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Team:Amsterdam/Project/Safety
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| - | Safety is of primary concern in every profession, including professions in research. Because the iGEM contest inevitably involves genetically modified organisms (GMOs), working safely is of utmost importance to its participants and their environments. The Amsterdam team has | + | Safety is of primary concern in every profession, including professions in research. Because the iGEM contest inevitably involves genetically modified organisms (GMOs), working safely is of utmost importance to its participants and their environments. The Amsterdam team has analysed the threats to safety involved with, and putatively caused by, their work. We conclude that, while caution and proper lab procedure should of course be maintained, the safety of the public, the environment, our colleagues and ourselves should be in no significant danger during or following work on the project. |
==Researcher safety== | ==Researcher safety== | ||
While the labs in which we work are generally full of chemicals, they are stored securely and at all times are treated with appropriate (pre)caution, as per ML-I regulations. Gloves, labcoats, masks and safety glasses are used to protect against harmful chemicals, and material safety datasheets are available within the lab in printed and digital form. | While the labs in which we work are generally full of chemicals, they are stored securely and at all times are treated with appropriate (pre)caution, as per ML-I regulations. Gloves, labcoats, masks and safety glasses are used to protect against harmful chemicals, and material safety datasheets are available within the lab in printed and digital form. | ||
| - | + | The strain of ''E. coli'' used in our experiments (DH5α) is not pathogenic, and the CryoBricks we develop don't encode substances that are known or suspected to be toxic, or involved with virulence or infection. Because of this, we deemed standard lab safety regulations sufficient for work on the project, and no additional considerations were taken into account. Note that while plans are being made to characterize the effect of our CryoBricks in bacterial species other than ''E. coli'', these organisms will also be selected for non-pathogenicity. | |
| - | + | ||
==Environmental safety== | ==Environmental safety== | ||
| - | Efforts are made to restrain the GMOs we work with to a controlled lab environment. All waste is handled in accordance with general safety regulations. Chemicals are treated as specified by their supplier | + | Efforts are made to restrain the GMOs we work with to a controlled lab environment. All waste is handled in accordance with general safety regulations. Chemicals are treated as specified by their supplier. Organic waste is disposed via biohazard containers, and where appropriate even autoclaved and/or treated with bleach beforehand. The windows are kept closed, and hands are washed upon entering and leaving the lab. |
| + | |||
| + | If all these precautions are still insufficient to prevent GMOs from leaving the lab uncontrolled - for example, when they're accidentally flushed down the drain - they will find themselves in an environment to which they're not adapted to survive. While the cold resistance genes we equip our bacteria with may relieve the stress caused to the cells by no longer being in a comfortable 37°C stove, this is only one of many problems ''E. coli'' will face outside of the lab. We expect nutrient availability to be a strongly limiting factor to its putative growth outside the academic environment, which is further exacerbated by other, presumably better adapted species' fierce competition over these resources. | ||
| + | |||
| + | ==Public safety== | ||
| + | As explained above, undesirable exposure to the bacteria is unlikely because 1) they're treated with care and restrained to the lab environment and 2) they aren't likely to thrive in more publics environments. Even if such exposure occurs, a non-pathogenic strain of ''E. coli'' is used in our experiments. It forms no threat to people exposed in its vicinity. | ||
==Biosafety at the UvA== | ==Biosafety at the UvA== | ||
One of our chief advisors, Dr. Pernette J. Verschure, is tasked with supervising responsible handling of GMOs, with respect to biosafety, at the Nuclear Organization Group (NOG) of the Swammerdam Institute for Life Sciences (SILS). Among others, she takes care of the NOG's GMO database, and official registration of GMOs (i.e. GGO 01-045, 01-052 and 02-241). Dr. Verschure is closely involved with the project, attends all our meetings, and keeps an eye out to ensure we maintain a safe working attitude. | One of our chief advisors, Dr. Pernette J. Verschure, is tasked with supervising responsible handling of GMOs, with respect to biosafety, at the Nuclear Organization Group (NOG) of the Swammerdam Institute for Life Sciences (SILS). Among others, she takes care of the NOG's GMO database, and official registration of GMOs (i.e. GGO 01-045, 01-052 and 02-241). Dr. Verschure is closely involved with the project, attends all our meetings, and keeps an eye out to ensure we maintain a safe working attitude. | ||
| + | |||
| + | Because of the team members' previous experience with labwork, all of them being 1st year MSc students with at least a degree of practical background, no special training or workshops were arranged to familiarize us with safety or labwork. Two tours of the lab, one two weeks prior to and one on the first day of labwork, clarified what type of waste went where and how it was to be treated. The close involvement of our instructors further saw to it that we worked safely and securely. | ||
==But what if...== | ==But what if...== | ||
| - | In the unlikely scenario the precautions described above are insufficient to prevent GMOs from leaving the lab uncontrolled, a safety hazard exists mainly in the shape of horizontal gene transfer. ''E. coli'' is adapted to survival in the intestines of endotherms, where increased cold tolerance is not very beneficial. However, it is not unthinkable that an ''E. coli'' comprising CryoBricks can transfer these bricks to other bacteria via conjugation. This | + | In the unlikely scenario the precautions described above are insufficient to prevent GMOs from leaving the lab uncontrolled, a safety hazard exists mainly in the shape of horizontal gene transfer. ''E. coli'' is adapted to survival in the intestines of endotherms, where increased cold tolerance is not very beneficial. However, it is not unthinkable that an ''E. coli'' comprising CryoBricks can transfer these bricks to other bacteria via conjugation. This can theoretically grant the recipient an increased cold resistance. |
| + | |||
| + | Uncontrolled spreading of CryoBricks may enhance a bacterium's ability to survive in various environments, which can have widespread consequences. For example, a bacterium that can't normally grow in a common household refrigerator might gain this ability by picking up a CryoBrick. This may lead to a "fridge infection", but can easily be prevented by keeping the refrigerator clean, and properly wrapping or packaging food. An increased risk of fridge infections is but one of many consequences spreading of CryoBricks may have. Speculations about the precise extent of these consequences are difficult, but we expect no substantial threats to human or animal well-being, or the state of the natural environment. | ||
| - | Note that in order to reduce the environmental impact of a putative CryoBrick-equipped ''E. coli'' outbreak, | + | Note that in order to reduce the environmental impact of a putative CryoBrick-equipped ''E. coli'' outbreak, some of our bricks are placed under control of an "on" switch. In particular, the CryoBricks comprising a (derivative of the) pBAD promoter will only be transcribed in presence of the sugar arabinose. This sugar is a viable carbon source for many different bacteria, and will be rapidly consumed in absence of a more preferred carbon source such as glucose. In a lab environment, glucose concentrations can be kept artifically high. Because glucose is a more preferred carbon source, this results in catabolite repression and preventing the consumption of arabinose, keeping the switch "on". In natural environments, catabolite repression is more of a dynamic process and arabinose is likely to suffer quick degradataion, returning the CryoBrick to its default "off" state. We feel such a simple 'safety catch' should be considered in any experiment involving GMOs, and suggest that each iGEM team discusses similar safety guidelines and considerations on their wiki. We hope that, by showing our attitude towards safety on this website, fellow researchers (including other iGEM teams) will share our sense of responsibility, and that any concerns of the public community regarding Synthetic Biology may be alleviated. |
{{:Team:Amsterdam/Footer}} | {{:Team:Amsterdam/Footer}} | ||
Revision as of 09:54, 30 August 2011
Safety is of primary concern in every profession, including professions in research. Because the iGEM contest inevitably involves genetically modified organisms (GMOs), working safely is of utmost importance to its participants and their environments. The Amsterdam team has analysed the threats to safety involved with, and putatively caused by, their work. We conclude that, while caution and proper lab procedure should of course be maintained, the safety of the public, the environment, our colleagues and ourselves should be in no significant danger during or following work on the project.
Researcher safety
While the labs in which we work are generally full of chemicals, they are stored securely and at all times are treated with appropriate (pre)caution, as per ML-I regulations. Gloves, labcoats, masks and safety glasses are used to protect against harmful chemicals, and material safety datasheets are available within the lab in printed and digital form.
The strain of E. coli used in our experiments (DH5α) is not pathogenic, and the CryoBricks we develop don't encode substances that are known or suspected to be toxic, or involved with virulence or infection. Because of this, we deemed standard lab safety regulations sufficient for work on the project, and no additional considerations were taken into account. Note that while plans are being made to characterize the effect of our CryoBricks in bacterial species other than E. coli, these organisms will also be selected for non-pathogenicity.
Environmental safety
Efforts are made to restrain the GMOs we work with to a controlled lab environment. All waste is handled in accordance with general safety regulations. Chemicals are treated as specified by their supplier. Organic waste is disposed via biohazard containers, and where appropriate even autoclaved and/or treated with bleach beforehand. The windows are kept closed, and hands are washed upon entering and leaving the lab.
If all these precautions are still insufficient to prevent GMOs from leaving the lab uncontrolled - for example, when they're accidentally flushed down the drain - they will find themselves in an environment to which they're not adapted to survive. While the cold resistance genes we equip our bacteria with may relieve the stress caused to the cells by no longer being in a comfortable 37°C stove, this is only one of many problems E. coli will face outside of the lab. We expect nutrient availability to be a strongly limiting factor to its putative growth outside the academic environment, which is further exacerbated by other, presumably better adapted species' fierce competition over these resources.
Public safety
As explained above, undesirable exposure to the bacteria is unlikely because 1) they're treated with care and restrained to the lab environment and 2) they aren't likely to thrive in more publics environments. Even if such exposure occurs, a non-pathogenic strain of E. coli is used in our experiments. It forms no threat to people exposed in its vicinity.
Biosafety at the UvA
One of our chief advisors, Dr. Pernette J. Verschure, is tasked with supervising responsible handling of GMOs, with respect to biosafety, at the Nuclear Organization Group (NOG) of the Swammerdam Institute for Life Sciences (SILS). Among others, she takes care of the NOG's GMO database, and official registration of GMOs (i.e. GGO 01-045, 01-052 and 02-241). Dr. Verschure is closely involved with the project, attends all our meetings, and keeps an eye out to ensure we maintain a safe working attitude.
Because of the team members' previous experience with labwork, all of them being 1st year MSc students with at least a degree of practical background, no special training or workshops were arranged to familiarize us with safety or labwork. Two tours of the lab, one two weeks prior to and one on the first day of labwork, clarified what type of waste went where and how it was to be treated. The close involvement of our instructors further saw to it that we worked safely and securely.
But what if...
In the unlikely scenario the precautions described above are insufficient to prevent GMOs from leaving the lab uncontrolled, a safety hazard exists mainly in the shape of horizontal gene transfer. E. coli is adapted to survival in the intestines of endotherms, where increased cold tolerance is not very beneficial. However, it is not unthinkable that an E. coli comprising CryoBricks can transfer these bricks to other bacteria via conjugation. This can theoretically grant the recipient an increased cold resistance.
Uncontrolled spreading of CryoBricks may enhance a bacterium's ability to survive in various environments, which can have widespread consequences. For example, a bacterium that can't normally grow in a common household refrigerator might gain this ability by picking up a CryoBrick. This may lead to a "fridge infection", but can easily be prevented by keeping the refrigerator clean, and properly wrapping or packaging food. An increased risk of fridge infections is but one of many consequences spreading of CryoBricks may have. Speculations about the precise extent of these consequences are difficult, but we expect no substantial threats to human or animal well-being, or the state of the natural environment.
Note that in order to reduce the environmental impact of a putative CryoBrick-equipped E. coli outbreak, some of our bricks are placed under control of an "on" switch. In particular, the CryoBricks comprising a (derivative of the) pBAD promoter will only be transcribed in presence of the sugar arabinose. This sugar is a viable carbon source for many different bacteria, and will be rapidly consumed in absence of a more preferred carbon source such as glucose. In a lab environment, glucose concentrations can be kept artifically high. Because glucose is a more preferred carbon source, this results in catabolite repression and preventing the consumption of arabinose, keeping the switch "on". In natural environments, catabolite repression is more of a dynamic process and arabinose is likely to suffer quick degradataion, returning the CryoBrick to its default "off" state. We feel such a simple 'safety catch' should be considered in any experiment involving GMOs, and suggest that each iGEM team discusses similar safety guidelines and considerations on their wiki. We hope that, by showing our attitude towards safety on this website, fellow researchers (including other iGEM teams) will share our sense of responsibility, and that any concerns of the public community regarding Synthetic Biology may be alleviated.
