http://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&feed=atom&action=historyTeam:BCCS-Bristol/Wetlab/signal soil - Revision history2024-03-28T09:07:39ZRevision history for this page on the wikiMediaWiki 1.16.5http://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&diff=192901&oldid=prevAmaty at 19:09, 27 October 20102010-10-27T19:09:30Z<p></p>
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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;">=Signal Visibility in Soil=</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:BCCS-Bristol/newtoc}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:BCCS-Bristol/newtoc}}</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;">==Motivation==</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: #eee; color:black; font-size: smaller;"><div>For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed ''E. coli'' constitutively expressing GFP in soil and imaged and photographed them under a stereo-microscope, mimicking the CCD-based method we envision farmers using to detect fluorescence were this project to be used commercially.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed ''E. coli'' constitutively expressing GFP in soil and imaged and photographed them under a stereo-microscope, mimicking the CCD-based method we envision farmers using to detect fluorescence were this project to be used commercially.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Experiment==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Experiment==</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The soil cultures were left overnight at 37°C.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The soil cultures were left overnight at 37°C.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Soil samples viewed under fluorescence microscope. Controls used were as follows:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Soil samples viewed under fluorescence microscope. Controls used were as follows:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Results and Conclusion==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Results and Conclusion==</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>All test soil samples showed growth of ''E.coli'' expressing GFP. As might have been expected, a significant increase in growth was observed in the sterile samples when compared to the non-sterile samples at similar dilutions of bacteria/g soil, suggesting our lab-safe MG1655s had been out-competed by more robust wild-type bacteria strains.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All test soil samples showed growth of ''E.coli'' expressing GFP. As might have been expected, a significant increase in growth was observed in the sterile samples when compared to the non-sterile samples at similar dilutions of bacteria/g soil, suggesting our lab-safe MG1655s had been out-competed by more robust wild-type bacteria strains.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click [https://2010.igem.org/Team:BCCS-Bristol/Wetlab/Lab_photos/First_GFP_Experiment here] for some example images from the test.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click [https://2010.igem.org/Team:BCCS-Bristol/Wetlab/Lab_photos/First_GFP_Experiment here] for some example images from the test.</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>It quickly became clear that using <del class="diffchange diffchange-inline">'</del>E. coli<del class="diffchange diffchange-inline">' </del>spread freely in the soil was not going to yield a strong enough signal to detect from relatively low tech equipment attached to the back of a tractor. It was because of this that we invented the bead method of spreading our bacteria.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>It quickly became clear that using <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>spread freely in the soil was not going to yield a strong enough signal to detect from relatively low tech equipment attached to the back of a tractor. It was because of this that we invented the bead method of spreading our bacteria.</div></td></tr>
</table>Amatyhttp://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&diff=191302&oldid=prevTtodd at 18:21, 27 October 20102010-10-27T18:21:14Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Motivation==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Motivation==</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed 'E. coli' constitutively expressing GFP in soil and imaged and photographed them under a stereo-microscope, <del class="diffchange diffchange-inline">mimicing </del>the CCD-based method we envision farmers using to detect fluorescence were this project to be used commercially.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed <ins class="diffchange diffchange-inline">'</ins>'E. coli<ins class="diffchange diffchange-inline">'</ins>' constitutively expressing GFP in soil and imaged and photographed them under a stereo-microscope, <ins class="diffchange diffchange-inline">mimicking </ins>the CCD-based method we envision farmers using to detect fluorescence were this project to be used commercially.</div></td></tr>
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</table>Ttoddhttp://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&diff=190695&oldid=prevTtodd at 18:02, 27 October 20102010-10-27T18:02:08Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Signal Visibility in Soil=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Signal Visibility in Soil=</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">{{:Team:BCCS-Bristol/newtoc}}</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Motivation==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Motivation==</div></td></tr>
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</table>Ttoddhttp://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&diff=147770&oldid=prevKcoyte at 19:04, 25 October 20102010-10-25T19:04:51Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Signal Visibility in Soil=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Signal Visibility in Soil=</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;">==Motivation==</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed 'E. coli' constitutively expressing GFP in soil and imaged and photographed them under a stereo-microscope, mimicing the CCD-based method we envision farmers using to detect fluorescence were this project to be used commercially.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed 'E. coli' constitutively expressing GFP in soil and imaged and photographed them under a stereo-microscope, mimicing the CCD-based method we envision farmers using to detect fluorescence were this project to be used commercially.</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;">==Experiment==</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sample soil taken from local source (team member's garden). 6 x ~15g aliquots of soil were placed in 50mL centrifuge tubes, taking care to avoid including wildlife. 3 of the tubes were then sterilised using an autoclave. Meanwhile, a 1 in 10 dilution of the overnight culture of MG1655 cells + [http://partsregistry.org/Part:BBa_I13522 BBa_I13522] was found to have an A<sub>600</sub> value of ~0.5, roughly translating as 2.5x10<sup>9</sup> cells/mL in the original culture. The following table lists the rough figures for the 6 soil experiments set up. The lines notated with "S" were for the sterilised tubes, the lines notated with "N" were for the non-sterilised tubes:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sample soil taken from local source (team member's garden). 6 x ~15g aliquots of soil were placed in 50mL centrifuge tubes, taking care to avoid including wildlife. 3 of the tubes were then sterilised using an autoclave. Meanwhile, a 1 in 10 dilution of the overnight culture of MG1655 cells + [http://partsregistry.org/Part:BBa_I13522 BBa_I13522] was found to have an A<sub>600</sub> value of ~0.5, roughly translating as 2.5x10<sup>9</sup> cells/mL in the original culture. The following table lists the rough figures for the 6 soil experiments set up. The lines notated with "S" were for the sterilised tubes, the lines notated with "N" were for the non-sterilised tubes:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|A sample of the unsterilised soil with a 200μL aliquot of cell culture applied 10 minutes before visualisation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|A sample of the unsterilised soil with a 200μL aliquot of cell culture applied 10 minutes before visualisation</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 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;">==Results and Conclusion==</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All test soil samples showed growth of ''E.coli'' expressing GFP. As might have been expected, a significant increase in growth was observed in the sterile samples when compared to the non-sterile samples at similar dilutions of bacteria/g soil, suggesting our lab-safe MG1655s had been out-competed by more robust wild-type bacteria strains.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>All test soil samples showed growth of ''E.coli'' expressing GFP. As might have been expected, a significant increase in growth was observed in the sterile samples when compared to the non-sterile samples at similar dilutions of bacteria/g soil, suggesting our lab-safe MG1655s had been out-competed by more robust wild-type bacteria strains.</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click [https://2010.igem.org/Team:BCCS-Bristol/Wetlab/Lab_photos/First_GFP_Experiment here] for some example images from the test.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click [https://2010.igem.org/Team:BCCS-Bristol/Wetlab/Lab_photos/First_GFP_Experiment here] for some example images from the test.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It quickly became clear that using 'E. coli' spread freely in the soil was not going to yield a strong enough signal to detect from relatively low tech equipment attached to the back of a tractor. It was because of this that we invented the bead method of spreading our bacteria.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It quickly became clear that using 'E. coli' spread freely in the soil was not going to yield a strong enough signal to detect from relatively low tech equipment attached to the back of a tractor. It was because of this that we invented the bead method of spreading our bacteria.</div></td></tr>
</table>Kcoytehttp://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&diff=136830&oldid=prevAmaty at 20:03, 24 October 20102010-10-24T20:03:12Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Signal Visibility in Soil=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Signal Visibility in Soil=</div></td></tr>
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</table>Amatyhttp://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&diff=108189&oldid=prevKcoyte: /* Signal Visibility in Soil */2010-10-18T10:50:33Z<p><span class="autocomment">Signal Visibility in Soil</span></p>
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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;">'''22/07/2010 - Day Ten'''</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Soil samples viewed under fluorescence microscope. Controls used were as follows:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Soil samples viewed under fluorescence microscope. Controls used were as follows:</div></td></tr>
</table>Kcoytehttp://2010.igem.org/wiki/index.php?title=Team:BCCS-Bristol/Wetlab/signal_soil&diff=108185&oldid=prevKcoyte: New page: =Signal Visibility in Soil= For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed 'E. coli' constitutively expressing GFP ...2010-10-18T10:50:12Z<p>New page: =Signal Visibility in Soil= For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed 'E. coli' constitutively expressing GFP ...</p>
<p><b>New page</b></p><div>=Signal Visibility in Soil=<br />
<br />
For this project to work it was essential that a signal could actually be detected when in soil. To test this we mixed 'E. coli' constitutively expressing GFP in soil and imaged and photographed them under a stereo-microscope, mimicing the CCD-based method we envision farmers using to detect fluorescence were this project to be used commercially.<br />
<br />
Sample soil taken from local source (team member's garden). 6 x ~15g aliquots of soil were placed in 50mL centrifuge tubes, taking care to avoid including wildlife. 3 of the tubes were then sterilised using an autoclave. Meanwhile, a 1 in 10 dilution of the overnight culture of MG1655 cells + [http://partsregistry.org/Part:BBa_I13522 BBa_I13522] was found to have an A<sub>600</sub> value of ~0.5, roughly translating as 2.5x10<sup>9</sup> cells/mL in the original culture. The following table lists the rough figures for the 6 soil experiments set up. The lines notated with "S" were for the sterilised tubes, the lines notated with "N" were for the non-sterilised tubes:<br />
<br />
{|style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000"<br />
!style="border-style: solid; border-width: 1px"|S1 <br />
!style="border-style: solid; border-width: 1px"| ~10<sup>7</sup> cells/g soil <br />
!style="border-style: solid; border-width: 1px"| 100μL cell culture plus 900μL LB added to soil<br />
|-<br />
!style="border-style: solid; border-width: 1px"|S2 <br />
!style="border-style: solid; border-width: 1px"| ~10<sup>6</sup> cells/g soil <br />
!style="border-style: solid; border-width: 1px"| 100μL <sup>1</sup>/<sub>10</sub> dilution of cell culture plus 900μL LB added to soil<br />
|-<br />
!style="border-style: solid; border-width: 1px"|S3 <br />
!style="border-style: solid; border-width: 1px"| ~10<sup>5</sup> cells/g soil <br />
!style="border-style: solid; border-width: 1px"| 100μL <sup>1</sup>/<sub>100</sub> dilution of cell culture plus 900μL LB added to soil<br />
|-<br />
!style="border-style: solid; border-width: 1px"|N1 <br />
!style="border-style: solid; border-width: 1px"| ~10<sup>7</sup> cells/g soil <br />
!style="border-style: solid; border-width: 1px"| 100μL cell culture plus 900μL LB added to soil<br />
|-<br />
!style="border-style: solid; border-width: 1px"|N2 <br />
!style="border-style: solid; border-width: 1px"| ~10<sup>6</sup> cells/g soil <br />
!style="border-style: solid; border-width: 1px"| 100μL <sup>1</sup>/<sub>10</sub> dilution of cell culture plus 900μL LB added to soil<br />
|-<br />
!style="border-style: solid; border-width: 1px"|N3 <br />
!style="border-style: solid; border-width: 1px"| ~10<sup>5</sup> cells/g soil <br />
!style="border-style: solid; border-width: 1px"| 100μL <sup>1</sup>/<sub>100</sub> dilution of cell culture plus 900μL LB added to soil<br />
|}<br />
<br />
The soil cultures were left overnight at 37°C.<br />
<br />
<br />
'''22/07/2010 - Day Ten'''<br />
<br />
Soil samples viewed under fluorescence microscope. Controls used were as follows:<br />
{|<br />
|A 200μL aliquot of pure water<br />
|-<br />
|A 200μL aliquot of cell culture expressing GFP<br />
|-<br />
|A sample of the unsterilised soil<br />
|-<br />
|A sample of the unsterilised soil with a 200μL aliquot of cell culture applied 10 minutes before visualisation<br />
|}<br />
All test soil samples showed growth of ''E.coli'' expressing GFP. As might have been expected, a significant increase in growth was observed in the sterile samples when compared to the non-sterile samples at similar dilutions of bacteria/g soil, suggesting our lab-safe MG1655s had been out-competed by more robust wild-type bacteria strains.<br />
<br />
Click [https://2010.igem.org/Team:BCCS-Bristol/Wetlab/Lab_photos/First_GFP_Experiment here] for some example images from the test.<br />
<br />
It quickly became clear that using 'E. coli' spread freely in the soil was not going to yield a strong enough signal to detect from relatively low tech equipment attached to the back of a tractor. It was because of this that we invented the bead method of spreading our bacteria.</div>Kcoyte