http://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&feed=atom&action=historyTeam:Groningen/environment - Revision history2024-03-28T09:48:06ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=181075&oldid=prevAlicja at 20:54, 25 September 20122012-09-25T20:54:29Z<p></p>
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</table>Alicjahttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=163979&oldid=prevJparrish at 01:08, 25 September 20122012-09-25T01:08:55Z<p></p>
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</table>Jparrishhttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=163976&oldid=prevJparrish at 01:08, 25 September 20122012-09-25T01:08:24Z<p></p>
<a href="http://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=163976&oldid=155642">Show changes</a>Jparrishhttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=155642&oldid=prevIsmael at 11:57, 24 September 20122012-09-24T11:57:52Z<p></p>
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</table>Ismaelhttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=155635&oldid=prevIsmael at 11:57, 24 September 20122012-09-24T11:57:03Z<p></p>
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</table>Ismaelhttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=149997&oldid=prevIsmael at 19:05, 23 September 20122012-09-23T19:05:21Z<p></p>
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</table>Ismaelhttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=149947&oldid=prevJparrish at 18:58, 23 September 20122012-09-23T18:58:57Z<p></p>
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</table>Jparrishhttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=144026&oldid=prevAlicja at 01:43, 23 September 20122012-09-23T01:43:30Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For more insights into the safety aspects of our product in general and its possible effects on the environment, we invited Prof. J.D. van Elsas, head of the Microbial Ecology group of the University of Groningen. He is also a member of COGEM (see our 'in the lab' safety page for a description) and an expert on the environmental aspect of biosafety. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For more insights into the safety aspects of our product in general and its possible effects on the environment, we invited Prof. J.D. van Elsas, head of the Microbial Ecology group of the University of Groningen. He is also a member of COGEM (see our 'in the lab' safety page for a description) and an expert on the environmental aspect of biosafety. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>He explained that biosafety is divided between risk assessment and risk management. Risk is often difined as a multiplication of hazard and exposure.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>He explained that biosafety is divided between risk assessment and risk management. Risk is often difined as a multiplication of hazard and exposure.</div></td></tr>
</table>Alicjahttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=118492&oldid=prevAlicja at 00:52, 16 September 20122012-09-16T00:52:31Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br>We now use the harmless bacterium <i>Bacillus subtilis</i> as our chassis, but in the future we want to implement our insert in the food grade <i>B. subtilis natto</i> strain to make sure that the possible harm is even further minimized. <br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br>We now use the harmless bacterium <i>Bacillus subtilis</i> as our chassis, but in the future we want to implement our insert in the food grade <i>B. subtilis natto</i> strain to make sure that the possible harm is even further minimized. <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><FONT COLOR=#ff6700><b>Concluding, in our assessment the Food Warden bacterium does not create any hazard or risk to humans, animals or the environment.<b></FONT><br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700><b>Concluding, in our assessment the Food Warden bacterium does not create any hazard or risk to humans, animals or the environment.<<ins class="diffchange diffchange-inline">/</ins>b></FONT><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><FONT COLOR=#ff6700><b>But imagine that...</b></FONT><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700><b>But imagine that...</b></FONT><br></div></td></tr>
</table>Alicjahttp://2012.igem.org/wiki/index.php?title=Team:Groningen/environment&diff=118491&oldid=prevAlicja at 00:52, 16 September 20122012-09-16T00:52:13Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700>Hazard</FONT><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700<ins class="diffchange diffchange-inline">><b</ins>>Hazard<ins class="diffchange diffchange-inline"></b></ins></FONT><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Hazard is defined as the degree of harm a GM organism may cause, this depends on the nature of the insert or changed gene/operon. Hazardous effects to humans or other organisms can be divided in two types, namely the toxicity or allerginicity effects of the GMO. In addition to humans and animals, the environment can be exposed to harm. It is important to consider what the effect of the GMO is on ecological diversity or whether it has an effect on the functioning of the ecosystem.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Hazard is defined as the degree of harm a GM organism may cause, this depends on the nature of the insert or changed gene/operon. Hazardous effects to humans or other organisms can be divided in two types, namely the toxicity or allerginicity effects of the GMO. In addition to humans and animals, the environment can be exposed to harm. It is important to consider what the effect of the GMO is on ecological diversity or whether it has an effect on the functioning of the ecosystem.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700>Exposure</FONT><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700<ins class="diffchange diffchange-inline">><b</ins>>Exposure<ins class="diffchange diffchange-inline"></b></ins></FONT><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Exposure is the degree to which humans/animals/the environment come into contact with a hazard introduced by the GM organism. Exposure is caused by the release of GMOs. This release can be unintended or deliberate. Once a GMO is released, several things must be considered, including the survivability of the GMO (establishment, colonization), gene persistence of the genetically modified gene,operon or plasmid insert via horizontal gene transfer, and the effects on indigenous microbial communities. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Exposure is the degree to which humans/animals/the environment come into contact with a hazard introduced by the GM organism. Exposure is caused by the release of GMOs. This release can be unintended or deliberate. Once a GMO is released, several things must be considered, including the survivability of the GMO (establishment, colonization), gene persistence of the genetically modified gene,operon or plasmid insert via horizontal gene transfer, and the effects on indigenous microbial communities. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700>With this knowledge we can make a risk assessment of our Food Warden system.</FONT><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700<ins class="diffchange diffchange-inline">><b</ins>>With this knowledge we can make a risk assessment of our Food Warden system.<ins class="diffchange diffchange-inline"></b></ins></FONT><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our goal is to create a device that does not contain an antibiotic resistance marker. This is a main concern for environmental safety, because the potential risk of gene transfer of an antibiotic resistance marker to a different a possibly virulent bacteria. However, the backbone biobrick we created is a insertion vector, thereby minimizing the chance of transferring the insert into other organisms significantly.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our goal is to create a device that does not contain an antibiotic resistance marker. This is a main concern for environmental safety, because the potential risk of gene transfer of an antibiotic resistance marker to a different a possibly virulent bacteria. However, the backbone biobrick we created is a insertion vector, thereby minimizing the chance of transferring the insert into other organisms significantly.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br>We now use the harmless bacterium <i>Bacillus subtilis</i> as our chassis, but in the future we want to implement our insert in the food grade <i>B. subtilis natto</i> strain to make sure that the possible harm is even further minimized. <br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br>We now use the harmless bacterium <i>Bacillus subtilis</i> as our chassis, but in the future we want to implement our insert in the food grade <i>B. subtilis natto</i> strain to make sure that the possible harm is even further minimized. <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><FONT COLOR=#ff6700>Concluding, in our assessment the Food Warden bacterium does not create any hazard or risk to humans, animals or the environment.</FONT><br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700<ins class="diffchange diffchange-inline">><b</ins>>Concluding, in our assessment the Food Warden bacterium does not create any hazard or risk to humans, animals or the environment.<ins class="diffchange diffchange-inline"><b></ins></FONT><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><FONT COLOR=#ff6700>But imagine that...</FONT><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700<ins class="diffchange diffchange-inline">><b</ins>>But imagine that...<ins class="diffchange diffchange-inline"></b></ins></FONT><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Even in a worst case scenario, if our Food Warden bacterium is released into the environment, the plasmid will not provide an advantage for survival above the natural biodiversity, nor could any genes potentially transferred to other bacteria give those bacteria the ability to become virulent or dominant over other bacteria, which in turn could endanger biodiversity. The ability to produce a pigment will waste valuable energy within the bacteria, further lessening the strains survivability. Because the strain we use is naturally abundant, it will very unlikely cause shifts in the biodiversity.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Even in a worst case scenario, if our Food Warden bacterium is released into the environment, the plasmid will not provide an advantage for survival above the natural biodiversity, nor could any genes potentially transferred to other bacteria give those bacteria the ability to become virulent or dominant over other bacteria, which in turn could endanger biodiversity. The ability to produce a pigment will waste valuable energy within the bacteria, further lessening the strains survivability. Because the strain we use is naturally abundant, it will very unlikely cause shifts in the biodiversity.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700>...The reality: prevention</FONT><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><FONT COLOR=#ff6700<ins class="diffchange diffchange-inline">><b</ins>>...The reality: prevention<ins class="diffchange diffchange-inline"></b></ins></FONT><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Despite the precautions outlined above, the product is still not intended for release into the environment, since not everything is known or can be ruled out. This is the risk management part of the safety aspect. In case of release in the environment we need to think about ecological containment. This is divided into three categories; natural die-out of population, induced die-out of population (use of plasmid-derived toxin/antitoxin systems), and safety measures, for instance the steaming of soils.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Despite the precautions outlined above, the product is still not intended for release into the environment, since not everything is known or can be ruled out. This is the risk management part of the safety aspect. In case of release in the environment we need to think about ecological containment. This is divided into three categories; natural die-out of population, induced die-out of population (use of plasmid-derived toxin/antitoxin systems), and safety measures, for instance the steaming of soils.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We thought of the idea to use the induced die-out method by anchoring a gene producing a toxin for <i>B. subtilis</i> strongly in the genome the bacteria. This gene is placed behind a strong promoter that promotes a strongly responsive stress factor. Thus, in the case of stress/an unfavourable environment the bacteria will express these genes, producing the toxin that will kill the cell. So in the rare case that the sealing of the sticker is compromised and the bacteria is released, the most likely stressful environment will induce self destruction of the cell. Also, after the usage of the Food Warden system, the food supply in the sticker will run out which in turn triggers the stress/sporulation gene and thereby killing the bacteria.<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We thought of the idea to use the induced die-out method by anchoring a gene producing a toxin for <i>B. subtilis</i> strongly in the genome the bacteria. This gene is placed behind a strong promoter that promotes a strongly responsive stress factor. Thus, in the case of stress/an unfavourable environment the bacteria will express these genes, producing the toxin that will kill the cell. So in the rare case that the sealing of the sticker is compromised and the bacteria is released, the most likely stressful environment will induce self destruction of the cell. Also, after the usage of the Food Warden system, the food supply in the sticker will run out which in turn triggers the stress/sporulation gene and thereby killing the bacteria.<br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Another, very simple method to sterilize the bacteria after usage, would be the introduction of a third, breakable compartment inside our sticker. This compartment should contain a bacteriotoxic compound and a strong color, clearly different from the pigment. In this way, a consumer can kill the bacteria directly after use by breaking the compartment and releasing the toxin inside the sticker. One big drawback however is that the safety of this completely relies on the consumer: when he or she forgets to use the third compartment, the bacteria will stay alive. This is why a genetic system might be preferred.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Another, very simple method to sterilize the bacteria after usage, would be the introduction of a third, breakable compartment inside our sticker. This compartment should contain a bacteriotoxic compound and a strong color, clearly different from the pigment. In this way, a consumer can kill the bacteria directly after use by breaking the compartment and releasing the toxin inside the sticker. One big drawback however is that the safety of this completely relies on the consumer: when he or she forgets to use the third compartment, the bacteria will stay alive. This is why a genetic system might be preferred.<ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
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