Difference between revisions of "Team:Paris Bettencourt/Safety"

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<h1> Safety </h1>
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<p>Please visit <a href="https://2017.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>
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<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>
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<div id=header1 class="header">SAFETY</div>
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<h4>To make sure our project was fully ethical and implemented in a fully ethical way, we decided to consult with people who work in science and ethics.</h4>
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<div class=text2><div class=text2left>        We paid a visit to the DG research and Innovation in the EU in Brussels, Belgium. Where we met with a member on the ethical board, Dr. Joana Namorado. She walked us through the current EU laws set in place about ethical science and what to consider when designing our project to make sure it was safe. </div>
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<div class=text2right>        Finally she helped us use the Ethics self-assessment guide for the Horizon 2020 Programme set forth by the EU. </br> We used this framework to then make create an ethical and safe design for our project. </div>
 
</div>
 
</div>
  
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</br></br></br><div class="horiline"><hr></div></br></br>
  
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<div class="column full_size">
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<h1>Summary</h1></br></br>
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<h5>Safe Project Design</h5>
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<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>
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We focused on the parts that pertained to our project:
 +
<h4>Personal data</h4>
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We made sure our data collection from questionnaires, interviews, phone calls and video recordings were taken with full consent and were kept on a secure domain. This data will not be transferred and does not contain any personal data (sensitive or otherwise).
 +
<h4>Environment, Health and Safety</h4>
 +
<li>All of our team members were trained to work safely in the lab and taught about how to handle hazardous material, minimise transfer of genetic material and contamination and understand safety procedures. </li>
 +
<li>We designed our prototype to limit contamination.</li>
 +
<li>We designed our bacteria to have a safety kill-switch, based on a cell lysis part from bacteriophage.</li>
 +
<li>We considered the precautionary principle in relation to our project, and found that there was no adequate safety risk that should prevent us from undertaking the project. </li>
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<h4>Dual Use</h4>
 +
Although the
  
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<ul>
 
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<li>Choosing a non-pathogenic chassis</li>
 
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<li>Choosing parts that will not harm humans / animals / plants</li>
 
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<li>Substituting safer materials for dangerous materials in a proof-of-concept experiment</li>
 
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<li>Including an "induced lethality" or "kill-switch" device</li>
 
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</ul>
 
  
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</br></br></br><div class="horiline"><hr></div></br></br>
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<h1>Full Assessment</h1></br></br>
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<div class=text2><div class=text2left>
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Here is the list of the 8 different sections presented in the Horizon 2020 Programme set forth by the EU.
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<ul><li> 1) Human embryo and foetuses</li>
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<li> 2) Human beings</li>
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<li> 3) Human cells and tissues</li>
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<li> 4) Personal data</li>
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<li> 5) Animals</li></div>
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<div class=text2right>
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<li> 6) Non-EU countries</li>
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<li> 7) Environment, health & safety</li>
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<li> 8) Dual Use</li></ul>
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Section 1, 2, 3, 5 and 6 were not applicable to our project as  we are not using or implementing our design in any human or animal subjects or samples and all of our research was conducted in Paris, France.</div>
 
</div>
 
</div>
  
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<div class="column half_size">
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</br></br></br><div class="horiline"><hr></div></br></br>
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<h5>Safe Lab Work</h5>
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<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>
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<h1>Section 4 - Personal data</h1></br></br>
  
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<div class=text3><div class=text3left>To conduct market research for our project, we collected data from different sources both about fundamental researchers using our 3D tools as well as community biologists and fablab users about our bioprinter. </br></br>
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We based ourselves on the Data Protection Directive, a european directive adopted in 1995,  where personal data is defined as "any information relating to an identified or identifiable natural person ("data subject"); an identifiable person is one who can be identified, directly or indirectly, in particular by reference to an identification number or to one or more factors specific to his physical, physiological, mental, economic, cultural or social identity;" (art. 2 a). </div>
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<div class=text3center>This states that all data shall: </br>
 +
<li>be obtained and processed fairly and lawfully and shall not be processed unless certain conditions are met. </li>
 +
<li>be obtained for a specified and lawful purpose and shall not be processed in any manner incompatible with that purpose;</li>
 +
<li>be adequate, relevant and not excessive for those purposes;</li>
 +
<li>be accurate and kept up to date;</li>
 +
<li>not be kept for longer than is necessary for that purpose;</li>
 +
<li>be processed in accordance with the data subject's rights;</li>
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<li>be kept safe from unauthorised access, accidental loss or destruction;</li>
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<li>not be transferred to a country outside the European Economic Area, unless that country has adequate levels of protection for personal data.</li></br></div>
 +
 +
<div class=text3right>Therefore, we made sure that none of our data was transferred.</br> All our online market research is fully anonymised and is not linkable to the person and therefore is not personal data. </br>All video, skype, face to face interviews were done with full informed consent, either through written documents or through video recording of consent and were notified of how their input would be processed. </br> The data we collected does not include: sensitive personal data (classed as: health, sexual lifestyle, ethnicity, political opinion, religious or philosophical conviction), genetic information, tracking or observation. This information was not deemed necessary for our project and thus we did not pursue any of the topics that would require special processing. </br>Furthermore none of this data was further transferred and thus no additional legal requirements need to be met.</div>
 
</div>
 
</div>
  
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<div class="column half_size">
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</br></br></br><div class="horiline"><hr></div></br></br>
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<h5>Safe Shipment</h5>
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<p>Did you face any safety problems in sending your DNA parts to the Registry? How did you solve those problems?</p>
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<h1>Section 7 - Environment, health & safety</h1></br></br>
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 +
<div class=text2><div class=text2left><h4> Environment </h4></br>
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Because our research outcomes (including optogenetic tools for fundamental research, biomaterials for synthetic biology and materials research and bioprinter device) are all aimed at staying on contained laboratory settings, they do not pose any imminent threat to the environment and have minimal risk of being exposed. </br></br>
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 +
<b>DESIGN OF PROTOTYPE</b></br>
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The prototype for the 3D printer is fully contained, with glass doors allowing for the control of contamination as well as for the incubation of the bacteria at a correct temperature. The bacteria is contained in either a glass or plastic receptacle within the machine, which thus limit contamination within the machine. The interior of the machine is to be fully de-constructable and can be cleaned with ethanol. The design also includes a HEPA filter which would remove  99.97% of particles that have a size of 0.3 µm. A handbook of cleaning care would also be provided which would specify optimal cleaning protocols to limit contamination. Finally, This prototype was designed to be used only in labs and community spaces with level 1 criteria of biosafety, thus limiting hazardous contact with civilians.</br></br>
 +
 
 +
<b>BACTERIAL DESIGN</b></br>
 +
Furthermore, we designed a cell lysis part in our cells to ensure that our genetically engineered cells could be quickly lysed and contained through chemical induction.</div>
 +
 
 +
<div class=text2right><h4>Health and Safety</h4></br>
 +
Our lab work and materials are all classed under level 1 biosafety criteria, and all team members underwent safety training for working in a laboratory with a Level 1 Biosafety criteria. This training was conducted by the Biosafety officer for INSERM U1001 and followed the practices described by the WHO laboratory biosafety manual. </br>This included learning:
 +
<li>Using protective clothing and materials</li>
 +
<li>Decontamination and disposal methods </li>
 +
<li>Chemical handling and storing</li>
 +
<li>Use of Machines and Equipment </li>
 +
<li>Emergency procedures</li>
 +
<li>Hygiene standards and appropriate attire in the lab</li></br></div>
 
</div>
 
</div>
  
 +
 +
For Section 7, we considered the Precautionary Principle, detailed in Article 191 of the Treaty on the Functioning of the European Union, where three preliminary conditions must be met: identification of potentially adverse effects; evaluation of the scientific data available; the extent of scientific uncertainty.
 +
 +
Potentially adverse effects:
 +
None of the biomaterials we produce are dangerous and aside from the . Even if these microorganisms are exposed, they are a biosafety hazard level 1, posing minimal risk and none of what is being produced is harmful.
 +
 +
Evaluation of Scientific data available:
 +
The project was based on a preliminary extensive literature research, where we looked at the previous uses of the biomaterial production and applications, optogenetic parts, RNA scaffolding and are referenced throughout our project.
 +
 +
Extent of scientific uncertainty:
 +
All of the biomaterials used are naturally occurring and have also been previously synthesised in labs (1.,2.,3.)  as well as in iGEM projects. Although the CARP genes that were implemented in the Calcium Carbonate production have not been previously used in synthetic biology and in e.coli, the material and genes have been fully characterised.
 +
 +
The optogenetic tools used in the transmembrane circuitry, including the FixJ light receptor and Cph8 have been used in many previous works and are fully characterised. The Dronpa photoswitchable protein has previously characterised for use with enzymes and have also been characterised individually and thus we have reasonable scientific certainty of the function when combined with a transcription factor. The mApple photoswitchable protein is a protein that has been characterised individually and has high homology to the protein caging protein Dronpa. Therefore we can say with reasonable scientific certainty that mApple engineering will not create any dangerous adverse effects.
 +
 +
The hybrid promoters created were all previously modelled in silico and were based on a previous paper that follows the same methodology (ref).
 +
 +
 +
 +
</div>
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Revision as of 00:53, 24 October 2017

SAFETY

To make sure our project was fully ethical and implemented in a fully ethical way, we decided to consult with people who work in science and ethics.

We paid a visit to the DG research and Innovation in the EU in Brussels, Belgium. Where we met with a member on the ethical board, Dr. Joana Namorado. She walked us through the current EU laws set in place about ethical science and what to consider when designing our project to make sure it was safe.
Finally she helped us use the Ethics self-assessment guide for the Horizon 2020 Programme set forth by the EU.
We used this framework to then make create an ethical and safe design for our project.





Summary



We focused on the parts that pertained to our project:

Personal data

We made sure our data collection from questionnaires, interviews, phone calls and video recordings were taken with full consent and were kept on a secure domain. This data will not be transferred and does not contain any personal data (sensitive or otherwise).

Environment, Health and Safety

  • All of our team members were trained to work safely in the lab and taught about how to handle hazardous material, minimise transfer of genetic material and contamination and understand safety procedures.
  • We designed our prototype to limit contamination.
  • We designed our bacteria to have a safety kill-switch, based on a cell lysis part from bacteriophage.
  • We considered the precautionary principle in relation to our project, and found that there was no adequate safety risk that should prevent us from undertaking the project.

    • Dual Use

    Although the




    Full Assessment



    Here is the list of the 8 different sections presented in the Horizon 2020 Programme set forth by the EU.
    • 1) Human embryo and foetuses
    • 2) Human beings
    • 3) Human cells and tissues
    • 4) Personal data
    • 5) Animals
  • 6) Non-EU countries
  • 7) Environment, health & safety
  • 8) Dual Use
    • Section 1, 2, 3, 5 and 6 were not applicable to our project as we are not using or implementing our design in any human or animal subjects or samples and all of our research was conducted in Paris, France.





    Section 4 - Personal data



    To conduct market research for our project, we collected data from different sources both about fundamental researchers using our 3D tools as well as community biologists and fablab users about our bioprinter.

    We based ourselves on the Data Protection Directive, a european directive adopted in 1995, where personal data is defined as "any information relating to an identified or identifiable natural person ("data subject"); an identifiable person is one who can be identified, directly or indirectly, in particular by reference to an identification number or to one or more factors specific to his physical, physiological, mental, economic, cultural or social identity;" (art. 2 a).
    This states that all data shall:
  • be obtained and processed fairly and lawfully and shall not be processed unless certain conditions are met.
  • be obtained for a specified and lawful purpose and shall not be processed in any manner incompatible with that purpose;
  • be adequate, relevant and not excessive for those purposes;
  • be accurate and kept up to date;
  • not be kept for longer than is necessary for that purpose;
  • be processed in accordance with the data subject's rights;
  • be kept safe from unauthorised access, accidental loss or destruction;
  • not be transferred to a country outside the European Economic Area, unless that country has adequate levels of protection for personal data.

    • Therefore, we made sure that none of our data was transferred.
    All our online market research is fully anonymised and is not linkable to the person and therefore is not personal data.
    All video, skype, face to face interviews were done with full informed consent, either through written documents or through video recording of consent and were notified of how their input would be processed.
    The data we collected does not include: sensitive personal data (classed as: health, sexual lifestyle, ethnicity, political opinion, religious or philosophical conviction), genetic information, tracking or observation. This information was not deemed necessary for our project and thus we did not pursue any of the topics that would require special processing.
    Furthermore none of this data was further transferred and thus no additional legal requirements need to be met.





    Section 7 - Environment, health & safety



    Environment


    Because our research outcomes (including optogenetic tools for fundamental research, biomaterials for synthetic biology and materials research and bioprinter device) are all aimed at staying on contained laboratory settings, they do not pose any imminent threat to the environment and have minimal risk of being exposed.

    DESIGN OF PROTOTYPE
    The prototype for the 3D printer is fully contained, with glass doors allowing for the control of contamination as well as for the incubation of the bacteria at a correct temperature. The bacteria is contained in either a glass or plastic receptacle within the machine, which thus limit contamination within the machine. The interior of the machine is to be fully de-constructable and can be cleaned with ethanol. The design also includes a HEPA filter which would remove 99.97% of particles that have a size of 0.3 µm. A handbook of cleaning care would also be provided which would specify optimal cleaning protocols to limit contamination. Finally, This prototype was designed to be used only in labs and community spaces with level 1 criteria of biosafety, thus limiting hazardous contact with civilians.

    BACTERIAL DESIGN
    Furthermore, we designed a cell lysis part in our cells to ensure that our genetically engineered cells could be quickly lysed and contained through chemical induction.

    Health and Safety


    Our lab work and materials are all classed under level 1 biosafety criteria, and all team members underwent safety training for working in a laboratory with a Level 1 Biosafety criteria. This training was conducted by the Biosafety officer for INSERM U1001 and followed the practices described by the WHO laboratory biosafety manual.
    This included learning:
  • Using protective clothing and materials
  • Decontamination and disposal methods
  • Chemical handling and storing
  • Use of Machines and Equipment
  • Emergency procedures
  • Hygiene standards and appropriate attire in the lab

    • For Section 7, we considered the Precautionary Principle, detailed in Article 191 of the Treaty on the Functioning of the European Union, where three preliminary conditions must be met: identification of potentially adverse effects; evaluation of the scientific data available; the extent of scientific uncertainty. Potentially adverse effects: None of the biomaterials we produce are dangerous and aside from the . Even if these microorganisms are exposed, they are a biosafety hazard level 1, posing minimal risk and none of what is being produced is harmful. Evaluation of Scientific data available: The project was based on a preliminary extensive literature research, where we looked at the previous uses of the biomaterial production and applications, optogenetic parts, RNA scaffolding and are referenced throughout our project. Extent of scientific uncertainty: All of the biomaterials used are naturally occurring and have also been previously synthesised in labs (1.,2.,3.) as well as in iGEM projects. Although the CARP genes that were implemented in the Calcium Carbonate production have not been previously used in synthetic biology and in e.coli, the material and genes have been fully characterised. The optogenetic tools used in the transmembrane circuitry, including the FixJ light receptor and Cph8 have been used in many previous works and are fully characterised. The Dronpa photoswitchable protein has previously characterised for use with enzymes and have also been characterised individually and thus we have reasonable scientific certainty of the function when combined with a transcription factor. The mApple photoswitchable protein is a protein that has been characterised individually and has high homology to the protein caging protein Dronpa. Therefore we can say with reasonable scientific certainty that mApple engineering will not create any dangerous adverse effects. The hybrid promoters created were all previously modelled in silico and were based on a previous paper that follows the same methodology (ref).


    Centre for Research and Interdisciplinarity (CRI)
    Faculty of Medicine Cochin Port-Royal, South wing, 2nd floor
    Paris Descartes University
    24, rue du Faubourg Saint Jacques
    75014 Paris, France
    bettencourt.igem2017@gmail.com