Team:Edinburgh/Notebook/Safety

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Safety Issues

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

• research safety,
• public safety,
• environmental safety?

During the planning stages of the project, many ideas were abandoned due to safety issues. For example, the original idea of creating xenomorphs via the use of BioBricks and synthetic biology was discontinued due to the risk associated with these highly aggressive, unpredictable, and uncontrollable species, as documented in the records of the Nostromo, the Weyland-Yutani Corporation Terraforming Colony on LV-426, prison planet Fiorin 161, and the Science Vessel USM Auriga, as well as numerous unsubstantiated sources. The idea of bacterial synthesis of opiates was also abandoned due to a number of potential ethical, legal, and social problems, such as losing the ability to enter the United States of America, further destabilizing the countries of Central Asia and South America, and concerns that the criminal element might attempt to acquire this information through violent means. We also made a conscious decision not to work on biosensors of any form, or any other related applications, such that our project would not require the exposure or release of the engineered organism to people or the environment.

Of our final choice in project, we believe that the pairing of light-producing and light-sensing BioBricks does not raise any known safety issues to research, the public, or the environment. On the other hand, the BRIDGE construct might, since it involves directly editing the bacterial genome. While we see this as an advantage for work in synthetic biology (markerless additions of genes allowing for infinite replacements, more permanent method of inserting genes, no antibiotic resistance in the organism created, etc.), it also means that more care should be taken with the bacteria containing the edited genome (due to the markerless insertion, it could be potentially more difficult to figure out what had been deleted/inserted). The stability of the genome might mean that it would be more difficult to extract an added gene. On the other hand, we don't believe that this will be a major safety issue because any genetic material inserted by BRIDGE can be removed just as easily as plasmids by simply using the recombinase again.

From an engineering and scientific point of view, risk assessment deals with the probability that a certain hazard is going to happen. It is very unlikely that there could be an unplanned event or series of events involving our project that would result in undesired consequences; we have ensured that we are adhering to strict safety codes that mitigate such probability, and we are working with an experienced supervisor and a number of trained advisors to prevent such an occurrence. As stated above, our project does not require that our organism comes into contact with people or the environment.

Even if Sod's Law dictated that the statistical probabilities were against us, it would be unlikely that our device (when working properly) would represent a hazard to people or the environment. The BRIDGE protocol simply adapts an existing natural process to an existing problem in a new area of application, while glowing bacteria are unlikely to be much of a hazard in the wide world (the amount of energy they expend to glow would render them uncompetitive in any case). We are working with non-pathogenic laboratory strains of E. coli, and even after engineering it is not infectious, toxic, or interfering with human physiology or the environment. Our work focuses on intracellular proteins with no significant catalytic role, and thus a malfunction in our BioBrick parts would pose minimal threat to humans, other organisms, or laboratory equipment.

Should the absolute worst happen and our engineered organism is released to the environment, we predict a short spate of glowing trees and a decline in the sales of Christmas lights should the release be timed correctly. Barring the remote possibility that our colour-repressilating bacteria somehow mutate into the deadliest killer virus known to man, causing people to turn red, blue, and green (with different effects depending upon who is nearby) before exploding, we believe that the competitive disadvantage inherent in our bacteria will cause them to die out within a couple of weeks.

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

• did you document these issues in the Registry?
• how did you manage to handle the safety issue?
• How could other teams learn from your experience?

Currently, none of the BioBricks we have made (or are planning to make) raise any specific safety issues. For example, we do not plan to create BioBricks that encode for toxic proteins, and neither do we intend to extend the environmental range of a cell chassis; in fact, by developing a protocol for markerless insertion, we're trying to do the exact opposite (i.e. make engineered bacteria not resistant to antibiotics)!

All BioBricks should be fully documented in the Registry, and any pertinent safety issues are noted should they be seen to exist. On the other hand, the iGEM project timescale is insufficient for current techniques to conduct thorough analysis of BioBrick characteristics such as genetic reliability and performance reliability, and it is often the case that even parts that are fully documented do not perform as they should. Hence, it is important that work outside iGEM continue to make use of and add to the documentation in the Registry for safety concerns.

It is also important to create a centralised forum for discussion on safety issues, such that teams can learn from the experiences of others. This would also allow for the development of software that would integrate safety and security aspects into the design process such that the designer is automatically informed of possible safety problems.

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?

Yes, there is a biosafety committee at the University of Edinburgh. At the beginning of the project, we were required to fill out a risk assessment form for Health and Safety at the University of Edinburgh. We had to provide details about the recipient micro-organism (E. coli), any genetic material we would be adding into the recipient micro-organism, and the vectors we might use, with regards to the bacterial systems, the risks to health and safety for humans, the nature of the work, the associated risk for the environment, their respective classification and containment measures, and the waste disposal procedures and spillage protocol used in our lab. We also had to detail our own qualifications and experience. This form had to be approved by the School of Biological Science's GM Safety Committee before we could begin work. A draft version of the form has been uploaded here for the sake of completeness.

On a wider scale, we are subject to the Health and Safety Executive of the UK government. As part of the 2010 UK iGEM meet-up in Newcastle, we attended a detailed talk from Mr. Brian Cook that outlined the various rules and regulations that we are subject to as well as the future development of further laws that are suited to the growing importance of synthetic biology. From this, we were given a good overview of the biosafety rules and guidelines that we have to consider when working with engineered organisms.

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?

Some ideas that came up regarding how to deal with safety issues are as follows:

• Standardised guidelines for risk assessment and probability / hazard identification. Many informatics and engineering projects incorporate such guidelines that allow them to pre-assess the possibility of risk both before and throughout the project timeline; an accepted global standard for such a purpose may be useful for future iGEM competitions.
• A structured and comprehensive testing regime, coupled with defined standards as to how to characterise a BioBrick part in terms of its safety and a requirement (perhaps not restricted to iGEM, but certainly before the part is made available from the Registry).
• A strict and defined process for the release of engineered organisms into the environment, allowing for the potential commercialisation of iGEM projects. One such effort is being spearheaded by Kim de Mora at the University of Edinburgh, who was a member of the 2006 team that worked on the prize-winning arsenic detection device that also pioneered the field of biosensors within iGEM.
• The BRIDGE protocol, along with the ability to perform markerless insertion and targeted gene deletion, may be used to create a 'safer' host chassis as well as pave the way for releasing non-antibiotic-resistant organisms into the environment.