Team:HokkaidoU Japan/Safety

From 2014.igem.org

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<h1>Basic Safety Questions for iGEM 2014</h1>
+
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<h2>The organisms and parts that we use</h2>
+
 
-
       <table>
+
 
 +
<h1>Basic Safety Questions for iGEM 2013</h1>
 +
<div class="section">
 +
  <h2>The chassis organism(s) we are using for this project.</h2>
 +
  <div class="answer">
 +
    <ul>
 +
       <li><span class="italic">E.coli</span>(K 12) DH5&alpha;</li>
 +
      <li><span class="italic">E.coli</span>(K 12)  JM109</li>
 +
    </ul>
 +
  </div>
 +
 
 +
  <h3>Highest Risk Group Listed</h3>
 +
  <div class="answer">
 +
    Risk Group 1
 +
  </div>
 +
 
 +
  <h2>This is a list of our new coding regions in our projects.</h2>
 +
  <div class="answer">
 +
    <table>
       <tr>
       <tr>
         <th>Part number</th>
         <th>Part number</th>
         <th>Source of DNA</th>
         <th>Source of DNA</th>
 +
        <th>Species</th>
         <th>Risk group</th>
         <th>Risk group</th>
         <th>Function</th>
         <th>Function</th>
       </tr>
       </tr>
-
<tr><td><span class="italic">E.coli</span></td><td> DH5&alpha;</td><td>1</td><td>Plasmid</td></tr>
+
      <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>
 +
      <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>
 +
      <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>
 +
      <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_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_K1084014</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>Promoter</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_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_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_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_K1084104</td><td>Synthesised, Sigma Alderich</td><td><span class="italic">E.coli</span></td><td>1</td><td>RBS</td></tr>
 +
    </table>
 +
  </div>
-
<tr><td><span class="italic">E.coli</span> JM109</td><td> 1</td><td></tr>
 
-
<tr><td>BBa_K1524100</td>　Synthesised, Sigma Alderich<span class="italic"> E. coli</span> 1 stem-loop
 
-
<tr><td>BBa_K1524101</td> restribution kit <span class="italic">E. coli</span> 1 Reporter gene
 
-
<tr><td>BBa_K1524102</td> restribution kit <span class="italic">E. coli</span> 1 Reporter gene
 
-
<tr><td>BBa_K1524104</td> Synthesised, Sigma-Genosys <span class="italic">E. coli</span> 1 sense fragment
 
-
<tr><td>BBa_K1524105</td> Synthesised, Sigma-Genosys <span class="italic">E. coli</span> 1 sense fragment
 
-
<tr><td>BBa_K1524106</td> Synthesised, Sigma-Genosys <span class="italic">E. coli</span> 1 sense fragment
 
-
<tr><td>BBa_K1524107 </td>Synthesised, Sigma-Genosys <span class="italic">E. coli</span> 1 sense fragment
 
-
<tr><td>BBa_K1524108 </td>Synthesised, Sigma-Genosys <span class="italic">E. coli</span> 1 sense fragment
 
-
</table>
+
  <h2>Description of the biological materials we are using in the lab.</h2>
-
>Description of the biological meterials we are using in the lab.
+
  <h3>Risks to the safety and health of team members or others working in the lab.</h3>
-
Dangerous chemicals
+
  <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>
-
Chloroform - corrosive and toxic: must be used in fume hood
+
  <h3>Dangerous chemicals</h3>
-
Ethidium Bromide - intercalating agent: must be used with personal safety gear
+
  <div class="answer">
-
Ethanol - flammable: must not be used near open flame or in large quantities
+
    <dl>
-
Liquid Nitrogen - cryogenic container and cryogenic gloves must be used
+
      <dt>Chloroform</dt><dd>corrosive and toxic : must be used in fume hood</dd>
 +
      <dt>Ethidium Bromide</dt><dd>intercalating agent : must be used with personal safety gear</dd>
 +
      <dt>Ethanol</dt><dd>flammable : must not be used near open flame or in large quantities</dd>
 +
      <dt>Liquid Nitrogen</dt><dd>cryogenic container and cryogenic gloves must be used</dd>
 +
    </dl>
 +
  </div>
-
Procedures and equipment  
+
  <h3>Procedures and equipment</h3>
 +
  <div class="answer">
 +
    <dl>
 +
      <dt>Agarose gel production</dt><dd>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</dd>
 +
      <dt>Benson burner</dt><dd>fire risk: DO NOT use flammable materials especially ethanol near open fire</dd>
 +
      <dt>Centrifuge</dt><dd>high velocity: balance appropriately, observe the machine till it reaches top velocity</dd>
 +
      <dt>Autoclave</dt><dd>high pressure: check the water level, DO NOT open when pressurized</dd>
 +
      <dt>UV radiation</dt><dd>damage to eyes and skin: use glove and UV box or UV shield</dd>
 +
    </dl>
 +
  </div>
-
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
+
  <h3>Non-pathogenic bacteria (policy requires treating as pathogenic, as precaution)</h3>
-
Benson burner - fire risk: DO NOT use flammable materials especially ethanol near open fire
+
  <div class="answer">
-
Centrifuge - high velocity: balance appropriately, observe the machine till it reaches top velocity
+
    <ul>
-
Autoclave - high pressure: check the water level, DO NOT open when pressurized
+
      <li>DH5&alpha;</li>
-
UV radiation - damage to eyes and skin: use glove and UV box or UV shield
+
      <li>JM109</li>
 +
    </ul>
 +
    <p>
 +
      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
 +
    </p>
 +
  </div>
 +
  <h3>Safety equipment</h3>
 +
  <div class="answer">
 +
    <ul>
 +
      <li>Gloves</li>
 +
      <li>Coats</li>
 +
      <li>Goggles</li>
 +
      <li>UV Box</li>
 +
      <li>UV shield</li>
 +
    </ul>
 +
  </div>
-
Non-pathogenic bacteria (policy requires treating as pathogenic, as precaution)
+
  <h3>Waste disposal and sterilization</h3>
 +
  <div class="answer">
 +
    <ul>
 +
      <li>All equipment and waste coming in contact with bacterial is sterilized by autoclave or bleach.</li>
 +
      <li>All chemicals compounds were disposed according to requirements for their disposal.</li>
 +
      <li>All table surface used for work were sterilized with 70% ethanol before and after a procedure.</li>
 +
    </ul>
 +
  </div>
-
JM109
+
  <h3>Chemical Usage</h3>
-
DH5alpha
+
  <div class="answer">
-
Both of these are lab safe strains. As a precaution all materials coming in contact are sterilized before and after.
+
    All chemical compounds were used according to their manuals and respective material safety data sheet
-
Reference Federal Register, (1986) Vol. V1: 88, 6952–16985
+
  </div>
-
Safety equipment
+
-
Gloves
+
-
Coats
+
-
Goggles
+
-
UV Box
+
-
UV shield
+
-
Waste disposal and sterilization
+
  <h2>Genetic material</h2>
 +
  <div class="answer">
 +
    <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>.
 +
      Expressed proteins did not show any toxic effect to their host.
 +
      Our biobricks do not have any foreseeable selective advantage if released to the environment.
 +
      After consideration we could not find any usage pausing a security concern.
 +
    </p>
 +
  </div>
-
All equipment and waste coming in contact with bacterial is sterilized by autoclave or bleach. All chemicals compounds were disposed according to requirements for their disposal. All table surface used for work were sterilized with 70% ethanol before and after a procedure
+
  <h3>Risks to the safety and health of the general public, if released by design or by accident.</h3>
 +
  <div class="answer">
 +
    <p>
 +
      Some materials pose risks to the general public.
 +
      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>
 +
  </div>
-
Chemical Usage
+
  <h3>Risks to the environment, if released by design or by accident.</h3>
 +
  <div class="answer">
 +
    <p>
 +
      The <span class="italic">E.coli</span> strains we use in our lab, are lab sage strains.
 +
      As a precaution all materials coming in contact are sterilized before and after.
 +
      Reference Federal Register, (1986) Vol. V1: 88, 6952-16985
 +
    </p>
 +
  </div>
-
All chemical compounds were used according to their manuals and respective material safety data sheet
+
  <h3>Risks to security through malicious misuse by individuals, groups, or countries.</h3>
 +
  <div class="answer">
 +
    <p>
 +
      There is no foreseeable risk in misuse of our generated genetic material.
 +
      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>
 +
  </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>
 +
  <div class="answer">
 +
    <p>
 +
      Our project is about optimizing the expression of genes. Our device does not contain a coding site.
 +
      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>
 +
  </div>
 +
  <h2>Design features to address safety risks.</h2>
 +
  <div class="answer">
 +
    <p>
 +
      Our device only contains sequences that regulate the expression of genes.
 +
      (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>
 +
  </div>
-
> Genetic material
+
  <h2>Safety training we received.</h2>
-
Risks to the safety and health of team members, or other people working in the lab:
+
  <div class="answer">
-
All lab staff is trained according to safety manual provided by Hokkaido University.
+
    <p>
-
We took on ourselves to compile a shortlist of often used dangerous materials and safety procedures in our project.
+
      We all received a lecture class regarding gene recombination that were held in Hokkaido University.
 +
      It is based on 'Act on the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms'.
 +
    </p>
 +
  </div>
-
Risks to the safety and health of the general public (if any biological materials escaped from your lab):
+
  <h2>Biosafety provisions</h2>
-
Device which we make, will not code odd protein. There is no risk by themselves.
+
  <h3>Link to our institution biosafety guidelines.</h3>
 +
  <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>
 +
  </div>
-
Risks to the environment (from waste disposal, or from materials escaping from your lab):
+
  <h3>Our Institutional Biosafety Committee.</h3>
-
Biodevice which we make, will not code odd protein. There is no risk to environment.
+
  <div class="answer">
 +
    <p>
 +
      We have a permission to engage in the experiments from the safety officer of genetic recombination of Hokkaido University.
 +
      All members participating in the experiments are registered with this office.
 +
      All members are trained according to the safety demands of safety officer of genetic recombination.
 +
    </p>
 +
  </div>
-
Risks to security through malicious mis-use by individuals, groups, or countries:
+
  <h3>Our country’s national biosafety regulations and guidelines</h3>
-
Our project is about improving antisense RNA system to be useful. They don't code odd proteins.
+
  <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>
-
What measures are you taking to reduce these risks? (For example: safe lab practices, choices of which organisms to use.)
+
  <h3>Biosafety Level rating of our lab.</h3>
-
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.
+
  <div class="answer">
 +
    <p>
 +
      Our labs Bio safety level is 2.
 +
    </p>
 +
  </div>
 +
  <h3>The Risk Group of our chassis organisms.</h3>
 +
  <div class="answer">
 +
    <p>
 +
      The Risk Group of our chassis organisms is 1.
 +
    </p>
 +
  </div>
-
>Risks of Your Project in the Future
+
  <h2>Faculty Advisor</h2>
-
Our project aims to make silencing system more efficient by using antisense RNA. There are no risks because the system leads to only control expression of proteins.
+
  <div class="answer">
 +
    Yamazaki Ken-ichi
 +
  </div>
 +
</div>
-
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.
+
<!-- end contents / begin footer -->
-
 
+
    </div>
-
>Biosafety provisions
+
  </div>
-
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
+
-
 
+
-
</div>
+
<!--end contents-->
<!--end contents-->
<!--begin footer-->
<!--begin footer-->

Revision as of 06:41, 16 October 2014

Basic Safety Questions for iGEM 2013

The chassis organism(s) we are using for this project.

  • E.coli(K 12) DH5α
  • E.coli(K 12) JM109

Highest Risk Group Listed

Risk Group 1

This is a list of our new coding regions in our projects.

Part number Source of DNA Species Risk group Function
BBa_K1084009Synthesised, Sigma AlderichE.coli1Promoter
BBa_K1084010Synthesised, Sigma AlderichE.coli1Promoter
BBa_K1084011Synthesised, Sigma AlderichE.coli1Promoter
BBa_K1084012Synthesised, Sigma AlderichE.coli1Promoter
BBa_K1084013Synthesised, Sigma AlderichE.coli1Promoter
BBa_K1084014Synthesised, Sigma AlderichE.coli1Promoter
BBa_K1084015Synthesised, Sigma AlderichE.coli1Promoter
BBa_K1084101Synthesised, Sigma AlderichE.coli1RBS
BBa_K1084102Synthesised, Sigma AlderichE.coli1RBS
BBa_K1084103Synthesised, Sigma AlderichE.coli1RBS
BBa_K1084104Synthesised, Sigma AlderichE.coli1RBS

Description of the biological materials we are using in the lab.

Risks to the safety and health of team members or others working in the lab.

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.

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)

  • DH5α
  • JM109

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

Chemical Usage

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

Genetic material

All genes used in this project come from non-pathogenic bacterial strains of E.coli or R. eutropha. Expressed proteins did not show any toxic effect to their host. Our biobricks do not have any foreseeable selective advantage if released to the environment. After consideration we could not find any usage pausing a security concern.

Risks to the safety and health of the general public, if released by design or by accident.

Some materials pose risks to the general public. 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.

Risks to the environment, if released by design or by accident.

The E.coli strains we use in our lab, are lab sage strains. As a precaution all materials coming in contact are sterilized before and after. Reference Federal Register, (1986) Vol. V1: 88, 6952-16985

Risks to security through malicious misuse by individuals, groups, or countries.

There is no foreseeable risk in misuse of our generated genetic material. Our generated genetic material performs basic functions in biology. However, it is impossible to guard against the incorporation of our parts in malicious settings.

Risks which might arise when our project move from a small-scale lab study to become widely used as a commercial/industrial product.

Our project is about optimizing the expression of genes. Our device does not contain a coding site. 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.

Design features to address safety risks.

Our device only contains sequences that regulate the expression of genes. (Promoter, RBS, and terminator) Therefore, our device itself does not contain any safety risks and does not have design feature to address safety risks.

Safety training we received.

We all received a lecture class regarding gene recombination that were held in Hokkaido University. It is based on 'Act on the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms'.

Biosafety provisions

Link to our institution biosafety guidelines.

http://www.hokudai.ac.jp/jimuk/reiki/reiki_honbun/u010RG00000583.html

Our Institutional Biosafety Committee.

We have a permission to engage in the experiments from the safety officer of genetic recombination of Hokkaido University. All members participating in the experiments are registered with this office. All members are trained according to the safety demands of safety officer of genetic recombination.

Our country’s national biosafety regulations and guidelines

Japan is participating in cartagena act. Please refer to a link below.
http://www.bch.biodic.go.jp/english/cartagena/images/e_cartagena.pdf

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

Retrieved from "http://2014.igem.org/Team:HokkaidoU_Japan/Safety"