Team:British Columbia/Safety

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Latest revision as of 01:42, 4 October 2012

British Columbia - 2012.igem.org

Safety Page

1. Would any of your parts or project ideas raise safety issues?

A. Risks to the safety and health of team members or others in the lab?
No. Upon assessment, our engineered parts present a very low risk to the safety of the researcher, public, and the environment. Every team member has completed the introductory laboratory safety courses.

The main chassis we are working with, a derivative from Escherichia coli K12, is a non-pathogenic strain. It is not known to consistently cause disease in healthy adult humans and is of minimal potential hazard to laboratory personnel and the environment. There are no special biosafety protocols researchers have to follow, other than basic treatment of equipment and materials coming into contact with the organism (autoclaving, etc.).

We will also briefly work with Rhodococcus erythropolis, which is also non-pathogenic. Like the E. coli strain we used, R. erythropolis posed no health hazards if normal biological laboratory procedures are followed.

B. Risks to the safety and health of the general public if released by design or accident?
As explained in part (a), none of the organisms, parts or created compounds are pathogenic, infectious, or toxic at the safety levels we are working at. The team is also following proper disposal procedures. Given that the E. coli we use are of the K12 strain or a derivative, these bacteria are of relatively small concern.

C. Risks to environmental quality if released by design or accident?
The only component of our project that may pose an environmental risk is the chemical reagents and products involved in the desulfurization process. Petroleum fractions and dibenzothiopene are potential pollutants but storage, bench work and waste disposal are being carried out in accordance with UBC's chemical safety procedures.

D. Risks to security through malicious misuse by individuals, groups or states?
At the moment, it doesn't seem very feasible to maliciously misuse our organisms or desulfurization reagents, since they don't pose a serious or immediate health or environmental threat.

2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?

No, we do not believe that the BioBrick parts made this year raise any safety issues. Our biobrick parts consist of genes in amino acid synthesis pathways, fluorescent proteins, and the Dsz desulfurization pathway. The amino acid components are easily found in the laboratory and in nature, while fluorescent proteins pose no threat to safety. Desulfurization pathway enzymes were originally isolated in 1990 and have since been extensively characterized. Their specific activities are not expected to be harmful to researchers, the public or the environment.

3. Is there a local biosafety group, committee, or review board at your institution? If yes, what does your local biosafety group think about your project? If no, which specific biosafety rules or guidelines do you have to consider in your country?

A and B. Does your institution have its own biosafety rules? Does your institution have an Institutional Biosafety Committee? Have you discussed your project with them?
UBC's biosafety committee has the institutional biosafety rules on their biohazard policies website. They are part of the Risk Management Services at UBC which educates and ensures UBC staff follows safe laboratory procedures at all times. The biosafety committee governs whether or not research can be conducted at UBC. They are composed of UBC faculty, staff, a biosafety advisor and the manager of occupational safety. In order for research to be done, the principle investigator must submit an application that outlines: objectives, methods, procedures, biosafety, what work will be done and where, what materials will be used, and waste management procedures. After this is submitted, the UBC Biosafety Committee will either reject or approve the principle investigator to do his/her work. They are granted Biohazard Approval Certification for 4 years but they must renew their certification annually.

We specifically spoke with the safety adviser at UBC. We have the appropriate biosafety approval to do the wet lab portion of our iGEM project in the Life Sciences Centre at UBC. We are working in a lab that already has its principle investigator approved to do similar research and we are not testing new procedures which have not been approved yet.

C. Did you receive any biosafety and/or lab training before beginning your project?
Each student on our team has gone through basic laboratory safety courses put on by the Risk Management Services. The basic laboratory safety served to cover topics such as the Workplace Hazardous Material Information System (WHMIS), biohazards, hazardous chemicals, and radioactive materials.

Graduate student advisors and other researchers have all received in-depth safety training in biological and chemical safety and trained and directly supervised iGEM members during project experiments. The team also established general safe protocols.

D. Does your country have national biosafety regulations or guidelines?
The Canadian government has 2 bodies which overlook each biosafety committee at Canadian universities. The first is the Public Health Agency of Canada. They published the “Laboratory Biosafety Guidelines” – a booklet that outlines all the rules which biological labs must follow. The second group is the Canadian Food Inspection Agency which mostly deals with plants and animals.

Additionally, should we ever choose to commercialize and release a product, it would be into controlled reactor vessels of oil refineries. Even though the microorganisms are not directly released into the environment, we would have to go through numerous other agencies in Canada – most notably Environment Canada. It is only after strict screening and investigation that such a product would be allowed to be used commercially outside of laboratories.

4. 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?

Biosafety is a major aspect of our project this year. We are focusing on two ways to limit safety risks posed by released organisms:

1) Distributed pathways -- By taking a single pathway and distributing the necessary pieces among various members of a microbial consortia, the possibility of the entire pathway being transferred to wild organisms drastically decreases.

2) Effective kill switches -- The use of tested and effective kill switch mechanisms will control engineered organisms that are introduced to the environment. Through the standardized evaluation of kill-switch efficacy, will aid iGEM teams in choosing the best system for their project. Such an evaluation will be made possible by the protocol that is designed and tested as a result of the collaboration between the 2012 University of Calgary and University of British Columbia teams.

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-. Would any of your project ideas raise safety issues in terms of:
+<html>
+<style>
-a. researcher safety,
+#break {width:950px;float:left; background-color: white; margin-left: 8px;  margin-top:10px;}
-b. public safety, or
-c. environmental safety?
-. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
-a. did you document these issues in the Registry?
-b. how did you manage to handle the safety issue?
-c. how could other teams learn from your experience?
-. Is there a local biosafety group, committee, or review board at your institution?
-a. If yes, what does your local biosafety group think about your project?
-b. If no, which specific biosafety rules or guidelines do you have to consider in your country?
-. 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?
-{{Template:Template_HD_1}}
-<html><style>
-#logo {width:150px; float:left; background-color: white; margin-left: 8px;  margin-top:10px;}
-#other {width:780px; float:left; background-color: white; margin-left: 8px;  margin-top:10px;}
 </style>
+<div id=break></div>
-<div id="logo"></br>
+<p align=center><font face=arial narrow size=5><b>Safety Page</b></font></p><font face=arial narrow>
-</div><div id="other"></html>
-===1. Would any of your parts or project ideas raise safety issues?===
-'''A. Risks to the safety and health of team members or others in the lab?'''
+<font face=arial narrow size=4><b>1. Would any of your parts or project ideas raise safety issues?</b></br></br></font><font face=arial narrow>
+<b>A. Risks to the safety and health of team members or others in the lab?</b></br>
-No. Upon assessment, our engineered parts present a very low risk to the safety of the researcher, public and the environment. Every team member has completed the introductory biosafety courses.
+No. Upon assessment, our engineered parts present a very low risk to the safety of the researcher, public, and the environment. Every team member has completed the introductory laboratory safety courses. </br></br>
-The main chassis we are working with, a derivative from Escherichia coli K12, is a non-pathogenic strain, which not known to consistently cause disease in healthy adult humans, and of minimal potential hazard to laboratory personnel and the environment.
+The main chassis we are working with, a derivative from <i>Escherichia coli</i> K12, is a non-pathogenic strain.  It is not known to consistently cause disease in healthy adult humans and is of minimal potential hazard to laboratory personnel and the environment.  There are no special biosafety protocols researchers have to follow, other than basic treatment of equipment and materials coming into contact with the organism (autoclaving, etc.).</br></br>
-The G. clavigera bluestain fungus has not been shown to cause disease in humans and there are no special biosafety protocols researchers have to follow, other than basic treatment of equipment and materials coming into contact with the organism (autoclaving, etc.).
+We will also briefly work with <i>Rhodococcus erythropolis</i>, which is also non-pathogenic.  Like the <i>E. coli</i> strain we used, <i>R. erythropolis</i> posed no health hazards if normal biological laboratory procedures are followed. </br></br>
-The terpenes we will be working with (alpha-pinene, beta-pinene, 3-carene, limonene) are toxic at high concentrations if ingested and may also irritate the eyes, skin and airway. However, from previous studies, we expect terpene production of at most a couple hundred mg/L. Working with at most 50mL at a time, this puts potential exposure levels well below toxicity levels, which are on the order of several grams per kg body mass (if ingested). Safety precautions, including wearing gloves and safety glasses, will be taken to ensure researcher safety and prevent exposure. All work involving terpenes will be disposed of according to chemical waste disposal procedures as to not pollute the environment.
+<b>B. Risks to the safety and health of the general public if released by design or accident?</b></br>
-'''B. Risks to the safety and health of the general public if released by design or accident?'''
+As explained in part (a), none of the organisms, parts or created compounds are pathogenic, infectious, or toxic at the safety levels we are working at. The team is also following proper disposal procedures.  Given that the E. coli we use are of the K12 strain or a derivative, these bacteria are of relatively small concern.</br></br>
-As explained in part (a), none of the organisms, parts or created compounds are pathogenic, infectious or toxic at the safety levels we are working at. The team is also following proper disposal procedures.
+<b>C. Risks to environmental quality if released by design or accident?</b></br>
-Exposure to our yeast chassis and terpenes would be as hazardous as exposure to baker's yeast, unfiltered beer or an air freshener. The bluestain fungus is also not pathogenic to humans, although it is a reasonable assumption that deliberate ingestion or inhalation of a considerably large amount of this fungus like any other mold would result in detrimental effects to one's health.
+The only component of our project that may pose an environmental risk is the chemical reagents and products involved in the desulfurization process.  Petroleum fractions and dibenzothiopene are potential pollutants but storage, bench work and waste disposal are being carried out in accordance with UBC's chemical safety procedures. </br></br>
-'''C. Risks to environmental quality if released by design or accident?'''
+<b>D. Risks to security through malicious misuse by individuals, groups or states?</b></br>
-The only component of our project that may pose an environmental risk is the bluestain fungus, which forms a symbiotic relationship with the mountain pine beetle to facilitate its spread in the pine forests. However, it requires a vector, the mountain pine beetle, to allow it to colonize new trees, so even if spores were carried out of the lab by a researcher the chances of them infecting the local environment is extremely low.  Even other species of beetles found in infected trees have not been found to carry the fungus, so it is very specific to the mountain pine beetle.
+At the moment, it doesn't seem very feasible to maliciously misuse our organisms or desulfurization reagents, since they don't pose a serious or immediate health or environmental threat.</br>
-In order to cause deliberate harm to the environment, someone would have to breed mountain pine beetles with the bluestain fungus and travel out into the pine forests and release these beetles onto aged pine trees, which would eventually lead to an infestation over a few years. However, this would not be the start of something new e.g. introducing a competitive invasive species, because there is already a mountain pine beetle-bluestain fungus epidemic in North American pine forests.
+<div id=break></br></div>
-'''D. Risks to security through malicious misuse by individuals, groups or states?'''
+<font face=arial narrow size=4><b>2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</b></br></br></font><font face=arial narrow>
-At the moment, it doesn't seem very feasible to maliciously misuse our yeast, terpenes or bluestain fungus since they don't pose a serious or immediate health or environmental threat.
+No, we do not believe that the BioBrick parts made this year raise any safety issues. Our biobrick parts consist of genes in amino acid synthesis pathways, fluorescent proteins, and the Dsz desulfurization pathway. The amino acid components are easily found in the laboratory and in nature, while fluorescent proteins pose no threat to safety.  Desulfurization pathway enzymes were originally isolated in 1990 and have since been extensively characterized. Their specific activities are not expected to be harmful to researchers, the public or the environment.</br>
-<br>
+<div id=break></br></div>
-===2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?===
+<font face=arial narrow size=4><b>3. Is there a local biosafety group, committee, or review board at your institution? If yes, what does your local biosafety group think about your project? If no, which specific biosafety rules or guidelines do you have to consider in your country?</b></br></br></font><font face=arial narrow>
-No, we do not have any safety issues with the Biobrick parts made this year (refer to answer for question 1). Our biobrick parts consist of yeast promoters, genes encoding monoterpene synthases and S. cerevisiae mevalonate pathway genes. These components are easily found in the laboratory and in nature.
+<b>A and B. Does your institution have its own biosafety rules? Does your institution have an Institutional Biosafety Committee? Have you discussed your project with them?</b></br>
-<br>
+UBC's <a href="http://www.ors.ubc.ca/ors/biosafety">biosafety committee</a> has the institutional biosafety rules on their <a href="http://www.ors.ubc.ca/contents/biohazard-policies">biohazard policies website</a>. They are part of the Risk Management Services at UBC which educates and ensures UBC staff follows safe laboratory procedures at all times. The biosafety committee governs whether or not research can be conducted at UBC. They are composed of UBC faculty, staff, a biosafety advisor and the manager of occupational safety. In order for research to be done, the principle investigator must submit an application that outlines: objectives, methods, procedures, biosafety, what work will be done and where, what materials will be used, and waste management procedures. After this is submitted, the UBC Biosafety Committee will either reject or approve the principle investigator to do his/her work. They are granted Biohazard Approval Certification for 4 years but they must renew their certification annually.</br></br>
-===3. Is there a local biosafety group, committee, or review board at your institution? If yes, what does your local biosafety group think about your project? If no, which specific biosafety rules or guidelines do you have to consider in your country?===
+We specifically spoke with the safety adviser at UBC. We have the appropriate biosafety approval to do the wet lab portion of our iGEM project in the Life Sciences Centre at UBC. We are working in a lab that already has its principle investigator approved to do similar research and we are not testing new procedures which have not been approved yet.</br></br>
-'''A and B. Does your institution have its own biosafety rules? Does your institution have an Institutional Biosafety Committee? Have you discussed your project with them?'''
+<b>C. Did you receive any biosafety and/or lab training before beginning your project?</b></br>
-UBC's '''[http://www.ors.ubc.ca/ors/biosafety biosafety committee]''' has the institutional biosafety rules on their '''[http://www.ors.ubc.ca/contents/biohazard-policies biohazard policies site]'''. They are part of the Risk Management Services at UBC which educates and ensures UBC staff follows safe laboratory procedures at all times. Biosafety committee governs whether or not research can be conducted at UBC. They are composed of UBC faculty, staff, a biosafety advisor and the manager of occupational safety. In order for research to be done, the principle investigator must submit an application that outlines: objectives, methods, procedures, biosafety, what work will be done and where, what materials will be used, and waste management procedures. After this is submitted, the UBC Biosafety Committee will either reject or approve the principle investigator to do his/her work. They are granted Biohazard Approval Certification for 4 years but they must renew their certification annually.
-We specifically spoke with the safety adviser at UBC. We have the appropriate biosafety approval to do the wet lab portion of our iGEM project in the Michael Smith Laboratories at UBC. We are working in a lab that already has its principle investigator approved to do similar research and we are not testing new procedures which have not been approved yet.
-'''C. Did you receive any biosafety and/or lab training before beginning your project?'''
-Each student on our team has gone through basic biosafety courses put on by the Risk Management Services. The '''[http://riskmanagement.ubc.ca/courses/laboratory-chemical-safety chemical safety training]''' covered: chemical hazards, WHMIS, safe handling, storage, hazard recognition and control, waste management and emergency response. In the practical session, our students performed a spill clean-up, learn decontamination procedures and will practice chemical segregation for safe storage. The '''[http://riskmanagement.ubc.ca/courses/intro-lab-safety basic laboratory safety]''' served to increase our knowledge about the Workplace Hazardous Material Information System (WHMIS), biohazards, hazardous chemicals and radioactive materials.
+Each student on our team has gone through basic laboratory safety courses put on by the Risk Management Services. The <a href="http://riskmanagement.ubc.ca/courses/intro-lab-safety">basic laboratory safety</a> served to cover topics such as the Workplace Hazardous Material Information System (WHMIS), biohazards, hazardous chemicals, and radioactive materials. </br></br>
-Our faculty instructor, Dr. Joanne Fox went through a 3-day basic laboratory training course with the team in early June before they started working in the lab. The team also established '''[https://2011.igem.org/Team:British_Columbia/Protocols/Peace basic safety rules]''' to follow with the members of our host lab.
-Furthermore, the Michael Smith Laboratories has it's own local biosafety committee which is composed of members from each lab. They coordinate with each other to ensure each group knows the safety protocols specific to their labs and deal with lab specific matters when incidents arise.
-'''D. Does your country have national biosafety regulations or guidelines?'''
-The Canadian government has 2 bodies which overlook each biosafety committee at Canadian universities. The first is the '''[http://www.phac-aspc.gc.ca/index-eng.php Public Health Agency of Canada]'''. They published the '''[http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/ “Laboratory Biosafety Guidelines”]''' – a booklet that outlines all the rules which biological labs must follow. The second group is the '''[http://www.inspection.gc.ca/english/toce.shtml Canadian Food Inspection Agency]''' which mostly deals with plants and animals. They have established a '''[http://www.inspection.gc.ca/english/sci/bio/bioe.shtml containment standard]''' for labs dealing with plant pests.
-Additionally, should we ever choose to release a product into the wild, to limit (or stop) the spread of the pine beetle, we would have to go through numerous other agencies in Canada – most notably '''[http://www.ec.gc.ca/default.asp?lang=en Environment Canada]'''.
-<br>
-===4. 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?===
-We encourage the use of organisms that are well adapted to laboratory settings and are not competitive outside lab environment. If synthetic organisms are to be released into the environment, they should:
-(1) Contain a tracking system to detect their presence e.g. a non-coding DNA code akin to a fingerprint
-(2) Contain a suicide system to enable effective elimination of the organism when so desired
-<br>
-===5. Additional Comments===
-Since our project's vision is to release synthetic yeast into the environment to address the mountain pine beetle outbreak, we spoke to many experts in the field and collated their '''[https://2011.igem.org/Team:British_Columbia/Wild insights into the release of synthetic organisms]'''. We believe that this raises many important safety points that future researchers and iGEM teams should consider if they plan to release synthetic organisms into the environment. The interview transcripts and take-home messages can be found '''[https://2011.igem.org/Team:British_Columbia/Wild here]'''. Although our synthetic yeast is far from release into the environment, here are some of the questions we thought about:
-'''Are novel traits or a novel combination of traits introduced?''' (inspired by Dr. Riseman)
-Yes. These synthetic yeast are capable of producing monoterpenes associated with tree resistance to pine beetles/bluestain fungus.
-'''Do they compete with organisms in the wild and have any negative impacts on the environment?''' (inspired by Dr. Carroll and Dr. van Vuuren)
-Currently, our synthetic yeast is adapted to laboratory conditions and is not competitive with yeast in the wild. It is difficult to predict negative impacts since it is difficult to carry out trials of release in a closed system. However, since the yeast is not competitive, its impact should not be spatially far-reaching or long-term and it needs to be dispersed regularly to sustain its effects on the pine beetle epidemic. On the molecular level, monoterpenes can be either a defense compound or a nutrient to different organisms. However, beyond the molecular scale, we are not sure of the synthetic yeast's impact on other organisms and the physical environment. This consideration is beyond the scope of our project and will require vigorous testing and consultation with experts in the field.
+Graduate student advisors and other researchers have all received in-depth safety training in biological and chemical safety and trained and directly supervised iGEM members during project experiments. The team also established <a href="https://2012.igem.org/Team:British_Columbia/Protocols">general safe protocols</a>. </br></br>
-'''What quality controls have you performed?''' (inspired by Dr. van Vuuren)
+<b>D. Does your country have national biosafety regulations or guidelines?</b></br>
-We have confirmed that our monoterpene synthases are capable of producing monoterpenes using the gas chromatography mass spectrometry (GC-MS) technique. However, much more testing must be performed before release such as the analysis of the synthetic yeast proteome, transcriptome and metabolome in order to determine potential side effects of monoterpene production in yeast.
+The Canadian government has 2 bodies which overlook each biosafety committee at Canadian universities. The first is the <a href="http://www.phac-aspc.gc.ca/index-eng.php">Public Health Agency of Canada</a>. They published the <a href="http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/">“Laboratory Biosafety Guidelines”</a> – a booklet that outlines all the rules which biological labs must follow. The second group is the <a href="http://www.inspection.gc.ca/english/toce.shtml">Canadian Food Inspection Agency</a> which mostly deals with plants and animals.</br></br>
-'''What are the benefits of your synthetic organism? Are there alternatives?''' (inspired by all of our interviewees)
+Additionally, should we ever choose to commercialize and release a product, it would be into controlled reactor vessels of oil refineries.  Even though the microorganisms are not directly released into the environment, we would have to go through numerous other agencies in Canada – most notably <a href="http://www.ec.gc.ca/default.asp?lang=en">Environment Canada</a>. It is only after strict screening and investigation that such a product would be allowed to be used commercially outside of laboratories.</br></br>
-The benefits of our organism lie mostly in the relative harmlessness of yeast as compared to bacteria or toxic compounds that might be used against the pine beetle/bluestain fungus epidemic. Yeast is also a very well-studied model eukaryote that is already naturally found in the environment. If successful, this yeast could suppress the epidemic and also wane in population size together with the epidemic. Since it is not too competitive, its impact on the environment is also not lasting and far-reaching should we decide to terminate the program. In terms of alternative solutions to the pine beetle epidemic, there are different approaches such as harvesting or burning large circumferences of trees around infested areas to keep beetles infestations isolated. However, the epidemic is still spreading rapidly throughout the Americas and more solutions are needed to control the spread and preserve pine forests. It is predicted that 67% of all marketable pine trees will be lost by 2015 if we do not find new solutions.
+<div id=break></br></div>
-'''What have you done so far to attain public acceptance?''' (inspired by all of our interviewees)
+<font face=arial narrow size=4><b>4. 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?</b></br></br></font><font face=arial narrow>
-We have been probing '''[https://2011.igem.org/Team:British_Columbia/Perceptions public perception of synthetic biology]''' by asking the UBC community for their definitions of synthetic biology. We have also performed '''[https://2011.igem.org/Team:British_Columbia/Mentorship educational outreach]''' to high school students through the Vancouver Science World. We have also actively been presenting our project to the UBC science community. However, our project is not at a point where we are prepared to engage the general public and encourage a synthetic biology approach to the pine beetle epidemic. Nonetheless, we know that public acceptance has to be earned by open communication of not just the science but also the economic-social-environmental aspects of the project. We foresee that if a feasible product is achieved, there will need to be collaboration with non-science organizations such as the media and environmental and political groups to properly convey an understanding of our scientific approach in the context of a problem that is important to the public.
+Biosafety is a major aspect of our project this year.  We are focusing on two ways to limit safety risks posed by released organisms:</br></br>
+) Distributed pathways -- By taking a single pathway and distributing the necessary pieces among various members of a microbial consortia, the possibility of the entire pathway being transferred to wild organisms drastically decreases.</br> </br>
+) Effective kill switches -- The use of tested and effective kill switch mechanisms will control engineered organisms that are introduced to the environment.  Through the standardized evaluation of kill-switch efficacy, will aid iGEM teams in choosing the best system for their project.  Such an evaluation will be made possible by the protocol that is designed and tested as a result of the collaboration between the 2012 University of Calgary and University of British Columbia teams.</br></br>