Team:Paris Saclay/Safety

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='''Safety'''=
='''Safety'''=
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Use this page to answer the questions on the  [[Safety | safety page]].
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'''Safety forms were approved on September 22, 2013 by Evan Appleton.'''
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iGEM Safety Questions
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== iGEM Safety Questions ==
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'''<u>1. Would any of your project ideas raise safety issues in term of:</u>'''
 
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'''-researcher safety'''
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'''1. Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:'''
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We are using the bacteria Burkholderia xenovorans, Pseudomonas pseudoalcaligenes KF707,
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We used the strain ''E. coli'' K12, the MG1655 strain and its derivatives, which all belong to Risk group 1 (http://www.absa.org/riskgroups/bacteriasearch.php?genus=Escherichia&species=coli) and is not associated with disease in healthy adult humans.
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Rhodococcus jostii RHA1 and Escherichia coli DH5 a to build the biobrick parts, and
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especially Escherichia coli DH5 a as the host of our constructs. These strains are not pathogenic
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so they belong to the risk group 1 according to the WHO laboratory biosafety manual.
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These organisms have been manipulated with all the required precautions without any risk or
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danger for our researchers leading the experiments.
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Nevertheless, for our project a chemical pollutant the PCB (Polychlorinated Biphenyl) has
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been employed so as to test the efficiency of our constructs. This hydrophobic molecule can
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penetrate skin and latex, it is able to induct cardiovascular disease and maybe cancer, that is
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why we manipulated it with the material and methods introduced by the IOMC (Inter-Organization
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Program for the Sound Management of Chemicals) letting us manipulate it safely.
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http://www.chem.unep.ch/pops/pdf/pcbtranscap.pdf
 
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'''2. Highest Risk Group Listed:'''
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The highest risk group listed is 1.
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'''-public safety'''
 
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During the course of an experiment, we made sure members of the general public did not have
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'''3. List and describe all new or modified coding regions you will be using in your project. (If you use parts from the 2013 iGEM Distribution without modifying them, you do not need to list those parts.)'''
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access to the lab by keeping the door locked. The lack of pathogenic power of these strains
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avoided all danger of illness diffusion by an unlikely exposition.
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Concerning PCBs, their manipulation was done in confined conditions where anybody
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-
unexpected could be in contact with this pollutant.
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 +
{| class="wikitable centre" width="80%"
 +
|+
 +
|-align="center"
 +
! scope=col | Number
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! scope=col | Part Number
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! scope=col | Physical origin of DNA
 +
! scope=col | What species does this part originally come from?
 +
! scope=col | What is the Risk Group of the species?
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! scope=col |What is the function of this part, in its parent species?
 +
|-align="center"
 +
| width="10%" |
 +
1
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| width="19%" |
 +
BBa_K1155008
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| width="19%" |
 +
laboratory of Dr Philippe Bouloc (IGM, Université Paris-Sud)
 +
| width="19%" |
 +
''Escherichia coli'' DH5alpha
 +
| width="10%" |
 +
1
 +
| width="28%" |
 +
Transcriptional regulator, sensitive to oxygen
 +
|-align="center"
 +
| width="10%" |
 +
2
 +
| width="19%" |
 +
BBa_K1155009
 +
| width="19%" |
 +
DSMZ for the strain
 +
| width="19%" |
 +
''Pseudomonas pseudoalcaligenes'' KF 707
 +
| width="10%" |
 +
1
 +
| width="28%" |
 +
transcriptional regulator, sensitive to PCBs
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'''-environmental safety'''
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|}
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Our project has been made to be applied in the case of a confined environment where
 
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microorganisms won’t vanish within the air steering clear any DNA transfer with another
 
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form of life. If we expect the worst these genes would confer the ability of catalyze the degradation
 
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or detect PCBs what do not represent a real danger for environment if we do not care
 
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about the probability of mutations modifying their function or quite simply the ethical limits
 
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of GMOs released in nature.
 
 +
'''4. Do the biological materials used in your lab work pose any of the following risks? Please describe.'''
 +
'''a. Risks to the safety and health of team members or others working in the lab?'''
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'''<u>2.Do any of the BioBrick parts (or devices) that you made this year raise safety issues?</u>'''
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All  bacteria (Escherichia coli K12 and Pseudomonas pseudoalcaligenes KF 707) used in our project belong to the risk group 1, so they do not represent any risk for the health of the members of the team.
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Not really, this year the biobricks will concern the detection of PCBs and the coordination of
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'''b. Risks to the safety and health of the general public, if released by design or by accident?'''
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the biodegradation metabolism of those in E.Coli, the parts are not dangerous as they are.
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 +
Our final system or any of the intermediate strains constructed  do not represent any risk or danger for the general public as they are all derived from Escherichia coli K12 (belonging to the risk group 1), a strain that cannot colonize the human colon and does not produce toxins.
 +
'''c. Risks to the environment, if released by design or by accident?'''
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'''<u>3.Is there a local biosafety group, committee, or review board at your institution?</u>'''
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The strains used and constructed derive from E. coli K12, a strain whose survival  under environmental conditions (soil or water) is  limited. Moreover, the bacteria do not produce harmful compounds.
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There is, in every department of the Université Paris-Sud, a comity in charge of hygiene and
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Source: http://epa.gov/biotech_rule/pubs/fra/fra004.htm
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security. Consequently, the Institute of Genetics and Microbiology, where we performed our
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experiments, has a bureau in charge of hygiene and security whose GMO section is directed by one
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of our instructors: Jean-Luc Pernodet.
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His presence in the team helped us think of the dangers linked to disseminating GMOs into the
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environment, as well as ways to resolve these problems.
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We also learned about the specific safety rules of the laboratory where we carried our experiments
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with the person in charge of this laboratory (gas usage, handling of BEt (ethidium bromide),
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processing of chemical and biological waste...).
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We also payed attention to the security memorandum and signed the hygiene and security
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charter of the Institute of Genetics and Microbiology:
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Security memorandum
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Hygiene and security charter
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All experiments were carried out according to French Safety Regulations.
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 +
'''d. Risks to security through malicious misuse by individuals, groups, or countries?'''
 +
The risk of malicious misuses of our project system is limited as this system is built for bioremediation, namely the detection and the degradation of the PCB. The genes used in this system do not code for  toxins or for enzymes synthetizing products toxic to humans or harmful for the environment.
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'''<u>4. Do you have any other ideas how to deal with safety issues that could be useful for
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'''5. If your project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise? (Consider the different categories of risks that are listed in parts a-d of the previous question.) Also, what risks might arise if the knowledge you generate or the methods you develop became widely available? (Note: This is meant to be a somewhat open-ended discussion question.)'''
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future iGEM competitions? How parts devices and systems could be made even safer
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through biosafety engineering</u>'''
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The advocation by the iGEM competition of the restriction enzymes and particularly the 3A
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If used at the industrial scale, the risk of accidental release might increase. But in such a case, a different chassis could be used (different species, designed features to limit the impact of accidental release).
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assembly, even if we are fully aware of the fact that it’s a way to reach compatibility, could be, in
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terms of biosafety, a mean to increase the probability of DNA transfer between organisms because
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of the excessive use of restriction sites, in the prefix and the suffix, recognized by enzymes that can
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be easily found, in high levels, in most of organisms.
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Some ways using methods like Gibson Assembly should be more frequently employed to make the
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'''6. Does your project include any design features to address safety risks? (For example: kill switches, auxotrophic chassis,etc.) Note that including such features is not mandatory to participate in iGEM, but many groups choose to include them.'''
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constructs, even if the biobrick standard would be harder to approach.
+
 
 +
No, not at this stage. This project was a proof of concept. A different chassis could be used for the large scale implementation of this project. The GEMOTE system, imagined by the Paris-Saclay 2012 team, could for exemple be used to limit the survival of the strains outside a specific temperature range.
 +
 
 +
'''7. What safety training have you received (or plan to receive in the future)? Provide a brief description, and a link to your institution’s safety training requirements, if available.'''
 +
 
 +
We learned about laboratory safety rules with our advisors during the three months of lab work (gas usage, handling of BEt (ethidium bromide), processing of chemical and biological wastes, precautions with UV light, manipulation of hot melted media, use of phenol...).
 +
 
 +
'''8. Under what biosafety provisions will / do you work?
 +
a. Please provide a link to your institution biosafety guidelines.'''
 +
 
 +
Biosafety in CNRS: http://www.dgdr.cnrs.fr/cnps/guides/risques/pdf/GuideIGHS_p27.pdf
 +
 
 +
'''b. Does your institution have an Institutional Biosafety Committee, or an equivalent group? If yes, have you discussed your project with them? Describe any concerns they raised with your project, and any changes you made to your project plan based on their review.'''
 +
 
 +
There is in the Institute of Genetics and Microbiology (Université Paris-Sud) where we performed our experiments, a comity in charge of hygiene and security. One of our advisors,  J-L Pernodet, is in charge of questions regarding GMO. He made sure that we only manipulated class 1 micro-organisms.
 +
 
 +
'''c. Does your country have national biosafety regulations or guidelines? If so, please provide a link to these regulations or guidelines if possible.'''
 +
 
 +
<u>In France:</u>
 +
 
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INRS: http://www.inrs.fr/accueil/risques/biologiques/prevention-risques/cadre-prevention.html
 +
 
 +
Haut Conseil de Biotechnologies: http://www.hautconseildesbiotechnologies.fr/IMG/pdf/Manuel_HCB_utilisation_confinee_OGM.pdf
 +
 
 +
<u>In Europe:</u> http://europa.eu/legislation_summaries/employment_and_social_policy/health_hygiene_safety_at_work/
 +
 
 +
 
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'''d. According to the WHO Biosafety Manual, what is the BioSafety Level rating of your lab? (Check the summary table on page 3, and the fuller description that starts on page 9.) If your lab does not fit neatly into category 1, 2, 3, or 4, please describe its safety features [see 2013.igem.org/Safety for help].'''
 +
 
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The BioSafety Level rating of our lab is Class 1.
 +
 
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'''e. What is the Risk Group of your chassis organism(s), as you stated in question 1? If it does not match the BSL rating of your laboratory, please explain what additional safety measures you are taking.'''
 +
 
 +
Our chassis, ''Escherichia coli'' K12 MG1655, belongs to the biosafety risk group 1 and matches the BSL rating of the laboratory.
 +
 
 +
 
 +
 
 +
 
 +
Written by Eric
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However the risk of DNA transformation by homologous sequences remains in spite of the
 
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reduction of biohazard. Obviously it’s only a hypothesis whose hasn’t been checke
 
{{Team:Paris_Saclay/incl_fin}}
{{Team:Paris_Saclay/incl_fin}}

Latest revision as of 20:42, 3 October 2013

Labwork Overview Biobricks Protocols Primers Safety

Safety

Safety forms were approved on September 22, 2013 by Evan Appleton.

iGEM Safety Questions

1. Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:

We used the strain E. coli K12, the MG1655 strain and its derivatives, which all belong to Risk group 1 (http://www.absa.org/riskgroups/bacteriasearch.php?genus=Escherichia&species=coli) and is not associated with disease in healthy adult humans.


2. Highest Risk Group Listed:

The highest risk group listed is 1.


3. List and describe all new or modified coding regions you will be using in your project. (If you use parts from the 2013 iGEM Distribution without modifying them, you do not need to list those parts.)

Number Part Number Physical origin of DNA What species does this part originally come from? What is the Risk Group of the species? What is the function of this part, in its parent species?

1

BBa_K1155008

laboratory of Dr Philippe Bouloc (IGM, Université Paris-Sud)

Escherichia coli DH5alpha

1

Transcriptional regulator, sensitive to oxygen

2

BBa_K1155009

DSMZ for the strain

Pseudomonas pseudoalcaligenes KF 707

1

transcriptional regulator, sensitive to PCBs


4. Do the biological materials used in your lab work pose any of the following risks? Please describe.

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

All bacteria (Escherichia coli K12 and Pseudomonas pseudoalcaligenes KF 707) used in our project belong to the risk group 1, so they do not represent any risk for the health of the members of the team.

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

Our final system or any of the intermediate strains constructed do not represent any risk or danger for the general public as they are all derived from Escherichia coli K12 (belonging to the risk group 1), a strain that cannot colonize the human colon and does not produce toxins.

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

The strains used and constructed derive from E. coli K12, a strain whose survival under environmental conditions (soil or water) is limited. Moreover, the bacteria do not produce harmful compounds.

Source: http://epa.gov/biotech_rule/pubs/fra/fra004.htm

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

The risk of malicious misuses of our project system is limited as this system is built for bioremediation, namely the detection and the degradation of the PCB. The genes used in this system do not code for toxins or for enzymes synthetizing products toxic to humans or harmful for the environment.

5. If your project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise? (Consider the different categories of risks that are listed in parts a-d of the previous question.) Also, what risks might arise if the knowledge you generate or the methods you develop became widely available? (Note: This is meant to be a somewhat open-ended discussion question.)

If used at the industrial scale, the risk of accidental release might increase. But in such a case, a different chassis could be used (different species, designed features to limit the impact of accidental release).

6. Does your project include any design features to address safety risks? (For example: kill switches, auxotrophic chassis,etc.) Note that including such features is not mandatory to participate in iGEM, but many groups choose to include them.

No, not at this stage. This project was a proof of concept. A different chassis could be used for the large scale implementation of this project. The GEMOTE system, imagined by the Paris-Saclay 2012 team, could for exemple be used to limit the survival of the strains outside a specific temperature range.

7. What safety training have you received (or plan to receive in the future)? Provide a brief description, and a link to your institution’s safety training requirements, if available.

We learned about laboratory safety rules with our advisors during the three months of lab work (gas usage, handling of BEt (ethidium bromide), processing of chemical and biological wastes, precautions with UV light, manipulation of hot melted media, use of phenol...).

8. Under what biosafety provisions will / do you work? a. Please provide a link to your institution biosafety guidelines.

Biosafety in CNRS: http://www.dgdr.cnrs.fr/cnps/guides/risques/pdf/GuideIGHS_p27.pdf

b. Does your institution have an Institutional Biosafety Committee, or an equivalent group? If yes, have you discussed your project with them? Describe any concerns they raised with your project, and any changes you made to your project plan based on their review.

There is in the Institute of Genetics and Microbiology (Université Paris-Sud) where we performed our experiments, a comity in charge of hygiene and security. One of our advisors, J-L Pernodet, is in charge of questions regarding GMO. He made sure that we only manipulated class 1 micro-organisms.

c. Does your country have national biosafety regulations or guidelines? If so, please provide a link to these regulations or guidelines if possible.

In France:

INRS: http://www.inrs.fr/accueil/risques/biologiques/prevention-risques/cadre-prevention.html

Haut Conseil de Biotechnologies: http://www.hautconseildesbiotechnologies.fr/IMG/pdf/Manuel_HCB_utilisation_confinee_OGM.pdf

In Europe: http://europa.eu/legislation_summaries/employment_and_social_policy/health_hygiene_safety_at_work/


d. According to the WHO Biosafety Manual, what is the BioSafety Level rating of your lab? (Check the summary table on page 3, and the fuller description that starts on page 9.) If your lab does not fit neatly into category 1, 2, 3, or 4, please describe its safety features [see 2013.igem.org/Safety for help].

The BioSafety Level rating of our lab is Class 1.

e. What is the Risk Group of your chassis organism(s), as you stated in question 1? If it does not match the BSL rating of your laboratory, please explain what additional safety measures you are taking.

Our chassis, Escherichia coli K12 MG1655, belongs to the biosafety risk group 1 and matches the BSL rating of the laboratory.



Written by Eric


Retrieved from "http://2013.igem.org/Team:Paris_Saclay/Safety"