Team:HokkaidoU Japan/Safety

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      Extra Materials
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      Safety
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      </div>
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<ul style="margin-left:20px;">
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Introduction">Overview</a></li>
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Background">Overview</a></li>
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<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Introduction">Introduction</a></li>
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<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Background">Background</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Background">Background</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Achievements">Achievements</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Achievements">Achievements</a></li>
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<ul>
<ul>
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length">Length Variation</a></li>
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length">Length Variation</a></li>
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            <li class="ldd_contents"><a href="">Overview</a></li>
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            <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length">Overview</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Method">Method</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Method">Method</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Results">Results</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Results">Results</a></li>
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey">High-School</a></li>
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey">High School</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Education">Education</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Education">Education</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Survey">Survey</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Survey">Survey</a></li>
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion">Discussion</a></li>
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion">Discussion</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Background">Background</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Background">Background</a></li>
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<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Estimation">Evaluation</a></li>
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<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Evaluation">Evaluation</a></li>
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</ul>
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<h1>Basic Safety Questions for iGEM 2014</h1>
<h1>Basic Safety Questions for iGEM 2014</h1>
<div class="section">
<div class="section">
-
   <h2>The chassis organism(s) we are using for this project.</h2>
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   <h2> The organisms and parts that we use </h2>
-
  <div class="answer">
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-
    <ul>
+
-
      <li><span class="italic">E.coli</span>(K 12) DH5&alpha;</li>
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-
      <li><span class="italic">E.coli</span>(K 12) JM109</li>
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-
    </ul>
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-
  </div>
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-
 
+
-
  <h3>Highest Risk Group Listed</h3>
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-
  <div class="answer">
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-
    Risk Group 1
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-
  </div>
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-
  <h2>This is a list of our new coding regions in our projects.</h2>
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   <div class="answer">
   <div class="answer">
     <table>
     <table>
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         <th>Function</th>
         <th>Function</th>
       </tr>
       </tr>
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       <tr><td>BBa_K1084009</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</td></tr>
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       <tr><td><i>E. coli</i>(K 12) DH5α</td><td></td><td></td><td>1</td><td></td><tr>
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       <tr><td>BBa_K1084010</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</td></tr>
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-
      <tr><td>BBa_K1084011</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</td></tr>
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       <tr><td><i>E. coli</i>(K 12) JM109</td><td></td><td></td><td>1</td><td></td><tr>
-
       <tr><td>BBa_K1084012</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</td></tr>
+
       <tr><td>BBa_K1524100</td><td>Synthesised, Sigma-Genosys</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>stem-loop</td></tr>
-
       <tr><td>BBa_K1084013</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</td></tr>
+
       <tr><td>BBa_K1524101</td><td>distribution kit</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>Reporter gene</td></tr>
-
       <tr><td>BBa_K1084014</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</td></tr>
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       <tr><td>BBa_K1524102</td><td>distribution kit</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>Reporter gene</td></tr>
-
       <tr><td>BBa_K1084015</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</td></tr>
+
       <tr><td>BBa_K1524104</td><td>Synthesised, Sigma-Genosys</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>sense fragment</td></tr>
-
       <tr><td>BBa_K1084101</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>RBS</td></tr>
+
       <tr><td>BBa_K1524105</td><td>Synthesised, Sigma-Genosys</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>sense fragment</td></tr>
-
       <tr><td>BBa_K1084102</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>RBS</td></tr>
+
       <tr><td>BBa_K1524106</td><td>Synthesised, Sigma-Genosys</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>sense fragment</td></tr>
-
       <tr><td>BBa_K1084103</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>RBS</td></tr>
+
       <tr><td>BBa_K1524107</td><td>Synthesised, Sigma-Genosys</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>sense fragment</td></tr>
-
       <tr><td>BBa_K1084104</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>RBS</td></tr>
+
       <tr><td>BBa_K1524108</td><td>Synthesised, Sigma-Genosys</td><td><span class="italic"><i>E. coli</i></span></td><td>1</td><td>sense fragment</td></tr>
-
     </table>
+
     </table>  
   </div>
   </div>
-
 
+
-
  <h2>Description of the biological materials we are using in the lab.</h2>
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-
  <h3>Risks to the safety and health of team members or others working in the lab.</h3>
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-
  <div class="answer">
+
-
    Some materials pose risks to team members. For example, Ethidium Bromide is an intercalating agent so it must be used by with personal safety gear. All lab staff is trained according to safety manual provided by Hokkaido University, to prevent risks.
+
-
    We took on ourselves to compile a shortlist of often used dangerous materials and safety procedures in our project.
+
-
  </div>
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   <h3>Dangerous chemicals</h3>
   <h3>Dangerous chemicals</h3>
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       <dt>UV radiation</dt><dd>damage to eyes and skin: use glove and UV box or UV shield</dd>
       <dt>UV radiation</dt><dd>damage to eyes and skin: use glove and UV box or UV shield</dd>
     </dl>
     </dl>
-
   </div>
+
   </div>
   <h3>Non-pathogenic bacteria (policy requires treating as pathogenic, as precaution)</h3>
   <h3>Non-pathogenic bacteria (policy requires treating as pathogenic, as precaution)</h3>
   <div class="answer">
   <div class="answer">
     <ul>
     <ul>
-
       <li>DH5&alpha;</li>
+
       <li>JM109 </li>
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       <li>JM109</li>
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       <li>DH5alpha </li>
     </ul>
     </ul>
     <p>
     <p>
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   <div class="answer">
   <div class="answer">
     <ul>
     <ul>
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       <li>All equipment and waste coming in contact with bacterial is sterilized by autoclave or bleach.</li>
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       <li>All equipments and wastes coming in contact with bacterial are sterilized by autoclave or bleach.</li>
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       <li>All chemicals compounds were disposed according to requirements for their disposal.</li>
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       <li>All chemicals compounds are disposed according to requirements for their disposal.</li>
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       <li>All table surface used for work were sterilized with 70% ethanol before and after a procedure.</li>
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       <li>All table surface used for work are sterilized with 70% ethanol before and after a procedure.</li>
     </ul>
     </ul>
   </div>
   </div>
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   <h3>Chemical Usage</h3>
   <h3>Chemical Usage</h3>
   <div class="answer">
   <div class="answer">
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     All chemical compounds were used according to their manuals and respective material safety data sheet
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     All chemical compounds are used according to their manuals and respective material safety data sheet
   </div>
   </div>
   <h2>Genetic material</h2>
   <h2>Genetic material</h2>
 +
 +
  <h3>Risks to the safety and health of team members, or other people working in the lab:.</h3>
   <div class="answer">
   <div class="answer">
     <p>
     <p>
-
       All genes used in this project come from non-pathogenic bacterial strains of <span class="italic">E.coli</span> or <span class="italic">R. eutropha</span>.
+
       All lab staffs are trained according to safety manual provided by Hokkaido University.
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      Expressed proteins did not show any toxic effect to their host.
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       We took on ourselves to compile a shortlist of often used dangerous materials and safety procedures in our project.
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       Our biobricks do not have any foreseeable selective advantage if released to the environment.
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-
      After consideration we could not find any usage pausing a security concern.
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     </p>
     </p>
-
   </div>
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   </div>  
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   <h3>Risks to the safety and health of the general public, if released by design or by accident.</h3>
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   <h3>Risks to the safety and health of the general public (if any biological materials escaped from your lab): </h3>
   <div class="answer">
   <div class="answer">
     <p>
     <p>
-
       Some materials pose risks to the general public.
+
       Devices which we made, do not code odd proteins. There are no risk by themselves.  
-
      For example, Ethanol is a flammable solution so it must not be used by open fire.
+
-
      Not to release those materials, all lab staff is trained according to safety manual provided by Hokkaido University.
+
     </p>
     </p>
   </div>
   </div>
-
   <h3>Risks to the environment, if released by design or by accident.</h3>
+
   <h3>Risks to the environment (from waste disposal, or from materials escaping from your lab): </h3>
   <div class="answer">
   <div class="answer">
     <p>
     <p>
-
       The <span class="italic">E.coli</span> strains we use in our lab, are lab sage strains.
+
       Biodevices which we made, do not code odd proteins. There are no risk to environment.  
-
      As a precaution all materials coming in contact are sterilized before and after.
+
-
      Reference Federal Register, (1986) Vol. V1: 88, 6952-16985
+
     </p>
     </p>
   </div>
   </div>
-
   <h3>Risks to security through malicious misuse by individuals, groups, or countries.</h3>
+
   <h3>Risks to security through malicious mis-use by individuals, groups, or countries:  </h3>
   <div class="answer">
   <div class="answer">
     <p>
     <p>
-
      There is no foreseeable risk in misuse of our generated genetic material.
+
       Our project is about improving antisense RNA system to be useful. They don’t code odd proteins.  
-
       Our generated genetic material performs basic functions in biology.
+
-
      However, it is impossible to guard against the incorporation of our parts in malicious settings.
+
     </p>
     </p>
   </div>
   </div>
-
   <h3>Risks which might arise when our project move from a small-scale lab study to become widely used as a commercial/industrial product.</h3>
+
   <h3>What measures are you taking to reduce these risks? (For example: safe lab practices, choices of which organisms to use.)</h3>
   <div class="answer">
   <div class="answer">
     <p>
     <p>
-
       Our project is about optimizing the expression of genes. Our device does not contain a coding site.
+
       Our projects are only related to antisense RNA system. They are not toxic substances nor substances that influence nature. Therefore that designs are not need.
-
      Therefore, risk will arise when other users assemble our parts with dangerous coding sites.
+
-
      We have to caution the user when assembling with dangerous coding sites.
+
     </p>
     </p>
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   </div>
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   </div>  
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   <h2>Design features to address safety risks.</h2>
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   <h3>Risks of Your Project in the Future</h3>
   <div class="answer">
   <div class="answer">
     <p>
     <p>
-
       Our device only contains sequences that regulate the expression of genes.
+
       Our project aims to make silencing system more efficient by using antisense RNA. There are no risk because the system leads to only control expression of proteins.
-
      (Promoter, RBS, and terminator) Therefore, our device itself does not contain any safety risks and does not have design feature to address safety risks.
+
     </p>
     </p>
-
   </div>
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   </div>  
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   <h2>Safety training we received.</h2>
+
 +
 
 +
   <h2>Safety training we received</h2>
   <div class="answer">
   <div class="answer">
     <p>
     <p>
-
       We all received a lecture class regarding gene recombination that were held in Hokkaido University.
+
       We all received a lecture class regarding gene recombination that was held in Hokkaido University we belong to. It is based on ’Act on the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms’ , ’Regulations related to the Enforcement of the Law concerning the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms’ and ’The Ministerial Ordinance Providing Containment Measures to Be Taken in Type 2 Use of Living Modified Organisms for Research and Development’ , Japanese laws.  
-
      It is based on 'Act on the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms'.
+
     </p>
     </p>
   </div>
   </div>
   <h2>Biosafety provisions</h2>
   <h2>Biosafety provisions</h2>
-
   <h3>Link to our institution biosafety guidelines.</h3>
+
   <h3>Link to the laboratory safety training requirements of our institution. </h3>
   <div class="answer">
   <div class="answer">
-
     <a href="http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html">http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html</a>
+
  <p>
-
   </div>
+
     <a href="http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html#e000000477 ">http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html#e000000477 </a>
 +
    <br> (Biosafety guidelines of Hokkaido university, section 5-23)
 +
  <br> <a href="http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html">http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html</a>
 +
    <br>(Biosafety guidelines of Hokkaido University)
 +
  </p>
 +
   </div>  
-
   <h3>Our Institutional Biosafety Committee.</h3>
+
   <h3>Our country’s national biosafety regulations and guidelines</h3>
   <div class="answer">
   <div class="answer">
-
    <p>
+
  <p>
-
      We have a permission to engage in the experiments from the safety officer of genetic recombination of Hokkaido University.
+
    <a href="http://www.bch.biodic.go.jp/houreiList06.html">http://www.bch.biodic.go.jp/houreiList06.html</a><br>
-
      All members participating in the experiments are registered with this office.
+
    <a href="http://www.bch.biodic.go.jp/houreiList04.html">http://www.bch.biodic.go.jp/houreiList04.html</a><br>
-
      All members are trained according to the safety demands of safety officer of genetic recombination.
+
     <a href="http://www.bch.biodic.go.jp/houreiList01.html">http://www.bch.biodic.go.jp/houreiList01.html</a>
-
     </p>
+
    (Reference Ministry of the Environment)
 +
  </p>
   </div>
   </div>
-
  <h3>Our country’s national biosafety regulations and guidelines</h3>
+
 
-
  <div class="answer">
+
-
    <p>
+
-
      Japan is participating in cartagena act. Please refer to a link below.<br>
+
-
      <a href="http://www.bch.biodic.go.jp/english/cartagena/images/e_cartagena.pdf">http://www.bch.biodic.go.jp/english/cartagena/images/e_cartagena.pdf</a>
+
-
    </p>
+
-
  </div>
+
   <h3>Biosafety Level rating of our lab.</h3>
   <h3>Biosafety Level rating of our lab.</h3>
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Latest revision as of 15:33, 9 September 2015

Extra Materials
Safety

Basic Safety Questions for iGEM 2014

The organisms and parts that we use

 
Part number Source of DNA Species Risk group Function
E. coli(K 12) DH5α1
E. coli(K 12) JM1091
BBa_K1524100Synthesised, Sigma-GenosysE. coli1stem-loop
BBa_K1524101distribution kitE. coli1Reporter gene
BBa_K1524102distribution kitE. coli1Reporter gene
BBa_K1524104Synthesised, Sigma-GenosysE. coli1sense fragment
BBa_K1524105Synthesised, Sigma-GenosysE. coli1sense fragment
BBa_K1524106Synthesised, Sigma-GenosysE. coli1sense fragment
BBa_K1524107Synthesised, Sigma-GenosysE. coli1sense fragment
BBa_K1524108Synthesised, Sigma-GenosysE. coli1sense fragment

Dangerous chemicals

Chloroform
corrosive and toxic : must be used in fume hood
Ethidium Bromide
intercalating agent : must be used with personal safety gear
Ethanol
flammable : must not be used near open flame or in large quantities
Liquid Nitrogen
cryogenic container and cryogenic gloves must be used

Procedures and equipment

Agarose gel production
heating in sealed container (rupture risk), scalding hot and vicious during preparation (burn injury risk) - remove container lid before heating in microwave, use safety gear, wait for a few moments before removing from microwave
Benson burner
fire risk: DO NOT use flammable materials especially ethanol near open fire
Centrifuge
high velocity: balance appropriately, observe the machine till it reaches top velocity
Autoclave
high pressure: check the water level, DO NOT open when pressurized
UV radiation
damage to eyes and skin: use glove and UV box or UV shield

Non-pathogenic bacteria (policy requires treating as pathogenic, as precaution)

  • JM109
  • DH5alpha

Both of these are lab safe strains. As a precaution all materials coming in contact are sterilized before and after. Reference Federal Register, (1986) Vol. V1: 88, 6952–16985

Safety equipment

  • Gloves
  • Coats
  • Goggles
  • UV Box
  • UV shield

Waste disposal and sterilization

  • All equipments and wastes coming in contact with bacterial are sterilized by autoclave or bleach.
  • All chemicals compounds are disposed according to requirements for their disposal.
  • All table surface used for work are sterilized with 70% ethanol before and after a procedure.

Chemical Usage

All chemical compounds are used according to their manuals and respective material safety data sheet

Genetic material

Risks to the safety and health of team members, or other people working in the lab:.

All lab staffs are trained according to safety manual provided by Hokkaido University. We took on ourselves to compile a shortlist of often used dangerous materials and safety procedures in our project.

Risks to the safety and health of the general public (if any biological materials escaped from your lab):

Devices which we made, do not code odd proteins. There are no risk by themselves.

Risks to the environment (from waste disposal, or from materials escaping from your lab):

Biodevices which we made, do not code odd proteins. There are no risk to environment.

Risks to security through malicious mis-use by individuals, groups, or countries:

Our project is about improving antisense RNA system to be useful. They don’t code odd proteins.

What measures are you taking to reduce these risks? (For example: safe lab practices, choices of which organisms to use.)

Our projects are only related to antisense RNA system. They are not toxic substances nor substances that influence nature. Therefore that designs are not need.

Risks of Your Project in the Future

Our project aims to make silencing system more efficient by using antisense RNA. There are no risk because the system leads to only control expression of proteins.

Safety training we received

We all received a lecture class regarding gene recombination that was held in Hokkaido University we belong to. It is based on ’Act on the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms’ , ’Regulations related to the Enforcement of the Law concerning the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms’ and ’The Ministerial Ordinance Providing Containment Measures to Be Taken in Type 2 Use of Living Modified Organisms for Research and Development’ , Japanese laws.

Biosafety provisions

Link to the laboratory safety training requirements of our institution.

http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html#e000000477
(Biosafety guidelines of Hokkaido university, section 5-23)
http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html
(Biosafety guidelines of Hokkaido University)

Our country’s national biosafety regulations and guidelines

http://www.bch.biodic.go.jp/houreiList06.html
http://www.bch.biodic.go.jp/houreiList04.html
http://www.bch.biodic.go.jp/houreiList01.html (Reference Ministry of the Environment)

Biosafety Level rating of our lab.

Our labs Bio safety level is 2.

The Risk Group of our chassis organisms.

The Risk Group of our chassis organisms is 1.

Faculty Advisor

Yamazaki Ken-ichi

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