Team:Grenoble-EMSE-LSU/Documentation/Safety/KR

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This is why safety considerations and an analysis of consequences need to be taken into account, should biological material from the lab be released into the environment. In the case of our project, we analyse each individual part in terms of safety issues and try to imagine how they could interact with the environment if they should ever be accidentally or intentionally released.</p>  
This is why safety considerations and an analysis of consequences need to be taken into account, should biological material from the lab be released into the environment. In the case of our project, we analyse each individual part in terms of safety issues and try to imagine how they could interact with the environment if they should ever be accidentally or intentionally released.</p>  
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<strong>DO NOT EDIT THIS PAGE!!!</strong> </br>
 
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<h1>KillerRed</h1><br>
<h1>KillerRed</h1><br>
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                     <p>When working with proteins like <a href="https://2013.igem.org/Team:Grenoble-EMSE-LSU/Project/KR">KillerRed</a>, one can quickly raise safety issues. We have been contacted by the <a href="https://2013.igem.org/Team:ATOMS-Turkiye">ATOMS-Turkiye</a> iGEM team on the possible toxicity of KillerRed, for example. This shows why it is particularly important to study possible risks arising from use of new parts like this protein.<br>
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                     <p>When working with proteins like <a href="https://2013.igem.org/Team:Grenoble-EMSE-LSU/Project/KR">KillerRed</a>, one can quickly raise safety issues. We have been contacted by the <a href="https://2013.igem.org/Team:ATOMS-Turkiye">ATOMS-Turkiye</a> iGEM team on the possible toxicity of KillerRed, for example. This shows why it is particularly important to study possible risks arising from use of new parts like this protein.<br><br>
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First of all, we need to take into account all the parts that we bring together inside a single bacteria. This is done with the safety sheet. <a href="https://static.igem.org/mediawiki/igem.org/c/ca/IGEM_2013_Basic_Safety_Form_Grenoble_EMSE_LSU.pdf">Here</a> is a final version of our safety sheet as of 08/30/2013. The document is completed and signed.<br>
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The ATOMS-Turkiye iGEM team believe that communication about safety issues can improve overall safety levels in synthetic biology. Their outreach consisted in accumulating information on other teams' safety issues with their projects. We contributed our data on KillerRed, applied to analyse its potential risks and the consequent measures taken to ensure the safety of the researchers and the general public, as well as preservation of the external environment (see below).
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We hope the collaboration with the ATOMS-Turkiye team will help encourage other teams to communicate about Safety; as it is as essential as the synthetic biology we work on, communication and collaboration should be on the same level for both. Thus we put this collaboration on he same level as synthetic biology for our team's outreach effort.<br><br>
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To analyse the risks present in our project and their possible consequences, we need to take into account all the parts that we bring together inside a single bacteria. This is done with the safety sheet. <a href="https://static.igem.org/mediawiki/igem.org/c/ca/IGEM_2013_Basic_Safety_Form_Grenoble_EMSE_LSU.pdf">Here</a> is a final version of our safety sheet as of 08/30/2013. The document is completed and signed.<br>
In our project, KillerRed is the new part that we have to study in order to determine its potential effects. Before working with the actual DNA, <a href="https://2013.igem.org/Team:Grenoble-EMSE-LSU/Project/Biology">documenting</a> ourselves on the protein was necessary.<br>
In our project, KillerRed is the new part that we have to study in order to determine its potential effects. Before working with the actual DNA, <a href="https://2013.igem.org/Team:Grenoble-EMSE-LSU/Project/Biology">documenting</a> ourselves on the protein was necessary.<br>
For safety considerations, several aspects of the protein have to be taken into account:</p><br>
For safety considerations, several aspects of the protein have to be taken into account:</p><br>
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<dl>
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<ul class="list">
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<dd><strong>The protein function</strong></dd>
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<li>The protein function</li>
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<dd><strong>The protein structure</strong></dd>
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<li>The protein structure</li>
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</dl><br>
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</ul><br>
<p>In the case of KillerRed, the function is that of a fluorescent protein similar to EGFP or dsRed, but with photosensitizing properties increased 1000-fold. EGFP is used in many research applications as a reporter protein but is actually slightly toxic.[1,2]<br>
<p>In the case of KillerRed, the function is that of a fluorescent protein similar to EGFP or dsRed, but with photosensitizing properties increased 1000-fold. EGFP is used in many research applications as a reporter protein but is actually slightly toxic.[1,2]<br>
This phototoxicity is due to ROS (Reactive Oxygen Species) generation. This ROS generation is only possible with the presence of molecular oxygen as an electron donor [3,5]. with superoxide being the main ROS generated, and the main source of KillerRed's phototoxicity [3]. ROS are extremely unstable compounds that readily react with many substrates including lipids, proteins and DNA [4]. There are many possible reactions and most if not all damage the substrate, leading to cell death. Reactions with DNA can also lead to mutagenesis and it was necessary to take this risk into account when working with the protein.<br>
This phototoxicity is due to ROS (Reactive Oxygen Species) generation. This ROS generation is only possible with the presence of molecular oxygen as an electron donor [3,5]. with superoxide being the main ROS generated, and the main source of KillerRed's phototoxicity [3]. ROS are extremely unstable compounds that readily react with many substrates including lipids, proteins and DNA [4]. There are many possible reactions and most if not all damage the substrate, leading to cell death. Reactions with DNA can also lead to mutagenesis and it was necessary to take this risk into account when working with the protein.<br>
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                                         We show that interactions of our system with the environment or healthy organisms do not pose any more risk than interactions with wild-type bacteria. Yet this isn't all there is to biosecurity. As a general guideline for good laboratory practices, and by law, we are required to follow a set of rules. These are given by governmental organizations in France:<br><br></p>
                                         We show that interactions of our system with the environment or healthy organisms do not pose any more risk than interactions with wild-type bacteria. Yet this isn't all there is to biosecurity. As a general guideline for good laboratory practices, and by law, we are required to follow a set of rules. These are given by governmental organizations in France:<br><br></p>
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                                         <dl>
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                                         <ul class="list">
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<dd><strong>The High Council for Biotechnologies</strong></dd>
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<li>The High Council for Biotechnologies</li>
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<dd><strong>The Ministry of Higher Education and Research</strong></dd>
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<li>The Ministry of Higher Education and Research</li>
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                                         <dd><strong>The European Parliament</strong></dd>
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                                         <li>The European Parliament</li>
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</dl><br><br></p>
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</ul><br><br></p>
<p>Among the laws that have passed concerning the use of genetically modified organisms, the following laws concern us in particular:<br><br></p>
<p>Among the laws that have passed concerning the use of genetically modified organisms, the following laws concern us in particular:<br><br></p>
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                                         <dl>
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                                         <ul class="list">
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<dd><strong>European Directive 89/391/CEE</strong></dd>
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<li>European Directive 89/391/CEE</li>
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<dd><strong>European Directive 90/219/CEE</strong></dd>
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<li>European Directive 90/219/CEE</li>
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</dl><br><br></p>
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</ul><br><br></p>
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<p>
To sum up these different laws, we can make a list of good laboratory practices that we have to follow:<br><br></p>
To sum up these different laws, we can make a list of good laboratory practices that we have to follow:<br><br></p>
<p>
<p>
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                                         <dl>
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                                         <ul class="list">
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<dd><strong>1. Minimalise contamination of work areas and the environment with genetically modified organisms.</strong></dd>
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<li>1. Minimalise contamination of work areas and the environment with genetically modified organisms.</strong></li>
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<dd><strong>2. Take measures to control risks at their source (genetic and/or protein level) and then use personal protection equipment (blouses, protectice eyewear...) if needed.</strong></dd>
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<li>2. Take measures to control risks at their source (genetic and/or protein level) and then use personal protection equipment (blouses, protectice eyewear...) if needed.</li>
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                                         <dd><strong>3. Regularly check and maintain equipment and procedures used to control genetically modified organism proliferation (laminar flow hoods, bleach...).</strong></dd>
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                                         <li>3. Regularly check and maintain equipment and procedures used to control genetically modified organism proliferation (laminar flow hoods, bleach...).</li>
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                                         <dd><strong>4. Verify if genetically modified organisms can thrive outside of their defined containment zones, and check for their presence in the work area out of their containment zones.</strong></dd>
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                                         <li>4. Verify if genetically modified organisms can thrive outside of their defined containment zones, and check for their presence in the work area out of their containment zones.</li>
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                                         <dd><strong>5. Ensure that personnel are adequately trained (with updated training for new techniques, risks and organisms in the lab).</strong></dd>
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                                         <li>5. Ensure that personnel are adequately trained (with updated training for new techniques, risks and organisms in the lab).</li>
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                                         <dd><strong>6. Create groups or sub-groups dedicated  to matters of biosecurity within the lab or work areas.</strong></dd>
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                                         <li>6. Create groups or sub-groups dedicated  to matters of biosecurity within the lab or work areas.</li>
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                                         <dd><strong>7. Design and publish good laboratory practices manuals for personnel working in the lab.</strong></dd>
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                                         <li>7. Design and publish good laboratory practices manuals for personnel working in the lab.</li>
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                                         <dd><strong>8. The lab has to notify the relevant authorities of the genetically modified organisms kept in it.</strong></dd>
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                                         <li>8. The lab has to notify the relevant authorities of the genetically modified organisms kept in it.</dd>
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                                         <dd><strong>9. Lab personnel have to keep a record of their work on genetically modified organisms for tracability (the lab notebook!).</strong></dd>
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                                         <li>9. Lab personnel have to keep a record of their work on genetically modified organisms for tracability (the lab notebook!).</li>
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                                         <dd><strong>10. An emergency protocol has to be defined in the case of an emergency or accident involving the release of genetically modified organisms in the external environment, so that the health of researchers, the general public and the integrity of the environment can be protected.</strong></dd>
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                                         <li>10. An emergency protocol has to be defined in the case of an emergency or accident involving the release of genetically modified organisms in the external environment, so that the health of researchers, the general public and the integrity of the environment can be protected.</li>
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</dl><br><br></p>
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</ul><br><br></p>
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<p>
<p>
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                                         <dl>
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                                         <ul class="list">
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                                         <dd><strong>All chassis and used DNA sequence characteristics (function, known effects on humans and other organisms, origin...) have to be known and taken into account for risk evaluation.</strong></dd>
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                                         <li>All chassis and used DNA sequence characteristics (function, known effects on humans and other organisms, origin...) have to be known and taken into account for risk evaluation.</li>
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                                         <dd><strong>No pathogenic organism or known pathogenic DNA part may be used without special approval by the High Council for Biotechnologies</strong></dd>
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                                         <li>No pathogenic organism or known pathogenic DNA part may be used without special approval by the High Council for Biotechnologies</li>
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                                         </dl><br><br></p>
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                                         </ul><br><br></p>
<p>
<p>
The European Directive 90/219/CEE also classifies BSL levels and the corresponding level of equipment and safety measures that need to be executed in order to limit or prevent dissemination of genetically modified organisms into the external environment. The document can be freely accessed <a href="http://ec.europa.eu/health/files/eudralex/vol-1/dir_1990_219/dir_1990_219_fr.pdf">here</a> (in french).
The European Directive 90/219/CEE also classifies BSL levels and the corresponding level of equipment and safety measures that need to be executed in order to limit or prevent dissemination of genetically modified organisms into the external environment. The document can be freely accessed <a href="http://ec.europa.eu/health/files/eudralex/vol-1/dir_1990_219/dir_1990_219_fr.pdf">here</a> (in french).
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As there aren't only biological risks in a synthetic biology laboratory, we also need to take into account safety measures for the other risks. These are principally chemical risks relating to the use of certain chemicals in synthetic biology. These chemicals can be ethidium bromide (a known mutagen), guanidine hydrochloride (poisonous) or acrylamide (a known neurotoxin), among others present in the lab.
As there aren't only biological risks in a synthetic biology laboratory, we also need to take into account safety measures for the other risks. These are principally chemical risks relating to the use of certain chemicals in synthetic biology. These chemicals can be ethidium bromide (a known mutagen), guanidine hydrochloride (poisonous) or acrylamide (a known neurotoxin), among others present in the lab.
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The prevention measures put in place by the labor code in France include:<br><br></p>
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The prevention measures put in place by the labor code in France include: <br><br> </p>
<p>
<p>
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                                         <dl>
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                                         <ul class="list">
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                                         <dd><strong></strong></dd>
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                                         <li>1. The evaluation of risks in the laboratory</dd>
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                                         </dl>
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                                        <li>2. Adapting the work and the workplace to the individual rather than the reverse</li>
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                                        <li>3. Continuously keep work areas up to date with recent equipment</li>
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                                        <li>4. Replace dangerous chemicals with less dangerous chemicals where possible</li>
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                                        <li>5. Plan risk prevention, taking into account techniques, workplace organization, work conditions and social relations between employees and possible external factors.</strong></dd>
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                                         <li>6. Prefer collective protection measures over individual versions.</li>  
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                                        </ul>
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</p>
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<p>In order to set an example for safety, we have strived to respect these rules all along our project and will communicate them to the next Grenoble iGEM team in 2014.</p>
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  [5] Shawn Swavey and Matthew Tran (2013). Porphyrin and Phthalocyanine Photosensitizers as PDT Agents: A New Modality for the Treatment of Melanoma, Recent Advances in the Biology, Therapy and Management of Melanoma, Dr. Lester Davids (Ed.), ISBN: 978-953-51-0976-1, InTech, DOI: 10.5772/54940. Available from: http://www.intechopen.com/books/recent-advances-in-the-biology-therapy-and-management-of-melanoma/porphyrin-and-phthalocyanine-photosensitizers-as-pdt-agents-a-new-modality-for-the-treatment-of-mela<br>
  [5] Shawn Swavey and Matthew Tran (2013). Porphyrin and Phthalocyanine Photosensitizers as PDT Agents: A New Modality for the Treatment of Melanoma, Recent Advances in the Biology, Therapy and Management of Melanoma, Dr. Lester Davids (Ed.), ISBN: 978-953-51-0976-1, InTech, DOI: 10.5772/54940. Available from: http://www.intechopen.com/books/recent-advances-in-the-biology-therapy-and-management-of-melanoma/porphyrin-and-phthalocyanine-photosensitizers-as-pdt-agents-a-new-modality-for-the-treatment-of-mela<br>
                       [6] According to bioinformatics.org's <a href="http://www.bioinformatics.org/sms/prot_mw.html">protein molecular weight calculator</a>.
                       [6] According to bioinformatics.org's <a href="http://www.bioinformatics.org/sms/prot_mw.html">protein molecular weight calculator</a>.
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                      [7] <a href="http://ec.europa.eu/health/files/eudralex/vol-1/dir_1990_219/dir_1990_219_fr.pdf">Directive 90/219/CEE of the European Council regarding the use of confined genetically modified organisms</a>
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Latest revision as of 03:58, 5 October 2013

Grenoble-EMSE-LSU, iGEM


Grenoble-EMSE-LSU, iGEM

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