week, and so we didn't get to do all the experiments we wanted, including one with an inducible promoter and one with our signaling peptide coupled with ''RIP''. </ins></div></td></tr>
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</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=160709&oldid=prevMbarnkob at 00:01, 22 October 20092009-10-22T00:01:37Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:SDU-Denmark/menu}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:SDU-Denmark/menu}}</div></td></tr>
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</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=160417&oldid=prevMbarnkob: /* Results */2009-10-21T23:52:03Z<p><span class="autocomment">Results</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are currently testing the quorum-quenching effect on ''S. aureus'' biofilm formation and the results are promising. The big question is whether or not, ''RIP'' gets exported out of ''E. coli'' and past the peptideglycan layer and capsule. The final results will be presented at the Jamboree.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We are currently testing the quorum-quenching effect on ''S. aureus'' biofilm formation and the results are promising. The big question is whether or not, ''RIP'' gets exported out of ''E. coli'' and past the peptideglycan layer and capsule. The final results will be presented at the Jamboree.</div></td></tr>
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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;">===Problems===</ins></div></td></tr>
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</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=160199&oldid=prevMbarnkob at 23:45, 21 October 20092009-10-21T23:45:27Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This peptide will make it easier to fight infections and kill ''S. aureus'' with conventional antibiotics.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This peptide will make it easier to fight infections and kill ''S. aureus'' with conventional antibiotics.</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 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;">==Other stuff==</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 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;">* Check out all our [[Team:SDU-Denmark/Protocols|protocols]].</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 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;">* See what [[Team:SDU-Denmark/Tools|tools]] we used.</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 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;">* Read our [[Team:SDU-Denmark/Safety|safety]] page.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Content==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Content==</div></td></tr>
</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=159156&oldid=prevMbarnkob: /* Our project in 1 minute */2009-10-21T23:14:33Z<p><span class="autocomment">Our project in 1 minute</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:SDU-Denmark-Clock-Icon.gif|<del class="diffchange diffchange-inline">30px</del>|right]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:SDU-Denmark-Clock-Icon.gif|<ins class="diffchange diffchange-inline">20px</ins>|right]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td></tr>
</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=159116&oldid=prevMbarnkob: /* Our project in 1 minute */2009-10-21T23:13:20Z<p><span class="autocomment">Our project in 1 minute</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:SDU-Denmark-Clock-Icon.gif|<del class="diffchange diffchange-inline">20px</del>|right]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:SDU-Denmark-Clock-Icon.gif|<ins class="diffchange diffchange-inline">30px</ins>|right]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td></tr>
</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=159097&oldid=prevMbarnkob: /* Our project in 1 minute */2009-10-21T23:12:49Z<p><span class="autocomment">Our project in 1 minute</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td></tr>
</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=159070&oldid=prevMbarnkob at 23:11, 21 October 20092009-10-21T23:11:05Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We want to fight hospital infections, using a biological machine.</div></td></tr>
</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=158798&oldid=prevMbarnkob: /* Biofilm assay */2009-10-21T23:03:10Z<p><span class="autocomment">Biofilm assay</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The assay was made on a 4*6-well plate. ''S.aureus'' were grown in the wells, thereby making biofilms. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The assay was made on a 4*6-well plate. ''S.aureus'' were grown in the wells, thereby making biofilms. </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We then added different ''E. coli''components to the wells: supernatant, crushed pellet and living ''E. coli''. After 24 hours the wells were washed three times with sterile 1x PBS solution to remove planctonic bacteria. Cells remaining adhered to the wells are subsequently stained with violet blue, the solution stands for 15 minutes and was washed twice.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We then added different ''E. coli'' components to the wells: supernatant, crushed pellet and living ''E. coli''. After 24 hours the wells were washed three times with sterile 1x PBS solution to remove planctonic bacteria. Cells remaining adhered to the wells are subsequently stained with violet blue, the solution stands for 15 minutes and was washed twice.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>1 ml of 96% ethanol was added to each stained well to loosen the biofilm. The biofilm was tested by measuring the absorbance by transferring the crystal violet/ethanol solution from each well to a cuvette, and measure the optical density (OD) of each of these samples at a wavelength of 595 nm.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>1 ml of 96% ethanol was added to each stained well to loosen the biofilm. The biofilm was tested by measuring the absorbance by transferring the crystal violet/ethanol solution from each well to a cuvette, and measure the optical density (OD) of each of these samples at a wavelength of 595 nm.</div></td></tr>
</table>Mbarnkobhttp://2009.igem.org/wiki/index.php?title=Team:SDU-Denmark/Project&diff=158655&oldid=prevMbarnkob: /* RIP expression in E. coli */2009-10-21T22:59:37Z<p><span class="autocomment">RIP expression in E. coli</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:SDU-Denmark-Nothern-Blot-RIP.jpg|200px|thumb|right|Northern blot of our 4 brick part (<partinfo>K237002</partinfo>) and our RIP-Terminator part (<partinfo>S04235</partinfo>). As seen here only the 4 brick part (left) is transcribed into mRNA and hopefully further translated into peptide.]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:SDU-Denmark-Nothern-Blot-RIP.jpg|200px|thumb|right|Northern blot of our 4 brick part (<partinfo>K237002</partinfo>) and our RIP-Terminator part (<partinfo>S04235</partinfo>). As seen here only the 4 brick part (left) is transcribed into mRNA and hopefully further translated into peptide.]]</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 have successfully assembled a 4<del class="diffchange diffchange-inline">-</del>brick part containing a constitutive promotor with RBS, our novel ''RIP'' part and a terminator. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We have successfully assembled a 4 brick part containing a constitutive promotor with RBS, our novel ''RIP'' part and a terminator. </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>Sequencing confirmed the 4<del class="diffchange diffchange-inline">-</del>brick part DNA sequence and a northern blot analysis confirmed that our ''E. coli'' indeed transcribes the ''RIP'' gene. To our knowledge this is the first recombinant organism to harbour and transcribe the ''RIP'' gene. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Sequencing confirmed the 4 brick part DNA sequence and a northern blot analysis confirmed that our ''E. coli'' indeed transcribes the ''RIP'' gene. To our knowledge this is the first recombinant organism to harbour and transcribe the ''RIP'' gene. </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>[[Image:SDU-Denmark-MALDI.jpg|200px|thumb|right|Mass spectrometry of supernatant from our 4 part ''RIP'' colony (A and C) compared with a reference colony (B and D). No conclusive results could be gathered from this analysis.]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:SDU-Denmark-MALDI.jpg|200px|thumb|right|Mass spectrometry of supernatant from our 4 part ''RIP'' colony (A and C) compared with a reference colony (B and D). No conclusive results could be gathered from this analysis.]]</div></td></tr>
</table>Mbarnkob