"
Team:UANL Mty-Mexico/Safety/stability test
From 2013.igem.org
| (8 intermediate revisions not shown) | |||
| Line 2: | Line 2: | ||
<html> | <html> | ||
| + | |||
| + | <h2>Safety</h2> | ||
<h3>Stability Test</h3> | <h3>Stability Test</h3> | ||
| Line 11: | Line 13: | ||
<p>We followed the protocol found in <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013244" target="1">Bryksin and Matsumura, 2010</a>, with a 100 mL culture that was re-inoculated with 100 μL of the culture of the previous day.</p> | <p>We followed the protocol found in <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013244" target="1">Bryksin and Matsumura, 2010</a>, with a 100 mL culture that was re-inoculated with 100 μL of the culture of the previous day.</p> | ||
| - | <br>< | + | <br> |
| + | <center><h2>pUC 57</h2></center> | ||
<!--chart container (charts will appear where the container is put--><div id="chart-A" class="chart"></div> <!-- End container for Chart A --> | <!--chart container (charts will appear where the container is put--><div id="chart-A" class="chart"></div> <!-- End container for Chart A --> | ||
<!--Interactive javascript charts (highcharts.com licensed under Creative Commons Attribution-NonCommercial 3.0 License)--> | <!--Interactive javascript charts (highcharts.com licensed under Creative Commons Attribution-NonCommercial 3.0 License)--> | ||
| Line 57: | Line 60: | ||
</script> | </script> | ||
<!-- end pUC57 chart script--> | <!-- end pUC57 chart script--> | ||
| - | + | <br> | |
<p>We observed that after day 3 (generation 30), pUC showed a pronounced decrease on plasmid retention (from 30% to 1%) and reached 0% on day 5.</p> | <p>We observed that after day 3 (generation 30), pUC showed a pronounced decrease on plasmid retention (from 30% to 1%) and reached 0% on day 5.</p> | ||
<p>This allows us to conclude that, in the case of a release to the environment, when the retention of the plasmid is left to the effect of genetic drift, at least 30 generations will pass until almost no cell retains the plasmid pUC and its derivatives that harbor genes that do not confer a selective advantage.</p> | <p>This allows us to conclude that, in the case of a release to the environment, when the retention of the plasmid is left to the effect of genetic drift, at least 30 generations will pass until almost no cell retains the plasmid pUC and its derivatives that harbor genes that do not confer a selective advantage.</p> | ||
| - | + | <br> | |
| + | <center><h2>pSB 1C3</h2></center> | ||
<!--second chart container--><div id="chart-B" class="chart"></div> <!-- End container for Chart B --> | <!--second chart container--><div id="chart-B" class="chart"></div> <!-- End container for Chart B --> | ||
<!--begin pSb retention chart script--> | <!--begin pSb retention chart script--> | ||
| Line 106: | Line 110: | ||
</script> | </script> | ||
<!-- End psb retention chart script --> | <!-- End psb retention chart script --> | ||
| + | <br> | ||
<p>We observed that after day 8 (generation 80), pSB showed a decrease on plasmid retention (from up to 100% to 2%) and is suposed to reach 0% on day 10.</p> | <p>We observed that after day 8 (generation 80), pSB showed a decrease on plasmid retention (from up to 100% to 2%) and is suposed to reach 0% on day 10.</p> | ||
<p>In the case of a release to the environment, at least 90 generations will pass until almost no cell retains the plasmid pSB and its derivatives that harbor genes that do not confer a selective advantage.</p> | <p>In the case of a release to the environment, at least 90 generations will pass until almost no cell retains the plasmid pSB and its derivatives that harbor genes that do not confer a selective advantage.</p> | ||
| - | |||
<script src="http://code.highcharts.com/highcharts.js"></script> | <script src="http://code.highcharts.com/highcharts.js"></script> | ||
<script src="http://code.highcharts.com/modules/exporting.js"></script> | <script src="http://code.highcharts.com/modules/exporting.js"></script> | ||
| - | |||
<h3>Protocol</h3> | <h3>Protocol</h3> | ||
| + | |||
<p>Plasmid stability test in E. coli:</p> | <p>Plasmid stability test in E. coli:</p> | ||
<ol><li>Inoculate a flask with 10 ml of LB medium with the proper antibiotic.</li> | <ol><li>Inoculate a flask with 10 ml of LB medium with the proper antibiotic.</li> | ||
<li>Grow overnight until saturation is reached.</li> | <li>Grow overnight until saturation is reached.</li> | ||
<li>Inoculate 100 mL of fresh LB without antibiotic with 100 μL of the overnight culture. Simultaneosuly, inocculate a dilution series (from 10<sup>-4</sup> to 10<sup>-8</sup>) of the overnight culture on two series of plaques, one with the antibiotic and one without.</li> | <li>Inoculate 100 mL of fresh LB without antibiotic with 100 μL of the overnight culture. Simultaneosuly, inocculate a dilution series (from 10<sup>-4</sup> to 10<sup>-8</sup>) of the overnight culture on two series of plaques, one with the antibiotic and one without.</li> | ||
| - | <li>Repeat the procedure for eight days (approximately 80 generations, according to <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013244" target="1">Bryksin and Matsumura, 2010</a> | + | <li>Repeat the procedure for eight days (approximately 80 generations, according to <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013244" target="1">Bryksin and Matsumura, 2010</a>.</li> |
<li>Calculate each day the percentage of Colony Forming Units (CFUs) that retain the plasmid by dividing the number of cells growing in plaques with antibiotic by the number of cells growing without antibiotic.</li></ol></p> | <li>Calculate each day the percentage of Colony Forming Units (CFUs) that retain the plasmid by dividing the number of cells growing in plaques with antibiotic by the number of cells growing without antibiotic.</li></ol></p> | ||
| - | <center><img src="https://static.igem.org/mediawiki/2013/d/d6/StabilityProtocolthermocoli2013.jpg" class="img-rounded"></center> | + | <center><img src="https://static.igem.org/mediawiki/2013/d/d6/StabilityProtocolthermocoli2013.jpg" data="holder.js/600x300/auto" alt="Generic placeholder image" width="600px" height="400px"class="img-rounded"></center> |
| - | <center><p>Overview of protocol</p></center> | + | <center><p><h3>Overview of protocol</h3></p></center> |
Latest revision as of 01:56, 29 October 2013
Safety
Stability Test
In the case of an accidental release (or even an intentional) of our plasmids, we'd be interested in knowing for how long will our cells keep the DNA with put on them, that is, how stable a plasmid is in the absence of a selective pressure, such as the antibiotic commonly used to specifically grow transformed cells. Plasmid stability tests are commonly employed to determine for how many generations can a cell culture keep a foreign plasmid in non-selective conditions.
We started with the assumption that our constructions -RNATs and reporter proteins- do not confer a selective advantage to the cells. In other words, we assumed that the replication origin of each plasmid should be the main factor that affects plasmid stability.
The core plasmids we needed to test were pUC and pSB, since all of our constructions are based on this skeletons.
We followed the protocol found in Bryksin and Matsumura, 2010, with a 100 mL culture that was re-inoculated with 100 μL of the culture of the previous day.
pUC 57
We observed that after day 3 (generation 30), pUC showed a pronounced decrease on plasmid retention (from 30% to 1%) and reached 0% on day 5.
This allows us to conclude that, in the case of a release to the environment, when the retention of the plasmid is left to the effect of genetic drift, at least 30 generations will pass until almost no cell retains the plasmid pUC and its derivatives that harbor genes that do not confer a selective advantage.
pSB 1C3
We observed that after day 8 (generation 80), pSB showed a decrease on plasmid retention (from up to 100% to 2%) and is suposed to reach 0% on day 10.
In the case of a release to the environment, at least 90 generations will pass until almost no cell retains the plasmid pSB and its derivatives that harbor genes that do not confer a selective advantage.
Protocol
Plasmid stability test in E. coli:
- Inoculate a flask with 10 ml of LB medium with the proper antibiotic.
- Grow overnight until saturation is reached.
- Inoculate 100 mL of fresh LB without antibiotic with 100 μL of the overnight culture. Simultaneosuly, inocculate a dilution series (from 10-4 to 10-8) of the overnight culture on two series of plaques, one with the antibiotic and one without.
- Repeat the procedure for eight days (approximately 80 generations, according to Bryksin and Matsumura, 2010.
- Calculate each day the percentage of Colony Forming Units (CFUs) that retain the plasmid by dividing the number of cells growing in plaques with antibiotic by the number of cells growing without antibiotic.
Overview of protocol
