http://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&feed=atom&action=historyTeam:Calgary/Notebook/Journals/OLD ENTRIES - Revision history2024-03-29T05:14:01ZRevision history for this page on the wikiMediaWiki 1.16.0http://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203673&oldid=prevFwchung at 04:36, 29 September 20112011-09-29T04:36:50Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Finished growth experiment, results were as expected, the more naphthenic acid there was the slower the growth. Surprisingly the difference wasn’t large though, will repeat at different concentrations. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Finished growth experiment, results were as expected, the more naphthenic acid there was the slower the growth. Surprisingly the difference wasn’t large though, will repeat at different concentrations. </p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>The gel from the previous day did not turn up well <del class="diffchange diffchange-inline">(image) </del>so no conclusions were drawn from it. A growth curve experiment was performed for the <i>E. coli</i> cultred the previous day to assess what conditions (heat, shaking) the cells could grow in and to track the progression from lag to log to death phase. New agar plates were also made.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The gel from the previous day did not turn up well<ins class="diffchange diffchange-inline">, </ins>so no conclusions were drawn from it. A growth curve experiment was performed for the <i>E. coli</i> cultred the previous day to assess what conditions (heat, shaking) the cells could grow in and to track the progression from lag to log to death phase. New agar plates were also made.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 24, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 24, 2011</h4></div></td></tr>
</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203630&oldid=prevFwchung at 04:33, 29 September 20112011-09-29T04:33:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3>Project Participants</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h3>Project Participants</h3></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p> Everyone</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p> Everyone<ins class="diffchange diffchange-inline">.</ins></p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></br><h3>May 2, 2011 - May 5, 2011</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></br><h3>May 2, 2011 - May 5, 2011</h3></div></td></tr>
</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203622&oldid=prevFwchung at 04:33, 29 September 20112011-09-29T04:33:21Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>BNH: Felix created .4% by volume (0.01M) CPR stock solution. We ran tests on 10 and 100 times diluted solutions to characterize it. In the process we developed a new test protocol; We switched back to a voltage clamp set-up, the Faraday box was shown to be very effective (10 times less noise in box). We noticed that a higher concentration of CPR recovers faster from the voltage stress. In response to that we increased the time to at least 90 seconds to give all samples sufficient time to reach equilibrium while still keeping tests short. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>BNH: Felix created .4% by volume (0.01M) CPR stock solution. We ran tests on 10 and 100 times diluted solutions to characterize it. In the process we developed a new test protocol; We switched back to a voltage clamp set-up, the Faraday box was shown to be very effective (10 times less noise in box). We noticed that a higher concentration of CPR recovers faster from the voltage stress. In response to that we increased the time to at least 90 seconds to give all samples sufficient time to reach equilibrium while still keeping tests short. </p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Started an experiment to measure how well <del class="diffchange diffchange-inline">Pseudomonads </del>can grow on naphthenic acids by measuring OD over times and concentrations. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Started an experiment to measure how well <ins class="diffchange diffchange-inline"><i>pseudomonas</i> </ins>can grow on naphthenic acids by measuring OD over times and concentrations. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The culture from the previous day was miniprepped and restriction digested and a gel was run. Another culture of transformed <i>E. coli</i> was made for the viability assay planned this week to determine the viability of <i>E. coli</i> cells in different concentrations of NAs and in tailings water.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The culture from the previous day was miniprepped and restriction digested and a gel was run. Another culture of transformed <i>E. coli</i> was made for the viability assay planned this week to determine the viability of <i>E. coli</i> cells in different concentrations of NAs and in tailings water.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 24, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 24, 2011</h4></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><p>New project: a bioinformatics analysis of Pseudomonas putida and Pseudomonas fluorescens genomes to search for non-homologous genes/pathways. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>New project: a bioinformatics analysis of <ins class="diffchange diffchange-inline"><i></ins>Pseudomonas putida<ins class="diffchange diffchange-inline"></i> </ins>and <ins class="diffchange diffchange-inline"><i></ins>Pseudomonas fluorescens<ins class="diffchange diffchange-inline"></i> </ins>genomes to search for non-homologous genes/pathways. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The viability assay was performed and using the results of the previous day’s growth curve we managed to expose the <i>E. coli</i> cells to the different treatments (different concentrations of different types of NAs, and tailings water) when they were rapidly dividing in log phase. A culture was made of bacteria transformed with I732005.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The viability assay was performed and using the results of the previous day’s growth curve we managed to expose the <i>E. coli</i> cells to the different treatments (different concentrations of different types of NAs, and tailings water) when they were rapidly dividing in log phase. A culture was made of bacteria transformed with I732005.</p></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><p>The results of the assay showed that the <i>E. coli</i> did not survive in the naphthenic acid solutions but did survive in the tailings water (see NA viability Assays).</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The results of the assay showed that the <i>E. coli</i> did not survive in the naphthenic acid solutions but did survive in the tailings water (see NA viability Assays).</p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>The assay is going well, with the <del class="diffchange diffchange-inline">Pseudomonads </del>outperforming the <i>E. coli</i> so far. The race is on!</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The assay is going well, with the <ins class="diffchange diffchange-inline"><i>Pseudomonas</i> </ins>outperforming the <i>E. coli</i> so far. The race is on!</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 7, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 7, 2011</h4></div></td></tr>
</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203609&oldid=prevFwchung at 04:32, 29 September 20112011-09-29T04:32:15Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Finished growth experiment, results were as expected, the more naphthenic acid there was the slower the growth. Surprisingly the difference wasn’t large though, will repeat at different concentrations. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Finished growth experiment, results were as expected, the more naphthenic acid there was the slower the growth. Surprisingly the difference wasn’t large though, will repeat at different concentrations. </p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>The gel from the previous day did not turn up well (image) so no conclusions were drawn from it. A growth curve experiment was performed for the E. coli cultred the previous day to assess what conditions (heat, shaking) the cells could grow in and to track the progression from lag to log to death phase. New agar plates were also made.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The gel from the previous day did not turn up well (image) so no conclusions were drawn from it. A growth curve experiment was performed for the <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>cultred the previous day to assess what conditions (heat, shaking) the cells could grow in and to track the progression from lag to log to death phase. New agar plates were also made.</p></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><h4>June 24, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 24, 2011</h4></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><p>New project: a bioinformatics analysis of Pseudomonas putida and Pseudomonas fluorescens genomes to search for non-homologous genes/pathways. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>New project: a bioinformatics analysis of Pseudomonas putida and Pseudomonas fluorescens genomes to search for non-homologous genes/pathways. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The viability assay was performed and using the results of the previous day’s growth curve we managed to expose the E. coli cells to the different treatments (different concentrations of different types of NAs, and tailings water) when they were rapidly dividing in log phase. A culture was made of bacteria transformed with I732005.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The viability assay was performed and using the results of the previous day’s growth curve we managed to expose the <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>cells to the different treatments (different concentrations of different types of NAs, and tailings water) when they were rapidly dividing in log phase. A culture was made of bacteria transformed with I732005.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></br><h3>June 27, 2011 – July 1, 2011</h3></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></br><h3>June 27, 2011 – July 1, 2011</h3></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Examined the results of the viability assay and miniprepped the cultures of I732005 and another culture for I0500 + B0034 was also miniprepped. they were both digested and run on a gel and the gel from June 22, 2011 was repeated.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Examined the results of the viability assay and miniprepped the cultures of I732005 and another culture for I0500 + B0034 was also miniprepped. they were both digested and run on a gel and the gel from June 22, 2011 was repeated.</p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Created a Foght minimal media with no carbon source so we can test <del class="diffchange diffchange-inline">pseudomonas’ </del>ability to work with naphthenic acids. Made a test overnight culture to make sure it could grow in it (40mg/L naphthenic acids).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Created a Foght minimal media with no carbon source so we can test <ins class="diffchange diffchange-inline"><i>Pseudomonas</i>’ </ins>ability to work with naphthenic acids. Made a test overnight culture to make sure it could grow in it (40mg/L naphthenic acids).</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Ran through the general architecture of the wiki with the team. Seems to be approved. Uploaded images for the menu bar. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Ran through the general architecture of the wiki with the team. Seems to be approved. Uploaded images for the menu bar. </p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Started a viability assay with Pseudomonas and E.coli to see which we will use in our final product. Fun readings at 8am and pm for a week.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Started a viability assay with <ins class="diffchange diffchange-inline"><i></ins>Pseudomonas<ins class="diffchange diffchange-inline"></i> </ins>and <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>to see which we will use in our final product. Fun readings at 8am and pm for a week.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 6, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 6, 2011</h4></div></td></tr>
</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203592&oldid=prevFwchung at 04:30, 29 September 20112011-09-29T04:30:51Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 18, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 18, 2011</h4></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Patrick conducted a tutorial for the group on the parts registry and how to look up specific segments of DNA online. Also parts agar plates were made for culturing transformed E. coli. the registry parts R0040, K325219, K325100, K274002, K274003, K274004, K274100, and K274120 were selected for E. coli transformation.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Patrick conducted a tutorial for the group on the parts registry and how to look up specific segments of DNA online. Also parts agar plates were made for culturing transformed <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i></ins>. the registry parts R0040, K325219, K325100, K274002, K274003, K274004, K274100, and K274120 were selected for <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>transformation.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 19, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 19, 2011</h4></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 20, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 20, 2011</h4></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><p>BNH: Did first test readings with the amplifier. Since it was the first day most data we got turned out to be a learning experience. Since we were working with PAP, without knowing that it oxidizes in air and water, most of the readings were confusing. As a result we started working with a fixed current and measured the voltage, that setup gave us better readings with PAP. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>BNH: Did first test readings with the amplifier. Since it was the first day<ins class="diffchange diffchange-inline">, </ins>most data we got turned out to be a learning experience. Since we were working with PAP, without knowing that it oxidizes in air and water, most of the readings were confusing. As a result we started working with a fixed current and measured the voltage, that setup gave us better readings with PAP. </p></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;"></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><h4>June 21, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 21, 2011</h4></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><p>BNH: Took control measurements with pure <del class="diffchange diffchange-inline">H2O </del>and TPW. Measurements are (relatively) useless since we were still working with constant current, measured voltage.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>BNH: Took control measurements with pure <ins class="diffchange diffchange-inline">H<sub>2</sub>O </ins>and TPW. Measurements are (relatively) useless since we were still working with constant current, measured voltage.</p></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><p>After running comprehensive BLAST searches it was decided that our sequenced construct was not what we thought it was, we decided to make a culture (in the hopes of running a gel to confirm the identity) of the plate made from the third transformation of the construct made on June 7, 2011.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>After running comprehensive BLAST searches it was decided that our sequenced construct was not what we thought it was, we decided to make a culture (in the hopes of running a gel to confirm the identity) of the plate made from the third transformation of the construct made on June 7, 2011.</p></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: #eee; color:black; font-size: smaller;"><div><p>Started an experiment to measure how well Pseudomonads can grow on naphthenic acids by measuring OD over times and concentrations. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Started an experiment to measure how well Pseudomonads can grow on naphthenic acids by measuring OD over times and concentrations. </p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>The culture from the previous day was miniprepped and restriction digested and a gel was run. Another culture of transformed E. coli was made for the viability assay planned this week to determine the viability of E. coli cells in different concentrations of NAs and in tailings water.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The culture from the previous day was miniprepped and restriction digested and a gel was run. Another culture of transformed <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>was made for the viability assay planned this week to determine the viability of <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>cells in different concentrations of NAs and in tailings water.</p></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><img src="https://static.igem.org/mediawiki/2011/3/3e/UCAlgary2011_06.22.2011-restriction_digest_of_ORI_T-R.jpg" width="650px"></img></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2011/3/3e/UCAlgary2011_06.22.2011-restriction_digest_of_ORI_T-R.jpg" width="650px"></img></div></td></tr>
</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203568&oldid=prevFwchung at 04:28, 29 September 20112011-09-29T04:28:48Z<p></p>
<table style="background-color: white; color:black;">
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 5, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 5, 2011</h4></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><p>Glycerol stocks were prepared of the strain cultured the previous day, also the construct was sent for sequencing to confirm the identity. The viability assay (E. coli in NAs and tailings) design was improved and the assay was carried out (details of this can be found under the NA Viability Assays).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Glycerol stocks were prepared of the strain cultured the previous day, also the construct was sent for sequencing to confirm the identity. The viability assay (<ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>in NAs and tailings) design was improved and the assay was carried out (details of this can be found under the NA Viability Assays).</p></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><p>Ran through the general architecture of the wiki with the team. Seems to be approved. Uploaded images for the menu bar. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Ran through the general architecture of the wiki with the team. Seems to be approved. Uploaded images for the menu bar. </p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 6, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 6, 2011</h4></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><p>The results of the assay showed that the E. coli did not survive in the naphthenic acid solutions but did survive in the tailings water (see NA viability Assays).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The results of the assay showed that the <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>did not survive in the naphthenic acid solutions but did survive in the tailings water (see NA viability Assays).</p></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><p>The assay is going well, with the Pseudomonads outperforming the E.coli so far. The race is on!</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The assay is going well, with the Pseudomonads outperforming the <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>so far. The race is on!</p></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><h4>July 7, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>July 7, 2011</h4></div></td></tr>
</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203524&oldid=prevFwchung at 04:25, 29 September 20112011-09-29T04:25:39Z<p></p>
<table style="background-color: white; color:black;">
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 6, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 6, 2011</h4></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><p>A gel was run for the colony PCR performed over the weekend. Also all the previous stocks of I0500 were removed from the freezer and restriction digested then run on a gel. The I0500 that displayed complete digestion after 70 min was then selected to remake the construct made the previous week (I0050, I732019, 1AC3). <del class="diffchange diffchange-inline">the </del>construct was then used to transform top10 cells which were plated.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>A gel was run for the colony PCR performed over the weekend. Also all the previous stocks of I0500 were removed from the freezer and restriction digested then run on a gel. The I0500 that displayed complete digestion after 70 min was then selected to remake the construct made the previous week (I0050, I732019, 1AC3). <ins class="diffchange diffchange-inline">The </ins>construct was then used to transform top10 cells which were plated.</p></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><p>Discussed plans for the week. A poster for the ISMOS-3 conference on Monday is required. Patrick is working on this.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Discussed plans for the week. A poster for the ISMOS-3 conference on Monday is required. Patrick is working on this.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 7, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 7, 2011</h4></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><p>Hardly any colonies could be observed on the plates from the previous day in the morning so the construct was remade again and <del class="diffchange diffchange-inline">top10 </del>cells were transformed and then plated. Later in the day several colonies were observed on the plates containing the transformed cells from the previous day so the colonies were used to run a colony PCR and cultured overnight. <del class="diffchange diffchange-inline">Top10 </del>competent cells were also cultured overnight with the intention of generating new cells.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Hardly any colonies could be observed on the plates from the previous day in the morning so the construct was remade again and <ins class="diffchange diffchange-inline">TOP10 </ins>cells were transformed and then plated. Later in the day several colonies were observed on the plates containing the transformed cells from the previous day so the colonies were used to run a colony PCR and cultured overnight. <ins class="diffchange diffchange-inline">TOP10 </ins>competent cells were also cultured overnight with the intention of generating new cells.</p></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><p>BNH: Got the amplifier needed to test the electrical signal. started familiarization with software. we soon realized that we would need to shield the probe from electric interference to reduce noise. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>BNH: Got the amplifier needed to test the electrical signal. started familiarization with software. we soon realized that we would need to shield the probe from electric interference to reduce noise. </p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 8, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 8, 2011</h4></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><p>The PCR products from the previous night were run on a gel however the results of the gel indicated that the PCR was not successful, thus the colony PCR was repeated. the plates from the previous day showed many colonies but since they were not immediately needed the plates were sealed and put in storage. the cultures from the previous day were miniprepped; samples were restriction digested and run on a gel, the results confirmed the identity of the plasmid DNA. the <del class="diffchange diffchange-inline">top10 </del>cell cultures were used to produce new <del class="diffchange diffchange-inline">top10 </del>cells.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The PCR products from the previous night were run on a gel however the results of the gel indicated that the PCR was not successful, thus the colony PCR was repeated. the plates from the previous day showed many colonies but since they were not immediately needed the plates were sealed and put in storage. the cultures from the previous day were miniprepped; samples were restriction digested and run on a gel, the results confirmed the identity of the plasmid DNA. the <ins class="diffchange diffchange-inline">TOP10 </ins>cell cultures were used to produce new <ins class="diffchange diffchange-inline">TOP10 </ins>cells.</p></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><p>BNH: More familiarization with amplifier and software. We decided easiest way of shielding would be to construct a Faraday box from a shoebox and aluminium foil. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>BNH: More familiarization with amplifier and software. We decided easiest way of shielding would be to construct a Faraday box from a shoebox and aluminium foil. </p></div></td></tr>
</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203499&oldid=prevFwchung at 04:24, 29 September 20112011-09-29T04:24:03Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 3, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 3, 2011</h4></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><p>Everybody presented the findings of their research about different cells to the group. We determined to create a <del class="diffchange diffchange-inline">Biosensor </del>and discussed the specific requirements for it. <del class="diffchange diffchange-inline">one </del>of the most obvious problems was how the cells would react to the presence of naphthenic acids. The three options we decided to test were via pigment secretion, fluorescence, and an electrochemical response.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Everybody presented the findings of their research about different cells to the group. We determined to create a <ins class="diffchange diffchange-inline">biosensor </ins>and discussed the specific requirements for it. <ins class="diffchange diffchange-inline">One </ins>of the most obvious problems was how the cells would react to the presence of naphthenic acids. The three options we decided to test were via pigment secretion, fluorescence, and an electrochemical response.</p></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>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203484&oldid=prevFwchung at 04:23, 29 September 20112011-09-29T04:23:15Z<p></p>
<table style="background-color: white; color:black;">
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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: #eee; color:black; font-size: smaller;"><div><p>The results for the DNA sent for sequencing was received and the identity was confirmed. The strain carrying the DNA (I0500_B0034_I732005) was then plated on a plate containing X-gal and IPTG. The parts E0240, K325210, I0500, and R0040 were used to make constructs I0500_E0240, R0040_E0240, and R0040_K32510. These parts were then used to transform TOP10 cells. These fluorescent reporters systems present a possible avenue for an alternative reporter system to the proposed electrochemical LacZ reporter system.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The results for the DNA sent for sequencing was received and the identity was confirmed. The strain carrying the DNA (I0500_B0034_I732005) was then plated on a plate containing X-gal and IPTG. The parts E0240, K325210, I0500, and R0040 were used to make constructs I0500_E0240, R0040_E0240, and R0040_K32510. These parts were then used to transform TOP10 cells. These fluorescent reporters systems present a possible avenue for an alternative reporter system to the proposed electrochemical LacZ reporter system.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
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</table>Fwchunghttp://2011.igem.org/wiki/index.php?title=Team:Calgary/Notebook/Journals/OLD_ENTRIES&diff=203467&oldid=prevFwchung at 04:21, 29 September 20112011-09-29T04:21:58Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 04:21, 29 September 2011</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 31</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>May 31</h4></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>The parts from the previous day were ligated, then used to transform <del class="diffchange diffchange-inline">top10 </del>cells, the blue script plasmid was also used to transform <del class="diffchange diffchange-inline">top10 </del>cells which were then plated.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The parts from the previous day were ligated, then used to transform <ins class="diffchange diffchange-inline">TOP10 </ins>cells, the blue script plasmid was also used to transform <ins class="diffchange diffchange-inline">TOP10 </ins>cells which were then plated.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 1, 2011</h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4>June 1, 2011</h4></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>The transformed cells successfully produced colonies. <del class="diffchange diffchange-inline">the </del>colonies formed by the bacteria carrying the construct made previously were used to run a colony PCR and the products were kept for running an agarose gel to confirm them. cells from the colonies (two plates carrying the construct) were used to make an overnight culture.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>The transformed cells successfully produced colonies. <ins class="diffchange diffchange-inline">The </ins>colonies formed by the bacteria carrying the construct made previously were used to run a colony PCR and the products were kept for running an agarose gel to confirm them. cells from the colonies (two plates carrying the construct) were used to make an overnight culture.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Emily, Robert, and Patrick went to the town of Bassano, Alberta as volunteers for Let’s Talk Science. In exchange for helping do some of the labs, they introduced iGEM and microbiology research to students in grades 6, 8, 9, and 12.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Emily, Robert, and Patrick went to the town of Bassano, Alberta as volunteers for Let’s Talk Science. In exchange for helping do some of the labs, they introduced iGEM and microbiology research to students in grades 6, 8, 9, and 12.</p></div></td></tr>
</table>Fwchung