Difference between revisions of "Team:HokkaidoU Japan/Safety"

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{{HokkaidoU_Japan}}
 
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<html>
 
<html>
 +
<body>
 +
<br>
 +
<span class="nomal2">
  
 +
<h1>The chassis organism we are using for this project.</h1>
 +
<span class="nomal2"> 
 +
    <ul>
 +
      <li><span class="italic">E. coli</span> (K 12) DH5&alpha;</li>
  
−
<div class="column full_size">
+
    </ul>
 +
 
  
 +
  <h3>Highest Risk Group Listed</h3>
  
−
<p>Please visit <a href="https://2016.igem.org/Safety">the main Safety page</a> to find this year's safety requirements & deadlines, and to learn about safe & responsible research in iGEM.</p>
+
    Risk Group 1
 +
</span>
 +
<br>
 +
<br>
 +
<span class="nomal2">
 +
  <h1>This is a list of our new coding regions in our projects.</h1>
 +
 +
    <table>
 +
      <tr>
 +
        <th>Part number</th>
 +
        <th>Source of DNA</th>
 +
        <th>Species</th>
 +
        <th>Risk group</th>
 +
        <th>Function</th>
 +
      </tr>
 +
        <tr align="center"><td>BBa_K2015000</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>Self-assembling region (SAR) for the circularization of proteins</td></tr>
 +
        <tr align="center"><td>BBa_K2015001</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>One of self-assembling peptides</td></tr>
 +
        <tr align="center"><td>BBa_K2015002</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>One of self-assembling peptides</td></tr>
 +
        <tr align="center"><td>BBa_K2015003</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>G7 linker containing 7 Glycine</td></tr>
 +
        <tr align="center"><td>BBa_K2015004</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>This part can form disulfide bonds between Sulfur residues for multimerization of protein</td></tr>
 +
        <tr align="center"><td>BBa_K2015005</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>This part can form disulfide bonds between Sulfur residues for circularization of protein</td></tr>
 +
        <tr align="center"><td>BBa_K2015008</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>This part can be formed multimerized protein by using BBa_K2015002</td></tr>
 +
        <tr align="center"><td>BBa_K2015009</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>This part can be formed multimerized protein by using BBa_K2015001</td></tr>
 +
        <tr align="center"><td>BBa_K2015010</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>CDS for circularized protein</td></tr>
 +
      <tr align="center"><td>BBa_K2015011</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>LacI expression unit</td></tr>
 +
        <tr align="center"><td>BBa_K2015012</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>The sequences of downstream can be induced strictly by IPTG</td></tr>
 +
        <tr align="center"><td>BBa_K2015013</td><td> IDT gBlock DNA synthesis</td><td><span class="italic">E. coli</span></td><td>1</td><td>A part of circularized GFP</td></tr>
  
−
<p>On this page of your wiki, you should write about how you are addressing any safety issues in your project. The wiki is a place where you can <strong>go beyond the questions on the safety forms</strong>, and write about whatever safety topics are most interesting in your project. (You do not need to copy your safety forms onto this wiki page.)</p>
+
</table>
 +
</span>
  
−
</div>
 
  
  
−
<div class="column full_size">
+
<span class="nomal2">
−
<h5>Safe Project Design</h5>
+
<br>
 +
<br>
 +
  <h1>Description of the biological materials we are using in the lab.</h1>
 +
  <h3>Risks to the safety and health of team members or others working in the lab.</h3>
 +
 
 +
    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.
 +
 
  
−
<p>Does your project include any safety features? Have you made certain decisions about the design to reduce risks? Write about them here! For example:</p>
+
  <h3>Dangerous chemicals</h3>
 +
 
 +
    <dl>
 +
      <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>
 +
 
  
−
<ul>
 
−
<li>Choosing a non-pathogenic chassis</li>
 
−
<li>Choosing parts that will not harm humans / animals / plants</li>
 
−
<li>Substituting safer materials for dangerous materials in a proof-of-concept experiment</li>
 
−
<li>Including an "induced lethality" or "kill-switch" device</li>
 
−
</ul>
 
  
−
</div>
+
  <h3>Procedures and equipment</h3>
 +
 
 +
    <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 class="column half_size">
+
  <h3>Non-pathogenic bacteria (policy requires treating as pathogenic, as precaution)</h3>
−
<h5>Safe Lab Work</h5>
+
 
 +
    <ul>
 +
      <li>DH5&alpha;</li>
 +
    </ul>
  
−
<p>What safety procedures do you use every day in the lab? Did you perform any unusual experiments, or face any unusual safety issues? Write about them here!</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, 6952–1,6985
  
−
</div>
+
 
  
−
<div class="column half_size">
+
  <h3>Safety equipment</h3>
−
<h5>Safe Shipment</h5>
+
 
 +
    <ul>
 +
      <li>Gloves</li>
 +
      <li>Coats</li>
 +
      <li>Goggles</li>
 +
      <li>UV Box</li>
 +
      <li>UV shield</li>
 +
    </ul>
 +
 
  
−
<p>Did you face any safety problems in sending your DNA parts to the Registry? How did you solve those problems?</p>
+
  <h3>Waste disposal and sterilization</h3>
−
</div>
+
 
 +
    <ul>
 +
      <li>All equipments and wastes coming in contact with bacterial were sterilized by autoclave or bleach.</li>
 +
      <li>All chemical compounds were disposed according to requirements for their disposal.</li>
 +
      <li>Table surface used for work were sterilized with 70% ethanol before and after a procedure.</li>
 +
    </ul>
 +
 
  
 +
  <h3>Chemical Usage</h3>
  
 +
    All chemical compounds were used according to their manuals and respective material safety data sheets.
 +
 +
 +
<br>
 +
<br>
 +
  <h1>Genetic material</h1>
 +
 +
 +
      All genes used in this project come from non-pathogenic bacterial strains of <span class="italic">E. coli</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.
 +
 +
  <h3>Risks to the safety and health of the general public, if released by design or by accident.</h3>
 +
 
 +
 +
      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.
 +
 +
  <h3>Risks to the environment, if released by design or by accident.</h3>
 +
 +
 +
 +
      The <span class="italic">E. coli</span> strains we use in our lab, are saved in our lab.
 +
      As a precaution all materials coming in contact are sterilized before and after.
 +
  Reference Federal Register, (1986) Vol. V1: 88, 6952-16985.
 +
 
 +
 +
  <h3>Risks to security through malicious misuse by individuals, groups, or countries.</h3>
 +
 +
 +
 
 +
      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.
 +
 +
 +
  <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>
 +
 
 +
 +
 +
 +
      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 users when assembling with dangerous coding sites.
 +
 +
 
 +
 +
<br>
 +
<br>
 +
 +
 +
 +
  <h1>Design features to address safety risks.</h1>
 +
 +
 +
 +
      Our device only contains sequences that regulate the expression of genes
 +
      (Promoter, RBS, and terminator). Therefore, our device in itself does not contain any safety risks and does not have design feature to address safety risks.
 +
 +
 +
<br>
 +
<br>
 +
  <h1>Safety training we received.</h1>
 +
 +
      We all received a lecture class regarding gene recombination that was 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'.
 +
 
 +
 +
<br>
 +
<br>
 +
  <h1>Biosafety provisions</h1>
 +
  <h3>Link to our institution biosafety guidelines.</h3>
 +
 
 +
    <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>
 +
 +
 +
  <h3>Our Institutional Biosafety Committee.</h3>
 +
 
 +
 +
 +
      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.
 +
 +
 +
  <h3>Our country's national biosafety regulations and guidelines</h3>
 +
 
 +
 +
 +
      Japan is participating in cartagena act.
 +
 +
 +
  <h3>Biosafety Level rating of our lab.</h3>
 +
 
 +
 +
 +
 +
      Our labs Bio safety level is 2.
 +
 +
 
 +
 +
  <h3>The Risk Group of our chassis organisms.</h3>
 +
 
 +
 +
 +
 +
  The Risk Group of our chassis organisms is 1.
 +
 +
 +
 +
<br>
 +
<br>
 +
 +
 +
  <h1>Faculty Advisor</h1>
 +
 
 +
    Yamazaki Ken-ichi
 +
<br>
 +
Sone Teruo
 +
 +
</span>
 +
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Latest revision as of 19:03, 19 October 2016

Team:HokkaidoU Japan - 2016.igem.org

 

Team:HokkaidoU Japan

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The chassis organism we are using for this project.

  • E. coli (K 12) DH5α

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_K2015000 IDT gBlock DNA synthesisE. coli1Self-assembling region (SAR) for the circularization of proteins
BBa_K2015001 IDT gBlock DNA synthesisE. coli1One of self-assembling peptides
BBa_K2015002 IDT gBlock DNA synthesisE. coli1One of self-assembling peptides
BBa_K2015003 IDT gBlock DNA synthesisE. coli1G7 linker containing 7 Glycine
BBa_K2015004 IDT gBlock DNA synthesisE. coli1This part can form disulfide bonds between Sulfur residues for multimerization of protein
BBa_K2015005 IDT gBlock DNA synthesisE. coli1This part can form disulfide bonds between Sulfur residues for circularization of protein
BBa_K2015008 IDT gBlock DNA synthesisE. coli1This part can be formed multimerized protein by using BBa_K2015002
BBa_K2015009 IDT gBlock DNA synthesisE. coli1This part can be formed multimerized protein by using BBa_K2015001
BBa_K2015010 IDT gBlock DNA synthesisE. coli1CDS for circularized protein
BBa_K2015011 IDT gBlock DNA synthesisE. coli1LacI expression unit
BBa_K2015012 IDT gBlock DNA synthesisE. coli1The sequences of downstream can be induced strictly by IPTG
BBa_K2015013 IDT gBlock DNA synthesisE. coli1A part of circularized GFP

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
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, 6952–1,6985

Safety equipment

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

Waste disposal and sterilization

  • All equipments and wastes coming in contact with bacterial were sterilized by autoclave or bleach.
  • All chemical compounds were disposed according to requirements for their disposal.
  • 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 sheets.

Genetic material

All genes used in this project come from non-pathogenic bacterial strains of E. coli. 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 saved in our lab. 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 users 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 in 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 was 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.

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
Sone Teruo