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Revision as of 16:59, 1 September 2011

Safety

1. Would the materials used in your project and/or your final product pose:
a. Risks to the safety and health of team members or others in the lab?
No, we are not using any materials that pose risk to anyone’s safety or health. We are only working with level 1 safety organisms and are not working with any toxic or otherwise dangerous materials. The organisms we are working with are Escherichia coli K12 strains BL21 DE3, DH10B and 5alpha. In addition, we are using Bacillus subtilis ____ and Arabidopsis thaliana Columbia wt, DR5:GFP and DR:3VENUS strains. The products that will be produced by our bacteria are also not dangerous to humans.

b. Risks to the safety and health of the general public if released by design or accident?
No, our final product is an engineered E. coli producing auxin and expressing a plant exudate-responsive chemoreceptor. We have used harmless E. coli K12 strains, B. subtilis strains and A. thaliana which would not pose any threat to the public if released.

c. Risks to environmental quality if released by design or accident?
No, from consulting Dr Alexandru Milcu, an ecologist, and experts from Syngenta, we have confirmed that secretion of natural indole-3-acetic acid into soil would not pose any large-scale threat to its biodiversity. However, as there is always a given level of uncertainty when dealing with biological systems, we have also designed a plasmid containment device that stops horizontal transfer to bacteria in the environment.

d. Risks to security through malicious misuse by individuals, groups or states?
No. The parts we are engineering are not in themselves dangerous. However, it would be conceivable that, if combined with other parts and components, it would be possible to construct a dangerous organism. Nevertheless, this can be said of any synthetic biology part.

Please explain your responses (whether yes or no) to these questions.

Specifically, are any parts or devices in your project associated with (or known to cause):
- pathogenicity, infectivity, or toxicity?
Yes. The auxin producing pathway occurs naturally in soil bacteria that are plant pathogens. However, these bacteria use the auxin pathway in combination with virulence factors that are not present in our bacteria. The pathway is also used by plant symbionts and is not inherently dangerous and should not promote pathogenicity to the plants. The chemotaxis receptor we are engineering into our bacteria naturally occurs in Pseudomonas aeruginosa, a pathogen of various organisms including humans and plants. However, the receptor is not in itself dangerous. On the other hand, Holin is a bactericidial protein that works in conjunction endolysin. However, it will only be active in bacteria that actively take up the plasmid.

- threats to environmental quality?
No. Auxin secretion may favour some plants over others and this may skew the population in affected area. We are targeting areas that already have degraded soil and reduced biodiversity. We are hoping that the application of auxin will eventually increase biodiversity. The auxin should therefore not negatively influence the environment.

- security concerns?
No. There should not be any security concerns for any of the parts we are engineering. None of the parts should be damaging or a threat to security.

2. If your response to any of the questions above is yes:
a. Explain how you addressed these issues in project design and while conducting laboratory work.
We have addressed the issues by making doing various experiments on Arabidopsis thaliana and earthworms to see the effects of different auxin concentrations. This will inform our design by telling us how much auxin our bacteria should be able to produce with the help of modelling. Furthermore, to avoid horizontal gene transfer, we have come up with a design for a containment module. This module will make it so that if the auxin genes are ever transferred to any bacteria other than our own they will also be transferred with a holin and endolysin gene. These genes will lyse any cells that have obtained our plasmid.

b. Describe and document safety, security, health and/or environmental issues as you submit your parts to the Registry.

3. Under what biosafety provisions will / do you operate?
a. Does your institution have its own biosafety rules and if so what are they? Provide a link to them online if possible.
Imperial College does have its own biosafety rules. These rules limit the use of infective and GM modified organisms to certified laboratories and state the requirement to get approval for work with them and the requirement to dispose of the organisms appropriately and report any accidental release and accidents to the Health and Safety department. The policy can be found at http://www3.imperial.ac.uk/safety/policies/individualpolicies/pc-11dangerouspathogens. Another, more comprehensive outline of how to deal with specific biological agents can be found at http://www3.imperial.ac.uk/safety/subjects/biosafety.

b. Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them? Describe any concerns or changes that were made based on this review.
Yes, there is a biosafety committee at our institution and we have discussed our project with them. Following their advice, we used plastic rather than glass tubes for our worm experiment and prepared E coli solutions for plant root experiments in the labs we are using rather than in the plant room to prevent exposure of other plants to our E coli.

c. Will / did you receive any biosafety and/or lab training before beginning your project? If so, describe this training.
Before we were allowed into the lab we received a lab induction from our advisor (James Field) as well as the lab technicians. In this induction we were shown the proper ways of waste disposal and were also shown where the fume hoods are and the proper ways for handling GMO's. We were also given an induction for the plant lab and were told how to handle GM plants as well. We were also told where the emergency exits are and the proper assembly point in case of a fire.

d. Does your country have national biosafety regulations or guidelines? If so, provide a link to them online if possible.
There are national biosafety regulations in Britain. The full list can be found at http://www.hse.gov.uk/biosafety/biologagents.pdf

4. OPTIONAL QUESTION: Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?
We have designed a novel containment switch: the BacTrap. This device is able to kill non-engineered bacteria that take up the genetically engineered plasmid, thereby ensuring containment of the GM plasmid to engineered strains of bacteria.