Team:Newcastle/safety

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Ethics

Safety Issues

These are the safety questions for the judging form:

1. Would any of your project ideas raise safety issues in terms of:

Researcher Safety

We worked in the Centre for Bacterial Cell Biology (CBCB) at Newcastle University for the entire project, where there are clearly defined safety rules and regulations that all laboratory workers must follow. One of our advisors, Dr Wendy Smith, guided us through the safety procedures along with some of the basic techniques during the first introductory week, before any laboratory work on the project began. This included carrying out the following risk assessments to determine what control measures would be required.

(i)Chemical Hazards: At the beginning of the project written risk assessments were already available in the host laboratories for all procedures that involved potentially hazardous chemicals. These risk assessments were reviewed and the recommended control measures were strictly followed throughout. No additional chemical hazards specific to this project were identified.

(ii)Radioisotopes and carcinogens: None of these were used in this project.

(iii)Biological hazards: Throughout the project, we used the Escherichia coli strain DH5α, Bacillus subtilis strain 3610, Bacillus subtilis strain 168 and Bacillus sphaericus strain LMG 22257. Wild-type E. coli is classified as a hazard group 2 pathogen by the UK Advisory Committee on the Dangerous Pathogens (ACDP). However, E. coli strain DH5α is derived from a laboratory strain E. coli K12, which is recognised as disabled and equivalent to an ACDP hazard group 1 organism (i.e. unlikely to cause disease). E. coli K12 and its derivatives such as strain DH5α are unable to colonise in humans or animals and consequently pose negligible risk to human or animal health. Wild-type Bacillus subtilis (i.e. strain 3610) is classified as an ACDP hazard group 1 organism and its derivative B. subtilis strain 168 has disabling auxotrophs mutations (e.g. conferring a requirement for tryptophan, Zeigler et al, 2008) that makes it even less likely to colonise or cause harm to human or animal health. Also Bacillus sphaericus LMG 22257 is classified as an ADCP hazard group 1 organism making it unlikely to cause any harm to either human or animal health. The potential of any sequences cloned into these bacterial hosts during the project to pose additional hazards was also assessed. None of these sequences were associated with pathogenic traits or traits that might significantly enhance the survival outside the lab. Therefore, no specific safety issues, other than those associated with use of any non-pathogenic microorganism, were identified. It was concluded that containment level 1(CL1) would be sufficient to ensure researcher safety. Nonetheless, all work was carried out in strict compliance with the host laboratory's standard safety procedures, which were more stringent that those required for CL1.

(iv)Other hazards: The project also involved conducting some work in the Engineering structures laboratory, where we made and broke concrete 'blocks'. Appropriate safety regulations for the type of work in this laboratory were followed. When we were in the structures lab, we wore safety goggles, steel toe cap boots and gloves.

Public Safety

Our project concerns repairing cracks on concrete surfaces by spraying these surfaces with spores of engineered derivatives of Bacillus subtilis 168. Before releasing engineered bacteria into the environment, considerable further research and testing would be necessary. However, if the project was deemed safe, workers carrying out the spraying should wear an appropriate face mask to minimize inhaling of spores. During the spraying procedure there is a risk that spores could escape into the surrounding environment. As outlined above, B. subtilis 168 is non-pathogenic and therefore very unlikely to pose a risk to public safety, particularly since any escaping spores would be unable to germinate in the absence of culture media.

Environmental Safety

For reasons outlined above, the E. coli strain DH5α has very limited ability to survive outside the laboratory so taht in the event of escape, it would be unable to survive, disseminate, or displace other organisms. Therefore no specific environmental hazards associated with the E. coli strain were identified.

Bacillus subtilis strain 3610 and Bacillus sphaericus strain LMG22257 are both equivalent to wild type strains that are already widespread in the environment. They have not been modified to enhance their ability to survive, disseminate or displace other organisms. Therefore no specific environmental hazards associated with the Bacillus subtilis strain 3610 or Bacillus sphaericus strain LMG22257 were identified.

GM derivatives of Bacillus subtilis strain 168 will be released deliberately. This is a strain that has been maintained in the lab for 52 years, during which it has accumulated disabling mutations, such as the tryptophan auxotrophy mentioned above, which greatly diminishes its ability to survive and disseminate outside the laboratory (Zeigler et al., 2008). It is very unlikely that it could compete effectively and replace wild-type B. subtilis. Nonetheless, the release of any GMO into the environment has been a concern since early days of genetic engineering and one of our instructors (Prof. Anil Wipat) has previously studied such issues (Wipat, 1990). To minimise concerns about environmental safety, in this project we designed the Non-target-environment kill switch genetic part to prevent dissemination after release into the environment.

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

We do not see any safety issues for the new Biobricks parts that we made this year.

3. Is there a local biosafety group, committee, or review board at your institution?

Yes there is a biosafety group at the Centre for Bacterial Cell Biology and Institute of Cell and Molecular Biosciences, which includes the Institute Safety Officer (SSO), Biological Safety Supervisor (BSS), Genetic Modification Chairperson (GMC), Radiation Protection Supervisor (RPS), Laser Protection Officer and Lab Heads. They have reviewed the safety of the lab regularly during the duration of the project.

If yes, what does your local biosafety group think about your project?

They are aware of the project and have reviewed it thoroughly with the team. They discussed about each Biobrick part in detail and found no safety issues with any of them.

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?

A full risk assessment should be carried out before the work begins. This should consider: (i) Consequences of any identifiable hazard and (ii) The likelihood of the hazard arising. The risk can then be defined and appropriate control measures can be introduced to minimise the risk.

The inclusion of a safety kill switch, such as that detailed in our project, could help reduce the risk of accidental release. In addition, strains should be marked with unique barcodes to allow them to be tracked, should they accidently escape.

Ethics

Synthetic Biology: Background

Synthetic biology is a new research field that has a big potential in coming up with solutions for our everyday problems. However, ethical issues have been raised since the start of development in this field. Here we will discuss the ethical issues that our project will bring.

Biohackers

In this field, there are always people that view synthetic biology's negative aspects with concern, like worrying about the production of pathogens to be used as weapons. Their fears are that people will hack into systems to obtain data that might be used to do this. Therefore, we have to be very careful with the products of our research so that they remain safe in our hands.

Playing God!!!

In synthetic biology, we control the lives of bacteria. We insert proteins into bacteria to make them do what we want them to do. We make them kill themselves at the end of their job because they might be released into the environment and be harmful to other living things. It shows that we do not really treat the single-celled organism as life. However, we are coming up with a novel solution for the environment by healing concrete cracks.

Biosecurity

Bacteria might be harmful to the environment and living things around. Considering the fact that they are such small organisms and could not be spotted with the naked-eye if they are released in air, we make them kill themselves with the ‘kill switch’ biobrick. This can be very inconsiderate standing in a bacteria’s point of view, but it is the novel thing to do to avoid them hurting other living organisms.

Construction: Background

Cracks form in concrete structures as soon as they set. These cracks continue to grow in size if they are not repaired due to the weight of the structure, imposed load, freeze-thaw effect and wind loading. The bigger the cracks are, the higher the rate of water seeping into the steel reinforcements, causing them to corrode and thus weakening the structure. Therefore, we would like to use Bacilla Filla to fill up these cracks before things get worse.

Environmental Disaster

Concrete is a very widely used material in construction. In fact, cement that is used to make concrete is the second most widely used substance in the world after water. Some building structures have to be demolished because the cracks formed appear to be threatening the strength of the structures. These buildings have to be rebuilt in order to reinforce its tensile strength. This is an unsustainable method of recovery because cement is a material that requires a lot of energy to be produced. In the production of cement, the rotating kiln requires the temperature to be between 1350°C-1400°C, which not only uses up a lot of energy resources, but also produces a lot of carbon dioxide. These carbon dioxide contributes to the green house effect which then leads to global warming. Therefore, our project can help to reduce renovation of buildings which in turn lowers the amount of cement that has to be produced each year.

Post-Chernobyl Disaster

The nuclear power plant combustion that occurred in Chernobyl on 26 April 1986 has allowed radioactive elements to be released into the environment, threatening the health of people living within close proximity of the plant. Therefore, a shelter, the Shelter Implementation Plan (SIP) which will be completed in 2012 is currently being built to cover up the area that where the accident occurred so as to make it environmentally friendly. However, if cracks were to form, something that inevitably occurs for building structures, those radioactive elements will still be dispersed into the environment. With the help of our project, those cracks will be able to be filled-up and the area will be safe again.

[1] Wipat, A. (1990). "Release and detection of geneticaly engineered streptomycetes in soil". PhD thesis, Microbiology Department, John Moores University.

[2] Zeigler DR, Prágai Z, Rodriguez S, Chevreux B, Muffler A, Albert T et al. (2008). "The origins of 168, W23, and other Bacillus subtilis legacy strains". Journal of Bacteriology, 190(21), 6983-95.

@@ Line 7: / Line 7: @@
 '''1. Would any of your project ideas raise safety issues in terms of:'''
-*Researcher Safety:
+=====Researcher Safety=====
-We worked in the Centre for Bacterial Cell Biology (CBCB) at Newcastle University for the entire project, where there are clearly defined Class II microbiology safety rules and regulations (UK).  One of our advisors, Dr Wendy Smith, guided us through the first [[Team:Newcastle/14_June_2010|introductory]] week, before any laboratory work began. This included carrying out the following risk assessments to determine what control measures would be required.
+We worked in the Centre for Bacterial Cell Biology (CBCB) at Newcastle University for the entire project, where there are clearly defined safety rules and regulations that all laboratory workers must follow.  One of our advisors, Dr Wendy Smith, guided us through the safety procedures along with some of the basic techniques during the first [[Team:Newcastle/14_June_2010|introductory]] week, before any laboratory work on the project began. This included carrying out the following risk assessments to determine what control measures would be required.
-(i)Chemical Hazards:
+(i)'''Chemical Hazards''':
 At the beginning of the project written risk assessments were already available in the host laboratories for all procedures that involved potentially hazardous chemicals. These risk assessments were reviewed and the recommended control measures were strictly followed throughout. No additional chemical hazards specific to this project were identified.
-(ii)Radioisotopes and carcinogens:
+(ii)'''Radioisotopes and carcinogens''':
+None of these were used in this project.
-None of them were used in this project.
+(iii)'''Biological hazards''':
+Throughout the project, we used the ''Escherichia coli'' strain DH5α, ''Bacillus subtilis'' strain 3610, ''Bacillus subtilis'' strain 168 and ''Bacillus sphaericus'' strain LMG 22257. Wild-type ''E. coli'' is classified as a hazard group 2 pathogen by the UK Advisory Committee on the Dangerous Pathogens (ACDP). However, ''E. coli'' strain DH5α is derived from a laboratory strain ''E. coli'' K12, which is recognised as disabled and equivalent to an ACDP hazard group 1 organism (i.e. unlikely to cause disease). ''E. coli'' K12 and its derivatives such as strain DH5α are unable to colonise in humans or animals and consequently pose negligible risk to human or animal health. Wild-type ''Bacillus subtilis'' (i.e. strain 3610) is classified as an ACDP hazard group 1 organism and its derivative ''B. subtilis'' strain 168 has disabling auxotrophs mutations (e.g. conferring a requirement for tryptophan, Zeigler ''et al'', 2008) that makes it even less likely to colonise or cause harm to human or animal health. Also ''Bacillus sphaericus'' LMG 22257 is classified as an ADCP hazard group 1 organism making it unlikely to cause any harm to either human or animal health. The potential of any sequences cloned into these bacterial hosts during the project to pose additional hazards was also assessed. None of these sequences were associated with pathogenic traits or traits that might significantly enhance the survival outside the lab. Therefore, no specific safety issues, other than those associated with use of any non-pathogenic microorganism, were identified. It was concluded that containment level 1(CL1) would be sufficient to ensure researcher safety. Nonetheless, all work was carried out in strict compliance with the host laboratory's standard safety procedures, which were more stringent that those required for CL1.
-(iii)Biological hazards:
+(iv)'''Other hazards''':
+The project also involved conducting some work in the Engineering structures laboratory, where we made and broke concrete 'blocks'. Appropriate safety regulations for the type of work in this laboratory were followed. When we were in the structures lab, we wore safety goggles, steel toe cap boots and gloves.
-Throughout the project, we used the ''Escherichia coli'' strain DH5α and the ''Bacillus subtilis'' strain 168. Wild-type ''E. coli'' is classified as a hazard group 2 pathogen by the UK Advisory Committee on the Dangerous Pathogens (ACDP).
+=====Public Safety=====
+Our project concerns repairing cracks on concrete surfaces by spraying these surfaces with spores of engineered derivatives of ''Bacillus subtilis'' 168. Before releasing engineered bacteria into the environment, considerable further research and testing would be necessary. However, if the project was deemed safe, workers carrying out the spraying should wear an appropriate face mask to minimize inhaling of spores. During the spraying procedure there is a risk that spores could escape into the surrounding environment. As outlined above, ''B. subtilis'' 168 is non-pathogenic and therefore very unlikely to pose a risk to public safety, particularly since any escaping spores would be unable to germinate in the absence of culture media.
-We also got to make and break concrete in the structures lab, which requires appropriate safety regulations to be obeyed. When we were in the structures lab, we wore safety goggles, steel toe cap boots and gloves, which will be able to protect us from lab based accidents.
+=====Environmental Safety=====
+For reasons outlined above, the ''E. coli'' strain DH5α has very limited ability to survive outside the laboratory so taht in the event of escape, it would be unable to survive, disseminate, or displace other organisms. Therefore no specific environmental hazards associated with the ''E. coli'' strain were identified.
-* Public Safety:
+''Bacillus subtilis'' strain 3610 and ''Bacillus sphaericus'' strain LMG22257  are both equivalent to wild type strains that are already widespread in the environment. They have not been modified to enhance their ability to survive, disseminate or displace other organisms. Therefore no specific environmental hazards associated with the ''Bacillus subtilis'' strain 3610 or ''Bacillus sphaericus'' strain LMG22257 were identified.
-Our project is about repairing cracks formed on the concrete surface with ''Bacillus subtilis'' 168. It is a lab strain and is non-pathogenic. Before spraying onto the concrete surface, there is a chance of them escaping into the environment. Spores in the absence of media won't be able to germinate and spread in the wild. At the same time, to prevent humans from inhaling the spores, it is advisable that while spraying the spores onto the concrete surface by a sprayer, the personnel should wear a face mask. Also if the spores are ingested by humans by mistake, then they will be able to pass through the alimentary canal without causing any reaction in the body.
-* Environmental Safety:
+GM derivatives of ''Bacillus subtilis'' strain 168 will be released deliberately. This is a strain that has been maintained in the lab for 52 years, during which it has accumulated disabling mutations, such as the tryptophan auxotrophy mentioned above, which greatly diminishes its ability to survive and disseminate outside the laboratory (Zeigler ''et al.'', 2008). It is very unlikely that it could compete effectively and replace wild-type ''B. subtilis''. Nonetheless, the release of any GMO into the environment has been a concern since early days of genetic engineering and one of our instructors (Prof. Anil Wipat) has previously studied such issues (Wipat, 1990). To minimise concerns about environmental safety, in this project we designed the [[Team:Newcastle/Non-target-environment kill switch|Non-target-environment kill switch]] genetic part to prevent dissemination after release into the environment.
-The ''Bacillus subtilis'' 168 that we chose to use for this project has been a lab strain for 52 years therefore it has lost some of the genes which are important for them to survive in the wild like synthesizing tryptophan (auxotroph), an essential amino acid which due to reductive evolution, has lost the ability to produce it, thus it requires a medium containing tryptophan for its growth and survival (Zeigler ''et al.'', 2008). Although they are non-pathogenic, releasing genetically engineered bacteria into the environment has been an issue since the 1970s. There are numerous reviews which discuss the issues relating to the safety of introducing genetically engineered organisms into systems such as soil. One of our intructors (Prof. Anil Wipat) studied issues relating to the release of genetically engineered microorganisms into the soil as part of his PhD (Wipat A., 1990). Many systems have been proposed to try to ensure the safety of GM organisms in the environment. For example, we designed the [[Team:Newcastle/Non-target-environment_kill_switch|kill switch]] genetic part which will allow the bacteria to kill themselves after sensing the environment around them. Therefore even if it escapes away from the lab, it will not be able to survive in the wild.
 '''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?'''
@@ Line 37: / Line 39: @@
 '''3. Is there a local biosafety group, committee, or review board at your institution?'''
-Yes there is a biosafety group at the Centre for Bacterial Cell Biology and Institute of Cell and Molecular Biosciences, which includes the Institute Safety Officer (SSO), Biological Safety Supervisor (BSS), Genetic Modification Chairperson (GMC), Radiation Protection Supervisor (RPS), Laser Protection Officer and Lab Heads. They have reviewed the safety of the lab from time to time during the duration of the project.
+Yes there is a biosafety group at the Centre for Bacterial Cell Biology and Institute of Cell and Molecular Biosciences, which includes the Institute Safety Officer (SSO), Biological Safety Supervisor (BSS), Genetic Modification Chairperson (GMC), Radiation Protection Supervisor (RPS), Laser Protection Officer and Lab Heads. They have reviewed the safety of the lab regularly during the duration of the project.
 * If yes, what does your local biosafety group think about your project?
-They are aware about the whole project and they reviewed it thoroughly with the whole team. They discussed about each and every Biobrick part in detail and found no safety issues with it.
+They are aware of the project and have reviewed it thoroughly with the team. They discussed about each Biobrick part in detail and found no safety issues with any of them.
 '''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?'''
+A full risk assessment should be carried out before the work begins. This should consider:
+(i) Consequences of any identifiable hazard and
+(ii) The likelihood of the hazard arising.
+The risk can then be defined and appropriate control measures can be introduced to minimise the risk.
+The inclusion of a safety kill switch, such as that detailed in our project, could help reduce the risk of accidental release. In addition, strains should be marked with unique barcodes to allow them to be tracked, should they accidently escape.
+==Ethics==
+===Synthetic Biology: Background===
+Synthetic biology is a new research field that has a big potential in coming up with solutions for our everyday problems. However, ethical issues have been raised since the start of development in this field. Here we will discuss the ethical issues that our project will bring.
+====Biohackers====
+In this field, there are always people that view synthetic biology's negative aspects with concern, like worrying about the production of pathogens to be used as weapons. Their fears are that people will hack into systems to obtain data that might be used to do this. Therefore, we have to be very careful with the products of our research so that they remain safe in our hands.
+====Playing God!!!====
+In synthetic biology, we control the lives of bacteria. We insert proteins into bacteria to make them do what we want them to do. We make them kill themselves at the end of their job because they might be released into the environment and be harmful to other living things. It shows that we do not really treat the single-celled organism as life. However, we are coming up with a novel solution for the environment by healing concrete cracks.
+====Biosecurity====
+Bacteria might be harmful to the environment and living things around. Considering the fact that they are such small organisms and could not be spotted with the naked-eye if they are released in air, we make them kill themselves with the ‘kill switch’ biobrick. This can be very inconsiderate standing in a bacteria’s point of view, but it is the novel thing to do to avoid them hurting other living organisms.
+===Construction: Background===
+Cracks form in concrete structures as soon as they set. These cracks continue to grow in size if they are not repaired due to the weight of the structure, imposed load, freeze-thaw effect and wind loading. The bigger the cracks are, the higher the rate of water seeping into the steel reinforcements, causing them to corrode and thus weakening the structure. Therefore, we would like to use Bacilla Filla to fill up these cracks before things get worse.
+====Environmental Disaster====
+Concrete is a very widely used material in construction. In fact, cement that is used to make concrete is the second most widely used substance in the world after water. Some building structures have to be demolished because the cracks formed appear to be threatening the strength of the structures. These buildings have to be rebuilt in order to reinforce its tensile strength. This is an unsustainable method of recovery because cement is a material that requires a lot of energy to be produced. In the production of cement, the rotating kiln requires the temperature to be between 1350°C-1400°C, which not only uses up a lot of energy resources, but also produces a lot of carbon dioxide. These carbon dioxide contributes to the green house effect which then leads to global warming. Therefore, our project can help to reduce renovation of buildings which in turn lowers the amount of cement that has to be produced each year.
+====Post-Chernobyl Disaster====
+The nuclear power plant combustion that occurred in Chernobyl on 26 April 1986 has allowed radioactive elements to be released into the environment, threatening the health of people living within close proximity of the plant. Therefore, a shelter, the Shelter Implementation Plan (SIP) which will be completed in 2012 is currently being built to cover up the area that where the accident occurred so as to make it environmentally friendly. However, if cracks were to form, something that inevitably occurs for building structures, those radioactive elements will still be dispersed into the environment. With the help of our project, those cracks will be able to be filled-up and the area will be safe again.
+[1] Wipat, A. (1990). "''Release and detection of geneticaly engineered streptomycetes in soil''". PhD thesis, Microbiology Department, John Moores University.
+[2] Zeigler DR, Prágai Z, Rodriguez S, Chevreux B, Muffler A, Albert T et al. (2008). "''The origins of 168, W23, and other Bacillus subtilis legacy strains''". Journal of Bacteriology, 190(21), 6983-95.
-[1] Zeigler DR, Prágai Z, Rodriguez S, Chevreux B, Muffler A, Albert T et al. (2008). "''The origins of 168, W23, and other Bacillus subtilis legacy strains''". Journal of bacteriology, 190(21), 6983-95.
-[2] Wipat, A. (1990). "''Release and detection of geneticaly engineered streptomycetes in soil''". Unpublished PhD thesis, Microbiology Department, John Moores University.
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