http://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&feed=atom&action=historyTeam:ETH Zurich/labblog/20140825 - Revision history2024-03-28T10:46:48ZRevision history for this page on the wikiMediaWiki 1.16.5http://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=192937&oldid=prevClormeau at 15:10, 11 October 20142014-10-11T15:10:10Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td></tr>
</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=192610&oldid=prevClormeau at 14:31, 11 October 20142014-10-11T14:31:42Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td></tr>
</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=172469&oldid=prevClormeau at 01:36, 8 October 20142014-10-08T01:36:22Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:ETH_Zurich_Diffusion4.JPG|center|500px|thumb|Diffusion experiment with beads. Click [https://2014.igem.org/Team:ETH_Zurich/Video3 here] to watch the video.]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:ETH_Zurich_Diffusion4.JPG|center|500px|thumb|Diffusion experiment with beads. Click [https://2014.igem.org/Team:ETH_Zurich/Video3 here] to watch the video.]]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><html<del class="diffchange diffchange-inline">> <p class="read-more"><a href="#diffusionexp" class="button twolines">Read More</a></p</del>> </article></html></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><html> </article></html></div></td></tr>
</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=172373&oldid=prevClormeau at 00:44, 8 October 20142014-10-08T00:44:05Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td></tr>
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</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=172237&oldid=prevClormeau at 23:18, 7 October 20142014-10-07T23:18:46Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Diffusion Experiments == </div></td></tr>
</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=109836&oldid=prevClormeau: /* Monday, 25th August */2014-09-09T11:48:46Z<p><span class="autocomment">Monday, 25th August</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Three main experiment designs were tested and modified: the agar-design, the liquid-design and the beads-design. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Three main experiment designs were tested and modified: the agar-design, the liquid-design and the beads-design. </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>For the agar-design we filled the chamber and channels with LB-agar or in a second attempt with agarose only. Subsequently, we punched a cylindric hole in each chamber. The capacities were filled with regulator/sensor strain culture or AHL/AHL producer strain culture, respectively. After 3 to 4 h at 37 °C we could observe an increase in the sfGFP signal. Since we used comparably high concentration of AHL in our first attempts, we could not detect a delayed sfGFP signal for chambers connected by a longer channel. The experiment will be repeated using lower concentrations. However, conducting the experiment using the agar-design, we encountered a problem: after some hours the LB-agar/agarose started to shrink and dried out. Thus, the agar-design cannot be used without modifications for experiments of longer duration. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>For the agar-design we filled the chamber and channels with LB-agar or in a second attempt with agarose only. Subsequently, we punched a cylindric hole in each chamber. The capacities were filled with regulator/sensor strain culture or AHL/AHL producer strain culture, respectively. After 3 to 4 h at 37 °C we could observe an increase in the sfGFP signal. Since we used comparably high concentration of AHL in our first attempts, we could not detect a delayed sfGFP signal for chambers connected by a longer channel. The experiment will be repeated using lower concentrations. However, conducting the experiment using the agar-design, we encountered a problem: after some hours the LB-agar/agarose started to shrink and dried out. Thus, the agar-design cannot be used without modifications for experiments of longer duration. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>In an attempt we only left a small agar fragment in each channel and filled the rest with liquid medium, so as to decrease chance of it drying out, while avoiding at the same time that bacteria from one chamber reach the other chamber. </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>The bead-design consists of an alginate bead for each chamber and liquid medium in between. The beads either contained regulator/sensor-bacteria or AHL.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In an attempt we only left a small agar fragment in each channel and filled the rest with liquid medium, so as to decrease chance of it drying out, while avoiding at the same time that bacteria from one chamber reach the other chamber. </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>The bead-design consists of an alginate bead for each chamber and liquid medium in between. The beads either contained regulator/sensor-bacteria or AHL.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=109835&oldid=prevClormeau: /* Monday, 25th August */2014-09-09T11:48:05Z<p><span class="autocomment">Monday, 25th August</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Now that we tested the different constructs for leakiness, dose response and cross talk, we are investigating in the diffusion rate of AHL. Therefore we designed a chip with chambers connected by channels of different length (see figure). In one chamber we added a strain containing a regulator and a sensor plasmid, to the second chamber we added AHL or an AHL producer strain. As soon as AHL is diffused to the former chamber it induces sfGFP production on the sensor plasmid. The time it takes until we can measure the sfGFP signal and the length of the channel gives us information about the velocity of AHL diffusion.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Now that we tested the different constructs for leakiness, dose response and cross talk, we are investigating in the diffusion rate of AHL. Therefore we designed a chip with chambers connected by channels of different length (see figure). In one chamber we added a strain containing a regulator and a sensor plasmid, to the second chamber we added AHL or an AHL producer strain. As soon as AHL is diffused to the former chamber it induces sfGFP production on the sensor plasmid. The time it takes until we can measure the sfGFP signal and the length of the channel gives us information about the velocity of AHL diffusion.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:Channelchip.jpg|<del class="diffchange diffchange-inline">x300px</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:Channelchip.jpg|<ins class="diffchange diffchange-inline">center|300px|thumb|PDMS millifluidic chip used for diffusion experiments</ins>]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Three main experiment designs were tested and modified: the agar-design, the liquid-design and the beads-design. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Three main experiment designs were tested and modified: the agar-design, the liquid-design and the beads-design. </div></td></tr>
</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=109833&oldid=prevClormeau: /* Monday, 25th August */2014-09-09T11:47:06Z<p><span class="autocomment">Monday, 25th August</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Channelchip.jpg|x300px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Channelchip.jpg|x300px]]</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">Two </del>main experiment designs were tested and modified: the agar-design and the beads-design. For the agar-design we filled the chamber and channels with LB-agar or in a second attempt with agarose only. Subsequently, we punched a cylindric hole in each chamber. The capacities were filled with regulator/sensor strain culture or AHL/AHL producer strain culture, respectively. After 3 to 4 h at 37 °C we could observe an increase in the sfGFP signal. Since we used comparably high concentration of AHL in our first attempts, we could not detect a delayed sfGFP signal for chambers connected by a longer channel. The experiment will be repeated using lower concentrations. However, <del class="diffchange diffchange-inline">the </del>conducting the experiment using the agar-design, we encountered a problem: after some hours the LB-agar/agarose started to shrink and dried out. Thus, the agar-design cannot be used without modifications for experiments of longer duration. In an attempt we only left a small agar fragment in each channel, so as to decrease chance of it drying out, while avoiding at the same time that bacteria from one chamber reach the other chamber. <del class="diffchange diffchange-inline">At the moment, we are optimising the agar-design.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Three </ins>main experiment designs were tested and modified: the agar<ins class="diffchange diffchange-inline">-design, the liquid</ins>-design and the beads-design. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The bead-design consists of an alginate bead for each chamber and <del class="diffchange diffchange-inline">a </del>liquid medium in between. The beads either contained regulator/sensor-bacteria or AHL.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>For the agar-design we filled the chamber and channels with LB-agar or in a second attempt with agarose only. Subsequently, we punched a cylindric hole in each chamber. The capacities were filled with regulator/sensor strain culture or AHL/AHL producer strain culture, respectively. After 3 to 4 h at 37 °C we could observe an increase in the sfGFP signal. Since we used comparably high concentration of AHL in our first attempts, we could not detect a delayed sfGFP signal for chambers connected by a longer channel. The experiment will be repeated using lower concentrations. However, conducting the experiment using the agar-design, we encountered a problem: after some hours the LB-agar/agarose started to shrink and dried out. Thus, the agar-design cannot be used without modifications for experiments of longer duration. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In an attempt we only left a small agar fragment in each channel <ins class="diffchange diffchange-inline">and filled the rest with liquid medium</ins>, so as to decrease chance of it drying out, while avoiding at the same time that bacteria from one chamber reach the other chamber. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The bead-design consists of an alginate bead for each chamber and liquid medium in between. The beads either contained regulator/sensor-bacteria or AHL.</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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</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=109831&oldid=prevClormeau: /* Monday, 25th August */2014-09-09T11:42:46Z<p><span class="autocomment">Monday, 25th August</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Two main experiment designs were tested and modified: the agar-design and the beads-design. For the agar-design we filled the chamber and channels with LB-agar or in a second attempt with agarose only. Subsequently, we punched a cylindric hole in each chamber. The capacities were filled with regulator/sensor strain culture or AHL/AHL producer strain culture, respectively. After 3 to 4 h at 37 °C we could observe an increase in the sfGFP signal. Since we used comparably high concentration of AHL in our first attempts, we could not detect a delayed sfGFP signal for chambers connected by a longer channel. The experiment will be repeated using lower concentrations. However, the conducting the experiment using the agar-design, we encountered a problem: after some hours the LB-agar/agarose started to shrink and dried out. Thus, the agar-design cannot be used without modifications for experiments of longer duration. In an attempt we only left a small agar fragment in each channel, so as to decrease chance of it drying out, while avoiding at the same time that bacteria from one chamber reach the other chamber. At the moment, we are optimising the agar-design.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Two main experiment designs were tested and modified: the agar-design and the beads-design. For the agar-design we filled the chamber and channels with LB-agar or in a second attempt with agarose only. Subsequently, we punched a cylindric hole in each chamber. The capacities were filled with regulator/sensor strain culture or AHL/AHL producer strain culture, respectively. After 3 to 4 h at 37 °C we could observe an increase in the sfGFP signal. Since we used comparably high concentration of AHL in our first attempts, we could not detect a delayed sfGFP signal for chambers connected by a longer channel. The experiment will be repeated using lower concentrations. However, the conducting the experiment using the agar-design, we encountered a problem: after some hours the LB-agar/agarose started to shrink and dried out. Thus, the agar-design cannot be used without modifications for experiments of longer duration. In an attempt we only left a small agar fragment in each channel, so as to decrease chance of it drying out, while avoiding at the same time that bacteria from one chamber reach the other chamber. At the moment, we are optimising the agar-design.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The bead-design consists of an alginate bead for each chamber and a liquid medium in between. The beads either contained regulator/sensor-bacteria or AHL.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The bead-design consists of an alginate bead for each chamber and a liquid medium in between. The beads either contained regulator/sensor-bacteria or AHL.</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>
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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;">[[File:ETH_Zurich_Diffusion2.JPG|center|500px|thumb|Diffusion experiment with agar. Click [https://2014.igem.org/Team:ETH_Zurich/Video1 here] to watch the video.]]</ins></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;">[[File:ETH_Zurich_Diffusion3.JPG|center|500px|thumb|Diffusion experiment with liquid. Click [https://2014.igem.org/Team:ETH_Zurich/Video2 here] to watch the video. ]]</ins></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;">[[File:ETH_Zurich_Diffusion4.JPG|center|500px|thumb|Diffusion experiment with beads. Click [https://2014.igem.org/Team:ETH_Zurich/Video3 here] to watch the video.]]</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:ETH_Zurich/tpl/topbutton}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:ETH_Zurich/tpl/topbutton}}</div></td></tr>
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</table>Clormeauhttp://2014.igem.org/wiki/index.php?title=Team:ETH_Zurich/labblog/20140825&diff=102080&oldid=prevClormeau: /* Monday, 25th August */2014-09-03T13:36:13Z<p><span class="autocomment">Monday, 25th August</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Monday, 25th August ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Monday, 25th August ====</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Now that we tested the different constructs for leakiness, dose response and cross talk, we are investigating in the diffusion rate of AHL. <del class="diffchange diffchange-inline">Therefor </del>we designed a chip with chambers connected by channels of different length (see figure). In one chamber we added a strain containing a regulator and a sensor plasmid, to the second chamber we added AHL or an AHL producer strain. As soon as AHL is diffused to the former chamber it induces sfGFP production on the sensor plasmid. The time it takes until we can measure the sfGFP signal and the length of the channel gives us information about the velocity of AHL diffusion.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Now that we tested the different constructs for leakiness, dose response and cross talk, we are investigating in the diffusion rate of AHL. <ins class="diffchange diffchange-inline">Therefore </ins>we designed a chip with chambers connected by channels of different length (see figure). In one chamber we added a strain containing a regulator and a sensor plasmid, to the second chamber we added AHL or an AHL producer strain. As soon as AHL is diffused to the former chamber it induces sfGFP production on the sensor plasmid. The time it takes until we can measure the sfGFP signal and the length of the channel gives us information about the velocity of AHL diffusion.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Channelchip.jpg|x300px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Channelchip.jpg|x300px]]</div></td></tr>
</table>Clormeau