Team:UC Chile/Practices/Biosafety

From 2012.igem.org

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     <li><strong>Would any of your project ideas raise safety issues in terms of:
     <li><strong>Would any of your project ideas raise safety issues in terms of:
       </strong>
       </strong>
       <ul>
       <ul>
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         <li> researcher safety, </li>
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         <li><strong> researcher or public safety, </strong> </li>
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        <li> public safety, or </li>
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         <li> environmental safety? </li>
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No pathogenic microorganisms or dangerous genes are considered in our ideas, in consequence our intended projects, if executed, do not represent any risk to researchers nor public safety.
 +
 
 +
         <li><strong> environmental safety? </strong> </li>
 +
 
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As Synechocystis is a naturally competent environmental bacteria that undergoes homologous recombination, there is a posibility that if laboratory recombinant strains are leaked to the environment there may be environmental safety issues such as lateral DNA transference and endogenous species endangerment. We discuss this issue further in question number 4 (see below).
       </ul>
       </ul>
     </li>
     </li>
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     <li><strong> Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
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     <li><strong> Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?
       </strong>
       </strong>
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      <ul>
 
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        <li> did you document these issues in the Registry? </li>
 
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        <li> how did you manage to handle the safety issue? </li>
 
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        <li> How could other teams learn from your experience? </li>
 
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      </ul>
 
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      </li>
 
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    <li><strong>Is there a local biosafety group, committee, or review board at your institution? </strong>
 
 +
Yes, the release of biobricks made from Synechocystis genome´s sequences or at least with a region homologous to it raise the possibility of recombination by environmental cyanobacteria. To address this issue we have proposed and designed a biosafety mechanism discussed in question number 4 (see below).
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Furthermore, our laboratory practices enforce strict methods to handle any biological material. As DNA is always hermetically contained or discarded with other biological material according to standard protocols we believe that our practices will not produce any environmental hazard.
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Our lab follows the Manual of Biosafety, established by the Superior Counsel of Science and Technological Development, from the National Fund of Scientific and Technological Development of Chile (FONDECYT).
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      <ul>
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        <li><strong> did you document these issues in the Registry? </strong></li>
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<html>
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All issues regarding our biobricks will be documented once we send the parts to the registry.
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<a href="http://www.fondecyt.cl/578/articles-30555_recurso_1.pdf">Click here to download the Manual of Biosafety </a>
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</html>
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Additionally, the Comitee of Bioethics and Biosafety of the Faculty of Biological Sciences  of the Pontifical Catholic University of Chile has reviewed our work , and determined that the procedures involved in our project follow the bioethical and biosafety standards for research regulations provided by the Chilean Comission on Scientific and Technological Research (CONICYT).
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It has to be stated that any of the sequences designed and/or handled by our team are not <i>per se</i> dangerous nor they represent a fitness advantage to recombinant strains.  
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<html>
 
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<a href="http://2012.igem.org/wiki/images/0/0f/UC_Chile-Certificado_Final_ByB_iGEM_2012_R_Guti%C3%A9rrez.pdf">Click here to download our Certificate from the Comitee of Bioethics and Biosafety</a>
 
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</html>
 
 +
        <li><strong> how did you manage to handle the safety issue? </strong> </li>
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    </li>
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Our lab follows the Manual of Biosafety, established by the Superior Counsel of Science and Technological Development, from the National Fund of Scientific and Technological Development of Chile (FONDECYT).
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    <li><strong>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering? </strong></li>
+
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Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?
 
-
To prevent future problems and to encourage the construction of biosafe standard biological parts, we, UC_Chile team, propose the creation of the section “biosafety analysis” mandatory for all parts before their shipping to the registry. In this way, is assured that each new biobrick or device includes an assessment of the risks and biosafety advantages involved in its physical implementation.
 
 +
<html>
 +
<a href="http://www.fondecyt.cl/578/articles-30555_recurso_1.pdf">Click here to download the Manual of Biosafety (Spanish) </a>
 +
</html>
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Alongside the previous, we suggest the characterization of biosafety levels of other team’s constructs, making this practice analogous to the existing standard characterization of bricks.
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        <li><strong> How could other teams learn from your experience?  </strong> </li>
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The requirement of this biosafety assessment for a team to win the gold medal would be a strong incentive.
+
 +
To adress the possibility of recombinant Synechocystis cells being released from the lab, we've designed a recombination plasmid that knocks out the copS gene. This gene codes for a Cu-binding protein and is essential to Cu stress response in Synechocystis. It has been demonstrated that strains lacking this gene can´t survive in much lesser Cu concentrations than those found in drinking water or natural water bodies (2).
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Regarding to the molecular methods by which biosafety could be improved; we believe that the addition of a “bomb” gene to all iGEM plasmid backbones could be very useful.
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We advice every team working in this chassis to adopt similar strategies. By designing integrative plasmids which interrupt fitness related genes, recombinant strains will be auxotrophic and/or hiper-susceptible. Thus, their recombinant cyanobacterial strains will be unable to thrive in natural environments.
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This gene would kill the recombinant cells unless its action is inhibited by a molecule present in the lab culture media but with an insignificant concentration in the environment. (1)
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The best candidate we found is the phiX1714 phage lysis gene E. When placed under a constitutive promoter, this gene inhibits peptidoglycan biosynthesis and therefore lyses the cells (2).
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      </ul>
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It has been shown that the addition of aprox. 0.2 M MgSO4  to the medium (much less than the amount founded in common water) prevents cell death by the gene E (and lysis in general) even when its expression has already been induced (3).
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      </li>
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    <li><strong>Is there a local biosafety group, committee, or review board at your institution? </strong> </li>
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To ensure cell lysis efficiency the optimized mutant gene mE, which produces lysis in 99,999% of cells (4), should be used.
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Yes, there is a local biosafety panel in our institution. The Comitee of Bioethics and Biosafety of the Biological Sciences Faculty of the Pontifical Catholic University of Chile has reviewed our work and determined that the procedures involved in our project follow the bioethical and biosafety standards for research regulations provided by the Chilean Comission of Scientific and Technological Research (CONICYT).
 +
<html>
 +
<a href="http://2012.igem.org/wiki/images/0/0f/UC_Chile-Certificado_Final_ByB_iGEM_2012_R_Guti%C3%A9rrez.pdf">Click here to download our Certificate from the Comitee of Bioethics and Biosafety</a>
 +
</html>
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Footnotes
 
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(1) Leduc M, Kasra R, van Heijenoort J. Induction and control of the autolytic system of Escherichia coli. J Bacteriol. 1982 Oct;152(1):26-34. PMID: 6181050 [PubMed - indexed for MEDLINE]
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    </li>
 +
    <li><strong>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering? </strong></li>
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(2) Young KD, Young R. Lytic action of cloned phi X174 gene E.J Virol. 1982 Dec;44(3):993-1002. PMID: 6294347 [PubMed - indexed for MEDLINE]
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To prevent future problems and to encourage the construction of biosafe standard biological parts, we, UC_Chile team, propose the creation of the section “biosafety analysis” mandatory for all parts before their shipping to the registry. This way, it is assured that each new biobrick or device includes an assessment of the risks and biosafety advantages involved in its physical implementation.
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+
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(3) Gschwender HH, Hofschneider PH. Lysis inhibition of phi-X174-, M12-, and Q-beta-infected Escherichia coli bacteria by magnesium ions. Biochim Biophys Acta. 1969 Oct 22;190(2):454-9.  
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(4) Yu SY, Peng W, Si W, Yin L, Liu SG, Liu HF, Zhao HL, Wang CL, Chang YH, Lin YZ. Enhancement of bacteriolysis of shuffled phage PhiX174 gene E. Virol J. 2011 May 6;8:206.
+
 +
Alongside the previous, we suggest the characterization of biosafety levels of other team’s constructs, making this practice analogous to the existing standard characterization of bricks.
 +
The requirement of this biosafety assessment for a team to win the gold medal would be a strong incentive to encourage the characterization of biosafety levels.
 +
Regarding to the molecular methods by which biosafety could be improved, we believe that the implementation of a lethal system to all iGEM plasmid backbones would prove essential. The system would kill the recombinant cells unless its action is inhibited by a compound present in the culture media but that its concentration in the environment is insignificant. In this way, recombinant cells which are leaked to the environment will have no possibility to thrive in environmental conditions.
-
    </ol></td>
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Concerning the last proposal, we have already thought of such a system. We have found a perfect candidate gen to be placed under a constitutive promoter that produces cell lysis. Soon we will document more information about it in our wiki.
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  <td><p>&nbsp;</p>    </td>
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</ol>
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</tr>
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</table>
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Latest revision as of 00:32, 8 September 2012

Cyanolux & SpiderColi - Pontificia Universidad Católica de Chile, iGEM 2012




  1. Would any of your project ideas raise safety issues in terms of:
    • researcher or public safety,
    • No pathogenic microorganisms or dangerous genes are considered in our ideas, in consequence our intended projects, if executed, do not represent any risk to researchers nor public safety.

    • environmental safety?
    • As Synechocystis is a naturally competent environmental bacteria that undergoes homologous recombination, there is a posibility that if laboratory recombinant strains are leaked to the environment there may be environmental safety issues such as lateral DNA transference and endogenous species endangerment. We discuss this issue further in question number 4 (see below).

  2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? Yes, the release of biobricks made from Synechocystis genome´s sequences or at least with a region homologous to it raise the possibility of recombination by environmental cyanobacteria. To address this issue we have proposed and designed a biosafety mechanism discussed in question number 4 (see below). Furthermore, our laboratory practices enforce strict methods to handle any biological material. As DNA is always hermetically contained or discarded with other biological material according to standard protocols we believe that our practices will not produce any environmental hazard.
    • did you document these issues in the Registry?
    • All issues regarding our biobricks will be documented once we send the parts to the registry.

      It has to be stated that any of the sequences designed and/or handled by our team are not per se dangerous nor they represent a fitness advantage to recombinant strains.


    • how did you manage to handle the safety issue?
    • Our lab follows the Manual of Biosafety, established by the Superior Counsel of Science and Technological Development, from the National Fund of Scientific and Technological Development of Chile (FONDECYT).


      Click here to download the Manual of Biosafety (Spanish)

    • How could other teams learn from your experience?
    • To adress the possibility of recombinant Synechocystis cells being released from the lab, we've designed a recombination plasmid that knocks out the copS gene. This gene codes for a Cu-binding protein and is essential to Cu stress response in Synechocystis. It has been demonstrated that strains lacking this gene can´t survive in much lesser Cu concentrations than those found in drinking water or natural water bodies (2).

      We advice every team working in this chassis to adopt similar strategies. By designing integrative plasmids which interrupt fitness related genes, recombinant strains will be auxotrophic and/or hiper-susceptible. Thus, their recombinant cyanobacterial strains will be unable to thrive in natural environments.

  3. Is there a local biosafety group, committee, or review board at your institution?
  4. Yes, there is a local biosafety panel in our institution. The Comitee of Bioethics and Biosafety of the Biological Sciences Faculty of the Pontifical Catholic University of Chile has reviewed our work and determined that the procedures involved in our project follow the bioethical and biosafety standards for research regulations provided by the Chilean Comission of Scientific and Technological Research (CONICYT).

    Click here to download our Certificate from the Comitee of Bioethics and Biosafety


  5. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?
  6. To prevent future problems and to encourage the construction of biosafe standard biological parts, we, UC_Chile team, propose the creation of the section “biosafety analysis” mandatory for all parts before their shipping to the registry. This way, it is assured that each new biobrick or device includes an assessment of the risks and biosafety advantages involved in its physical implementation.

    Alongside the previous, we suggest the characterization of biosafety levels of other team’s constructs, making this practice analogous to the existing standard characterization of bricks. The requirement of this biosafety assessment for a team to win the gold medal would be a strong incentive to encourage the characterization of biosafety levels.

    Regarding to the molecular methods by which biosafety could be improved, we believe that the implementation of a lethal system to all iGEM plasmid backbones would prove essential. The system would kill the recombinant cells unless its action is inhibited by a compound present in the culture media but that its concentration in the environment is insignificant. In this way, recombinant cells which are leaked to the environment will have no possibility to thrive in environmental conditions.

    Concerning the last proposal, we have already thought of such a system. We have found a perfect candidate gen to be placed under a constitutive promoter that produces cell lysis. Soon we will document more information about it in our wiki.