http://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&feed=atom&action=historyTeam:Dundee/Safety - Revision history2024-03-28T22:40:33ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=280361&oldid=prevJHAllan at 18:07, 3 October 20132013-10-03T18:07:28Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h2><b>Safety & Security</b> </h2<del class="diffchange diffchange-inline">><br><br</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h2><b>Safety & Security</b> </h2></div></td></tr>
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</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=280359&oldid=prevJHAllan at 18:07, 3 October 20132013-10-03T18:07:14Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h2><b>Safety & Security</b> </h2></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h2><b>Safety & Security</b> </h2<ins class="diffchange diffchange-inline">><br><br</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;"><i>Safety forms were approved on September 29, 2013 by the iGEM Safety Committee.</i><br><br></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li><a href ="#Q1">Question 1: Safety issues:</a></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li><a href ="#Q1">Question 1: Safety issues:</a></li></div></td></tr>
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</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=258309&oldid=prevJHAllan at 08:58, 1 October 20132013-10-01T08:58:32Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Even with these measures in place, <i>E. coli</i> and <i>B. subtilis</i> are not environmentally dangerous bacteria, with each being found as natural inhabitants of soil. Their presence would not obviously pose any threat to the environment. Nonetheless, the effects of a genetically modified organism in the environment may not be predicted accurately, thus their unprotected release in to the wild would be irresponsible.<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p>Even with these measures in place, <i>E. coli</i> and <i>B. subtilis</i> are not environmentally dangerous bacteria, with each being found as natural inhabitants of soil. Their presence would not obviously pose any threat to the environment. Nonetheless, the effects of a genetically modified organism in the environment may not be predicted accurately, thus their unprotected release in to the wild would be irresponsible.<br><br></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Due to the non-pathogenic, non-toxicogenic, and non-colonising nature of E. coli K12 and B. subtilis strains which we utilised and the harmless nature of our parts, we do not foresee any security concerns with our project. Our laboratory has secure entry to prevent unauthorised access. In the wrong hands, nothing harmful could be done with our parts or bacterial strains.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Due to the non-pathogenic, non-toxicogenic, and non-colonising nature of <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>K12 and <ins class="diffchange diffchange-inline"><i></ins>B. subtilis<ins class="diffchange diffchange-inline"></i> </ins>strains which we utilised and the harmless nature of our parts, we do not foresee any security concerns with our project. Our laboratory has secure entry to prevent unauthorised access. In the wrong hands, nothing harmful could be done with our parts or bacterial strains.</p></div></td></tr>
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</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=252543&oldid=prevJHAllan at 09:36, 30 September 20132013-09-30T09:36:11Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Threats ">iii. Security concerns</a></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Threats ">iii. Security concerns</a></h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p>Due to the non-pathogenic, non-toxicogenic, and non-colonising nature of E. coli K12 and B. subtilis strains which we utilised and the harmless nature of our parts, we do not foresee any security concerns with our project. Our laboratory has secure entry to prevent unauthorised access. In the wrong hands, nothing harmful could be done with our parts or bacterial strains.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p><ins class="diffchange diffchange-inline">Even with these measures in place, <i>E. coli</i> and <i>B. subtilis</i> are not environmentally dangerous bacteria, with each being found as natural inhabitants of soil. Their presence would not obviously pose any threat to the environment. Nonetheless, the effects of a genetically modified organism in the environment may not be predicted accurately, thus their unprotected release in to the wild would be irresponsible.<br><br></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>Due to the non-pathogenic, non-toxicogenic, and non-colonising nature of E. coli K12 and B. subtilis strains which we utilised and the harmless nature of our parts, we do not foresee any security concerns with our project. Our laboratory has secure entry to prevent unauthorised access. In the wrong hands, nothing harmful could be done with our parts or bacterial strains.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Q3">Question 3:</a> Do any of the new BioBricks parts (or devices) that you made this year raise any safety issues?</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Q3">Question 3:</a> Do any of the new BioBricks parts (or devices) that you made this year raise any safety issues?</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> Our biobricks do not raise any direct safety concerns.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> Our biobricks do not raise any direct safety concerns.<ins class="diffchange diffchange-inline"></p></ins></div></td></tr>
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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;">Regarding our mop device and microcystin detector containing bacteria, if they burst in the environment for any reason, they might spread lots of the toxin back into the water. Although, what binds to microcystin? – PP1, so if the cells burst, surely the toxin would bind to the protein phosphatase 1 in the water!<br><br></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;">We have considered how we might safely deploy the ToxiMop in the environment with the use of what we call the ‘ToxiTeabag’. A perforated bag with holes too large for bacteria to fit through but not water molecules, or more importantly, microcystin.</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> <h2><a id="Q5">Question 5:</a> Do we have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Q5">Question 5:</a> Do we have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> Perhaps future iGEM teams could be sent an information pack on lab safety and security issues so that every team member all around the world has had the same training before beginning their iGEM project. <br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> Perhaps future iGEM teams could be sent an information pack on lab safety and security issues so that every team member all around the world has had the same training before beginning their iGEM project. <br><br></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;">With regards to parts, devices and systems being made safer through biosafety engineering, perhaps each project should be reviewed by iGEM before it is allowed to go forward. This could be carried out to avoid any possible safety issues arising during the team’s project which could jeopardise the success of the project in the competition due. </del></div></td><td colspan="2"> </td></tr>
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</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=252519&oldid=prevJHAllan at 09:31, 30 September 20132013-09-30T09:31:02Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> We all attended a general health and safety induction at the beginning of our iGEM project and were given a safety tour of our lab. The tour included guidance with regards to disposal of sharps, biohazardous material and trace chemicals. The team were also trained in the relevant fire safety procedures; the locations of fire blankets, fire exits, etc. The team members wore disposable gloves and lab coats at all times when working in the wet lab and eliminated risk of contamination spreading outside the laboratory environment by ensuring they removed these items upon exit. Good laboratory practice, such as regular hand-washing and frequent cleaning of workbenches was enforced. <br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> We all attended a general health and safety induction at the beginning of our iGEM project and were given a safety tour of our lab. The tour included guidance with regards to disposal of sharps, biohazardous material and trace chemicals. The team were also trained in the relevant fire safety procedures; the locations of fire blankets, fire exits, etc. The team members wore disposable gloves and lab coats at all times when working in the wet lab and eliminated risk of contamination spreading outside the laboratory environment by ensuring they removed these items upon exit. Good laboratory practice, such as regular hand-washing and frequent cleaning of workbenches was enforced. <br><br></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>At all times, <del class="diffchange diffchange-inline">Safety </del>Operating Procedures (SOPs) for both equipment used in our project and general safety were closely followed. Protective goggles, masks and ear defenders were used when needed (e.g. for SDS-PAGE and exposure to UV light source, while sonicating cells etc.). While working in the lab, we were supervised by our instructors, advisors or lab technicians from Dundee University’s College of Life Sciences Learning & Teaching staff to ensure that we were safely carrying out procedures.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>At all times, <ins class="diffchange diffchange-inline">Standard </ins>Operating Procedures (SOPs) for both equipment used in our project and general safety were closely followed. Protective goggles, masks and ear defenders were used when needed (e.g. for SDS-PAGE and exposure to UV light source, while sonicating cells etc.). While working in the lab, we were supervised by our instructors, advisors or lab technicians from Dundee University’s College of Life Sciences Learning & Teaching staff to ensure that we were safely carrying out procedures.</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> To reduce risk to our health, we decided to use Qiagen kits (mini-prepping, gel extraction, PCR purification, etc.) rather than phenol based protocols. Ethidium bromide (EtBr) is an intercalating agent (it inserts itself into the DNA helix, unravelling the structure) commonly used as a fluorescent tag in molecular biology labs for agarose gel electrophoresis. By distorting the helical structure of DNA, Ethidium bromide is considered to be a mutagen. In order to avoid risk of exposure to ethidium bromide, we took it upon ourselves to use the GelRed staining for agarose gel electrophoresis instead.<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> To reduce risk to our health, we decided to use Qiagen kits (mini-prepping, gel extraction, PCR purification, etc.) rather than phenol based protocols. Ethidium bromide (EtBr) is an intercalating agent (it inserts itself into the DNA helix, unravelling the structure) commonly used as a fluorescent tag in molecular biology labs for agarose gel electrophoresis. By distorting the helical structure of DNA, Ethidium bromide is considered to be a mutagen. In order to avoid risk of exposure to ethidium bromide, we took it upon ourselves to use the GelRed staining for agarose gel electrophoresis instead.<br><br></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>As a safety precaution, all harmful chemicals were used within the sterile environment of <del class="diffchange diffchange-inline">the </del>fume cupboard and upon contamination were disposed of promptly and correctly according to the relevant Material Safety Data Sheet (MSDS). </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>As a safety precaution, all harmful chemicals were used within the sterile environment of <ins class="diffchange diffchange-inline">a </ins>fume cupboard and upon contamination were disposed of promptly and correctly according to the relevant Material Safety Data Sheet (MSDS). </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2>Biosafety</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2>Biosafety</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> We used safe bacteria types in the lab: E. coli and <del class="diffchange diffchange-inline">B. </del>subtilis. <del class="diffchange diffchange-inline">Escherichia </del>coli is a Gram-negative bacterium which is naturally found in the colon of warm-blooded organisms such as humans. Some strains of E. coli are the cause of serious food poisoning in humans, but the majority are harmless. On the other hand, <del class="diffchange diffchange-inline">Bacillus </del>subtilis is a Gram-positive bacterium and has the ability to form a tough, protective endospore. This allows the B. subtilis to tolerate extreme environmental conditions. <del class="diffchange diffchange-inline">Bacillus </del>subtilis inhabits the human gut, and is thought to be a natural gut commensal.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> We used safe bacteria types in the lab: <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>and <ins class="diffchange diffchange-inline"><i>Bacillus </ins>subtilis<ins class="diffchange diffchange-inline"></i>. <i>E</ins>. coli<ins class="diffchange diffchange-inline"></i> </ins>is a Gram-negative bacterium which is naturally found in the colon of warm-blooded organisms such as humans. Some strains of <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>are the cause of serious food poisoning in humans, but the majority are harmless. On the other hand, <ins class="diffchange diffchange-inline"><i>B. </ins>subtilis<ins class="diffchange diffchange-inline"></i> </ins>is a Gram-positive bacterium and has the ability to form a tough, protective endospore. This allows the <ins class="diffchange diffchange-inline"><i></ins>B. subtilis<ins class="diffchange diffchange-inline"></i> </ins>to tolerate extreme environmental conditions. <ins class="diffchange diffchange-inline"><i>B. </ins>subtilis<ins class="diffchange diffchange-inline"></i> </ins>inhabits the human gut, and is thought to be a natural gut commensal.<br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We used a few different bacterial strains throughout our project: <i>E. coli</i> MG1655, <del class="diffchange diffchange-inline">1061 </del>and DH5α. These are all disabled, non-pathogenic, non-toxicogenic, non-colonising, laboratory-adapted K12 strains, which are widely used for research purposes and present little hazard to human health. The <i>B. subtilis</i> strains which we used were NRS3086 strain (derived from the 1086 strain) and 3610.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We used a few different bacterial strains throughout our project: <i>E. coli</i> MG1655, <ins class="diffchange diffchange-inline">MC1061, JM110 </ins>and DH5α. These are all disabled, non-pathogenic, non-toxicogenic, non-colonising, laboratory-adapted K12 strains, which are widely used for research purposes and present little hazard to human health. The <i>B. subtilis</i> strains which we used were NRS3086 strain (derived from the 1086 strain) and 3610.<br><br></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>Although the bacterial strains we used are non-pathogenic, it is still important that we took measures to prevent any contamination. Any protocols which involved the transfer of bacterial cells or bacterial colonies between plates or tubes were carried out in sterile conditions. Otherwise, bacterial cells were stored in lidded containers/universal tubes with the caps sealed tightly. All of the biological waste was disposed of in accordance to lab waste disposal protocols, which involves autoclaving biological waste prior to discarding it. Reusable containers that had been in contact with live cells were soaked in Virkon solution to be disinfected before disposal and to ensure that no live cultures were poured into the sinks.<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Although the bacterial strains we used are non-pathogenic, it is still important that we took measures to prevent any contamination. Any protocols which involved the transfer of bacterial cells or bacterial colonies between plates or tubes were carried out in sterile conditions. Otherwise, bacterial cells were stored in lidded containers/universal tubes with the caps sealed tightly. All of the biological waste was disposed of in accordance to lab waste disposal protocols, which involves autoclaving biological waste prior to discarding it. Reusable containers that had been in contact with live cells were soaked in Virkon solution to be disinfected before disposal and to ensure that no live cultures were poured into the sinks.<br><br></div></td></tr>
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<td colspan="2" class="diff-lineno">Line 77:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="PublicSafety">ii. Public Safety</a></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="PublicSafety">ii. Public Safety</a></h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> While carrying out our project, we took utmost care to ensure that neither biological nor chemical materials were released from our lab accidentally. However, if unintentional release were to occur, the bacterial strains that we used would pose little to no danger to human health. With regards to the <i>E.coli</i> K12 strain derivatives which we used, the lack of danger to people is due to its poor ability to colonize the gut and establish infections. <i>E. coli</i> K12 also lacks the ability to produce large quantities of toxins that affect humans. The B. subtilis strains used were of minimal danger to the public as well.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> While carrying out our project, we took utmost care to ensure that neither biological nor chemical materials were released from our lab accidentally. However, if unintentional release were to occur, the bacterial strains that we used would pose little to no danger to human health. With regards to the <i>E.coli</i> K12 strain derivatives which we used, the lack of danger to people is due to its poor ability to colonize the gut and establish infections. <i>E. coli</i> K12 also lacks the ability to produce large quantities of toxins that affect humans. The <ins class="diffchange diffchange-inline"><i></ins>B. subtilis<ins class="diffchange diffchange-inline"></i> </ins>strains used were of minimal danger to the public as well <ins class="diffchange diffchange-inline">- this organism has never been associated with human infection and is in fact used as a food source in Japan (Netto)</ins>. <br><br></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>We used ampicillin resistant genes within our plasmids as a selectable marker for bacterial transformations. As we are fully aware of the issues surrounding horizontal gene transfer and multi-drug resistant bacteria, we followed university protocols regarding GMO waste disposal. The ultimate goal of our project, as with any other iGEM project, is for our modified bacteria to be used practically in the environment to treat algal blooms by removing microcystin. Our final step would be to remove antibiotic resistance from our plasmid prior to release of our bacteria into the environment.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We used ampicillin resistant genes within our plasmids as a selectable marker for bacterial transformations. As we are fully aware of the issues surrounding horizontal gene transfer and multi-drug resistant bacteria, we followed university protocols regarding GMO waste disposal. The ultimate goal of our project, as with any other iGEM project, is for our modified bacteria to be used practically in the environment to treat algal blooms by removing microcystin. Our final step would be to remove antibiotic resistance from our plasmid prior to release of our bacteria into the environment.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="EnvironmentalSafety">iii. Environmental Safety</a></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="EnvironmentalSafety">iii. Environmental Safety</a></h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> <del class="diffchange diffchange-inline">While carrying out our project, we took utmost care to ensure that neither biological nor chemical materials were released from our lab accidentally. However, if unintentional release were to occur, </del>the <del class="diffchange diffchange-inline">bacterial strains that we used would pose little to no danger to human health. With regards to the <i>E.coli</i> K12 strain derivatives which we used</del>, <del class="diffchange diffchange-inline">the lack </del>of <del class="diffchange diffchange-inline">danger to people </del>is <del class="diffchange diffchange-inline">due to its poor ability to colonize </del>the <del class="diffchange diffchange-inline">gut and establish infections. <i>E. coli</i> K12 also lacks </del>the <del class="diffchange diffchange-inline">ability </del>to <del class="diffchange diffchange-inline">produce large quantities of toxins that affect humans. The <i>B. subtilis</i> strains used were of minimal danger to the public as well</del>.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p><ins class="diffchange diffchange-inline">The use of genetically modified organisms in </ins>the <ins class="diffchange diffchange-inline">environment is a contentious issue</ins>, <ins class="diffchange diffchange-inline">however regardless </ins>of <ins class="diffchange diffchange-inline">your opinion it </ins>is <ins class="diffchange diffchange-inline">obvious that they must be kept isolated from </ins>the <ins class="diffchange diffchange-inline">wild in case they harm </ins>the <ins class="diffchange diffchange-inline">environment they have been engineered </ins>to <ins class="diffchange diffchange-inline">protect, improve or enhance</ins>.<br><br></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">We used ampicillin resistant genes within our plasmids as </del>a <del class="diffchange diffchange-inline">selectable marker for bacterial transformations</del>. <del class="diffchange diffchange-inline">As we are fully aware of </del>the <del class="diffchange diffchange-inline">issues surrounding horizontal gene transfer and multi-drug resistant </del>bacteria, we <del class="diffchange diffchange-inline">followed university protocols regarding GMO waste disposal. The ultimate goal of our project is </del>for our <del class="diffchange diffchange-inline">modified </del>bacteria to <del class="diffchange diffchange-inline">be used practically in </del>the environment to <del class="diffchange diffchange-inline">treat algal blooms by removing </del>microcystin<del class="diffchange diffchange-inline">. Our final step would be </del>to <del class="diffchange diffchange-inline">remove antibiotic resistance from our plasmid prior </del>to <del class="diffchange diffchange-inline">release of our bacteria into </del>the <del class="diffchange diffchange-inline">environment</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Since ToxiMop is an environmental clean-up tool, it was obvious to us that we could not just blindly inoculate water bodies with it, so we came up with </ins>a <ins class="diffchange diffchange-inline">clever way to mop and avoid releasing our bacteria in to the environment</ins>. <ins class="diffchange diffchange-inline">Where in </ins>the <ins class="diffchange diffchange-inline">past, mechanical filter systems have been proposed to contain synthetic </ins>bacteria, we <ins class="diffchange diffchange-inline">created the ToxiTeabag – a vessel </ins>for our bacteria to <ins class="diffchange diffchange-inline">interact with water while still remaining isolated from the rest of </ins>the environment<ins class="diffchange diffchange-inline">. The ToxiTeabag does exactly what it says on the tin, it is a dialysis bag filled with ToxiMop bacteria. Bacteria are too large </ins>to <ins class="diffchange diffchange-inline">escape the through the holes in the bag but water, but more importantly </ins>microcystin <ins class="diffchange diffchange-inline">is permitted </ins>to <ins class="diffchange diffchange-inline">flow freely allowing it </ins>to <ins class="diffchange diffchange-inline">be mopped up by PP1 expressed by </ins>the <ins class="diffchange diffchange-inline">bacteria</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Pathogenicity">i. Pathogenicity, infectivity, or toxicity</a></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Pathogenicity">i. Pathogenicity, infectivity, or toxicity</a></h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> The strains we used, which were derived from E. coli K12 <del class="diffchange diffchange-inline">are non-pathogenic and not capable </del>of <del class="diffchange diffchange-inline">colonising </del>the <del class="diffchange diffchange-inline">gut. Therefore they cannot cause </del>infection <del class="diffchange diffchange-inline">and do not have the ability to produce dangerous toxins in significant quantities</del>. <del class="diffchange diffchange-inline">The exact same information applies to the </del>B. subtilis <del class="diffchange diffchange-inline">strains </del>which <del class="diffchange diffchange-inline">we used</del>.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> The strains we used, which were derived from <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>K12 <ins class="diffchange diffchange-inline">lack many </ins>of the <ins class="diffchange diffchange-inline">virulence factors required for </ins>infection. <ins class="diffchange diffchange-inline"><i></ins>B. subtilis<ins class="diffchange diffchange-inline"></i> has never been associated with human infection. It has GRAS status </ins>which <ins class="diffchange diffchange-inline">means it is “generally recognized as safe”</ins>.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div><!-- Row End --></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div><!-- Row End --></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="span12"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Threats ">ii. Threats to environmental quality</a></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Threats ">ii. Threats to environmental quality</a></h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> <del class="diffchange diffchange-inline">As mentioned previously</del>, <del class="diffchange diffchange-inline">any E. coli K12 released into the environment would be expected </del>to <del class="diffchange diffchange-inline">survive poorly and would </del>not <del class="diffchange diffchange-inline">prove harmful </del>to <del class="diffchange diffchange-inline">plants</del>, <del class="diffchange diffchange-inline">microorganisms or other animals; </del>the <del class="diffchange diffchange-inline">same goes </del>for the <del class="diffchange diffchange-inline">B</del>. <del class="diffchange diffchange-inline">subtilis strains</del>.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> <ins class="diffchange diffchange-inline">Since ToxiMop is an environmental clean-up tool</ins>, <ins class="diffchange diffchange-inline">it was obvious </ins>to <ins class="diffchange diffchange-inline">us that we could </ins>not <ins class="diffchange diffchange-inline">just blindly inoculate water bodies with it, so we came up with a clever way </ins>to <ins class="diffchange diffchange-inline">mop and avoid releasing our bacteria in to the environment.<br><br></ins></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><ins class="diffchange diffchange-inline">Where in the past</ins>, <ins class="diffchange diffchange-inline">mechanical filter systems have been proposed to contain synthetic bacteria, we created </ins>the <ins class="diffchange diffchange-inline">ToxiTeabag – a vessel </ins>for <ins class="diffchange diffchange-inline">our bacteria to interact with water while still remaining isolated from </ins>the <ins class="diffchange diffchange-inline">rest of the environment</ins>. <ins class="diffchange diffchange-inline">The ToxiTeabag does exactly what it says on the tin, it is a dialysis bag filled with ToxiMop bacteria. Bacteria are too large to escape the through the holes in the bag but water, but more importantly microcystin is permitted to flow freely allowing it to be <a href="2013.igem.org/Team:Dundee/Project">mopped up by PP1 expressed by the bacteria</a></ins>.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div><!-- Row End --></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div><!-- Row End --></div></td></tr>
</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=168214&oldid=prevJHAllan at 11:19, 25 September 20132013-09-25T11:19:03Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> We used safe bacteria types in the lab: E. coli and B. subtilis. Escherichia coli is a Gram-negative bacterium which is naturally found in the colon of warm-blooded organisms such as humans. Some strains of E. coli are the cause of serious food poisoning in humans, but the majority are harmless. On the other hand, Bacillus subtilis is a Gram-positive bacterium and has the ability to form a tough, protective endospore. This allows the B. subtilis to tolerate extreme environmental conditions. Bacillus subtilis inhabits the human gut, and is thought to be a natural gut commensal.<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> We used safe bacteria types in the lab: E. coli and B. subtilis. Escherichia coli is a Gram-negative bacterium which is naturally found in the colon of warm-blooded organisms such as humans. Some strains of E. coli are the cause of serious food poisoning in humans, but the majority are harmless. On the other hand, Bacillus subtilis is a Gram-positive bacterium and has the ability to form a tough, protective endospore. This allows the B. subtilis to tolerate extreme environmental conditions. Bacillus subtilis inhabits the human gut, and is thought to be a natural gut commensal.<br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We used a few different bacterial strains throughout our project: E. coli MG1655, <del class="diffchange diffchange-inline"> </del>1061 and DH5α. These are all disabled, non-pathogenic, non-toxicogenic, non-colonising, laboratory-adapted K12 strains, which are widely used for research purposes and present <del class="diffchange diffchange-inline">absolutely no </del>hazard to human health. The B. subtilis strains which we used were <del class="diffchange diffchange-inline">Nrs3086 </del>strain (derived from the 1086 strain) and 3610.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We used a few different bacterial strains throughout our project: <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>MG1655, 1061 and DH5α. These are all disabled, non-pathogenic, non-toxicogenic, non-colonising, laboratory-adapted K12 strains, which are widely used for research purposes and present <ins class="diffchange diffchange-inline">little </ins>hazard to human health. The <ins class="diffchange diffchange-inline"><i></ins>B. subtilis<ins class="diffchange diffchange-inline"></i> </ins>strains which we used were <ins class="diffchange diffchange-inline">NRS3086 </ins>strain (derived from the 1086 strain) and 3610.<br><br></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>Although the bacterial strains we used are non-pathogenic <del class="diffchange diffchange-inline">(and therefore not labelled as a biohazard as such)</del>, it is still important that we took measures to prevent any contamination. Any protocols which involved the transfer of bacterial cells or bacterial colonies between plates or tubes were carried out in sterile conditions<del class="diffchange diffchange-inline">; close to a Bunsen flame</del>. Otherwise, bacterial cells were stored in lidded containers/universal tubes with the caps sealed tightly. All of the biological waste was disposed of in accordance to lab waste disposal protocols, which involves autoclaving biological waste prior to discarding it. Reusable containers that had been in contact with live cells were soaked in Virkon solution to be disinfected before disposal and to ensure that no live cultures were poured into the sinks.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Although the bacterial strains we used are non-pathogenic, it is still important that we took measures to prevent any contamination. Any protocols which involved the transfer of bacterial cells or bacterial colonies between plates or tubes were carried out in sterile conditions. Otherwise, bacterial cells were stored in lidded containers/universal tubes with the caps sealed tightly. All of the biological waste was disposed of in accordance to lab waste disposal protocols, which involves autoclaving biological waste prior to discarding it. Reusable containers that had been in contact with live cells were soaked in Virkon solution to be disinfected before disposal and to ensure that no live cultures were poured into the sinks.<br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Given that our project’s primary concern is the toxin microcystin, we made sure to be very safe regarding its use. The volumes at which we used microcystin for experiments were at levels so low they could present no hazard to human health.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Given that our project’s primary concern is the toxin microcystin, we made sure to be very safe regarding its use. The volumes at which we used microcystin for experiments were at levels so low they could present no hazard to human health.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="PublicSafety">ii. Public Safety</a></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="PublicSafety">ii. Public Safety</a></h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> While carrying out our project, we took utmost care to ensure that neither biological nor chemical materials were released from our lab accidentally. However, if unintentional release were to occur, the bacterial strains that we used would pose little to no danger to human health. With regards to the E.coli K12 strain derivatives which we used, the lack of danger to people is due to its poor ability to colonize the gut and establish infections. E. coli K12 also lacks the ability to produce large quantities of toxins that affect humans. The B. subtilis strains used were of minimal danger to the public as well.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> While carrying out our project, we took utmost care to ensure that neither biological nor chemical materials were released from our lab accidentally. However, if unintentional release were to occur, the bacterial strains that we used would pose little to no danger to human health. With regards to the <ins class="diffchange diffchange-inline"><i></ins>E.coli<ins class="diffchange diffchange-inline"></i> </ins>K12 strain derivatives which we used, the lack of danger to people is due to its poor ability to colonize the gut and establish infections. <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>K12 also lacks the ability to produce large quantities of toxins that affect humans. The B. subtilis strains used were of minimal danger to the public as well.<br><br></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>We used ampicillin resistant genes within our plasmids as a selectable marker for bacterial transformations. As we are fully aware of the issues surrounding horizontal gene transfer and multi-drug resistant bacteria, we followed university protocols regarding GMO waste disposal. The ultimate goal of our project, as with any other iGEM project, is for our modified bacteria to be used practically in the environment to treat algal blooms by removing microcystin. Our final step would be to remove antibiotic resistance from our plasmid prior to release of our bacteria into the environment.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We used ampicillin resistant genes within our plasmids as a selectable marker for bacterial transformations. As we are fully aware of the issues surrounding horizontal gene transfer and multi-drug resistant bacteria, we followed university protocols regarding GMO waste disposal. The ultimate goal of our project, as with any other iGEM project, is for our modified bacteria to be used practically in the environment to treat algal blooms by removing microcystin. Our final step would be to remove antibiotic resistance from our plasmid prior to release of our bacteria into the environment.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="EnvironmentalSafety">iii. Environmental Safety</a></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="EnvironmentalSafety">iii. Environmental Safety</a></h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> While carrying out our project, we took utmost care to ensure that neither biological nor chemical materials were released from our lab accidentally. However, if unintentional release were to occur, the bacterial strains that we used would pose little to no danger to human health. With regards to the E.coli K12 strain derivatives which we used, the lack of danger to people is due to its poor ability to colonize the gut and establish infections. E. coli K12 also lacks the ability to produce large quantities of toxins that affect humans. The B. subtilis strains used were of minimal danger to the public as well.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> While carrying out our project, we took utmost care to ensure that neither biological nor chemical materials were released from our lab accidentally. However, if unintentional release were to occur, the bacterial strains that we used would pose little to no danger to human health. With regards to the <ins class="diffchange diffchange-inline"><i></ins>E.coli<ins class="diffchange diffchange-inline"></i> </ins>K12 strain derivatives which we used, the lack of danger to people is due to its poor ability to colonize the gut and establish infections. <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>K12 also lacks the ability to produce large quantities of toxins that affect humans. The <ins class="diffchange diffchange-inline"><i></ins>B. subtilis<ins class="diffchange diffchange-inline"></i> </ins>strains used were of minimal danger to the public as well.<br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We used ampicillin resistant genes within our plasmids as a selectable marker for bacterial transformations. As we are fully aware of the issues surrounding horizontal gene transfer and multi-drug resistant bacteria, we followed university protocols regarding GMO waste disposal. The ultimate goal of our project<del class="diffchange diffchange-inline">, as with any other iGEM project, </del>is for our modified bacteria to be used practically in the environment to treat algal blooms by removing microcystin. Our final step would be to remove antibiotic resistance from our plasmid prior to release of our bacteria into the environment.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We used ampicillin resistant genes within our plasmids as a selectable marker for bacterial transformations. As we are fully aware of the issues surrounding horizontal gene transfer and multi-drug resistant bacteria, we followed university protocols regarding GMO waste disposal. The ultimate goal of our project is for our modified bacteria to be used practically in the environment to treat algal blooms by removing microcystin. Our final step would be to remove antibiotic resistance from our plasmid prior to release of our bacteria into the environment.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
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</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=168163&oldid=prevJHAllan at 11:13, 25 September 20132013-09-25T11:13:19Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2>Chemical</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2>Chemical</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> To reduce risk to our health, we decided to use Qiagen kits (mini-prepping, gel extraction, PCR purification, etc.) rather than phenol based protocols. Ethidium bromide (EtBr) is an intercalating agent (it inserts itself into the DNA helix, unravelling the structure) commonly used as a fluorescent tag in molecular biology labs for agarose gel electrophoresis. By distorting the helical structure of DNA, Ethidium bromide is considered to be a mutagen <del class="diffchange diffchange-inline">and carcinogen</del>. In order to avoid risk of exposure to <del class="diffchange diffchange-inline">Ethidium </del>bromide, we took it upon ourselves to use the GelRed staining <del class="diffchange diffchange-inline">method </del>for agarose gel electrophoresis instead.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> To reduce risk to our health, we decided to use Qiagen kits (mini-prepping, gel extraction, PCR purification, etc.) rather than phenol based protocols. Ethidium bromide (EtBr) is an intercalating agent (it inserts itself into the DNA helix, unravelling the structure) commonly used as a fluorescent tag in molecular biology labs for agarose gel electrophoresis. By distorting the helical structure of DNA, Ethidium bromide is considered to be a mutagen. In order to avoid risk of exposure to <ins class="diffchange diffchange-inline">ethidium </ins>bromide, we took it upon ourselves to use the GelRed staining for agarose gel electrophoresis instead.<br><br></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>As a safety precaution, all harmful chemicals were used within the sterile environment of the fume cupboard and upon contamination were disposed of promptly and correctly according to the relevant Material Safety Data Sheet (MSDS). </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As a safety precaution, all harmful chemicals were used within the sterile environment of the fume cupboard and upon contamination were disposed of promptly and correctly according to the relevant Material Safety Data Sheet (MSDS). </div></td></tr>
</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=168158&oldid=prevJHAllan at 11:12, 25 September 20132013-09-25T11:12:11Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> We all attended a general health and safety induction at the beginning of our iGEM project and were given a safety tour of our lab. The tour included guidance with regards to disposal of sharps, biohazardous material and trace chemicals. The team were also trained in the relevant fire safety procedures; the locations of fire blankets, fire exits, etc. The team members wore disposable gloves and lab coats at all times when working in the wet lab and eliminated risk of contamination spreading outside the laboratory environment by ensuring they removed these items upon exit. Good laboratory practice, such as regular hand-washing and frequent cleaning of workbenches was enforced. <br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p> We all attended a general health and safety induction at the beginning of our iGEM project and were given a safety tour of our lab. The tour included guidance with regards to disposal of sharps, biohazardous material and trace chemicals. The team were also trained in the relevant fire safety procedures; the locations of fire blankets, fire exits, etc. The team members wore disposable gloves and lab coats at all times when working in the wet lab and eliminated risk of contamination spreading outside the laboratory environment by ensuring they removed these items upon exit. Good laboratory practice, such as regular hand-washing and frequent cleaning of workbenches was enforced. <br><br></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>At all times, Safety Operating Procedures (SOPs) for both equipment used in our project and general safety were closely followed. Protective goggles, masks and ear defenders were used when needed (e.g. for SDS-PAGE and exposure to UV light source, while sonicating cells etc.). While working in the lab, we were supervised by our instructors, advisors or lab technicians from Dundee University’s <del class="diffchange diffchange-inline">School </del>of Life Sciences Learning & Teaching staff to ensure that we were safely carrying out procedures.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>At all times, Safety Operating Procedures (SOPs) for both equipment used in our project and general safety were closely followed. Protective goggles, masks and ear defenders were used when needed (e.g. for SDS-PAGE and exposure to UV light source, while sonicating cells etc.). While working in the lab, we were supervised by our instructors, advisors or lab technicians from Dundee University’s <ins class="diffchange diffchange-inline">College </ins>of Life Sciences Learning & Teaching staff to ensure that we were safely carrying out procedures.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></div></td></tr>
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</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=168145&oldid=prevJHAllan at 11:10, 25 September 20132013-09-25T11:10:56Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Q3">Question 3:</a> Do any of the new BioBricks parts (or devices) that you made this year raise any safety issues?</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Q3">Question 3:</a> Do any of the new BioBricks parts (or devices) that you made this year raise any safety issues?</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> Our <del class="diffchange diffchange-inline">BioBrick parts are all very safe as they are all natural components of the genetic code of harmless E. coli and B. subtilis strains. Regarding our mop device and microcystin detector containing bacteria, if they burst in the environment for </del>any <del class="diffchange diffchange-inline">reason, they might spread lots of the toxin back into the water</del>. <del class="diffchange diffchange-inline">Although, what binds to microcystin? – PP1, so if the cells burst, surely the toxin would bind to the protein phosphatase 1 in the water!<br><br></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> Our <ins class="diffchange diffchange-inline">biobricks do not raise </ins>any <ins class="diffchange diffchange-inline">direct safety concerns</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: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Nevertheless, the final stage of our project would be </del>our mop and <del class="diffchange diffchange-inline">detection </del>bacteria <del class="diffchange diffchange-inline">safely contained in a special ‘ToxiTeabag’</del>, <del class="diffchange diffchange-inline">which when dipped </del>in the <del class="diffchange diffchange-inline">algal bloom water</del>, the water <del class="diffchange diffchange-inline">(including </del>microcystin<del class="diffchange diffchange-inline">) would diffuse in</del>, <del class="diffchange diffchange-inline">but </del>the <del class="diffchange diffchange-inline">bacteria could not escape out as they are too big. Worst case scenario</del>, the <del class="diffchange diffchange-inline">bag bursts …but in the event of that happening, </del>the <del class="diffchange diffchange-inline">bacteria most likely won’t be able to survive </del>in the <del class="diffchange diffchange-inline">wild. Problem solved</del>! <<del class="diffchange diffchange-inline">/p</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Regarding </ins>our mop <ins class="diffchange diffchange-inline">device </ins>and <ins class="diffchange diffchange-inline">microcystin detector containing </ins>bacteria, <ins class="diffchange diffchange-inline">if they burst </ins>in the <ins class="diffchange diffchange-inline">environment for any reason</ins>, <ins class="diffchange diffchange-inline">they might spread lots of the toxin back into </ins>the water<ins class="diffchange diffchange-inline">. Although, what binds to </ins>microcystin<ins class="diffchange diffchange-inline">? – PP1</ins>, <ins class="diffchange diffchange-inline">so if </ins>the <ins class="diffchange diffchange-inline">cells burst</ins>, <ins class="diffchange diffchange-inline">surely </ins>the <ins class="diffchange diffchange-inline">toxin would bind to </ins>the <ins class="diffchange diffchange-inline">protein phosphatase 1 </ins>in the <ins class="diffchange diffchange-inline">water</ins>!<<ins class="diffchange diffchange-inline">br</ins>><<ins class="diffchange diffchange-inline">br</ins>></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del><<del class="diffchange diffchange-inline">/div</del>></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><ins class="diffchange diffchange-inline">We have considered how we might safely deploy the ToxiMop in the environment with the use of what we call the ‘ToxiTeabag’. A perforated bag with holes too large for bacteria to fit through but not water molecules, or more importantly, microcystin.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div><!-- Row End --></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div><!-- Row End --></div></td></tr>
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</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Safety&diff=74688&oldid=prevKyleharrison at 09:55, 16 August 20132013-08-16T09:55:31Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Q3">Question 3:</a> Do any of the new BioBricks parts (or devices) that you made this year raise any safety issues?</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <h2><a id="Q3">Question 3:</a> Do any of the new BioBricks parts (or devices) that you made this year raise any safety issues?</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p> Our BioBrick parts are all very safe as they are all natural components of the genetic code of harmless E. coli and B. subtilis strains. Regarding our mop device and microcystin detector containing bacteria, if they burst in the environment for any reason, they might spread lots of the toxin back into the water. Although, what binds to microcystin? – PP1, so if the cells burst, surely the toxin would bind to the protein phosphatase 1 in the water! Nevertheless, the final stage of our project would be our mop and detection bacteria safely contained in a special ‘ToxiTeabag’, which when dipped in the algal bloom water, the water (including microcystin) would diffuse in, but the bacteria could not escape out as they are too big. Worst case scenario, the bag bursts …but in the event of that happening, the bacteria most likely won’t be able to survive in the wild. Problem solved! </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p> Our BioBrick parts are all very safe as they are all natural components of the genetic code of harmless E. coli and B. subtilis strains. Regarding our mop device and microcystin detector containing bacteria, if they burst in the environment for any reason, they might spread lots of the toxin back into the water. Although, what binds to microcystin? – PP1, so if the cells burst, surely the toxin would bind to the protein phosphatase 1 in the water!<ins class="diffchange diffchange-inline"><br><br></ins></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>Nevertheless, the final stage of our project would be our mop and detection bacteria safely contained in a special ‘ToxiTeabag’, which when dipped in the algal bloom water, the water (including microcystin) would diffuse in, but the bacteria could not escape out as they are too big. Worst case scenario, the bag bursts …but in the event of that happening, the bacteria most likely won’t be able to survive in the wild. Problem solved! </p></div></td></tr>
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</table>Kyleharrison