Safety

1.Would any of your project ideas raise safety issues in terms of: * Researcher safety * Public safety * Environmental safety?

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?

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?

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?

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

• Researcher safety
• Public safety
• Environmental safety?

There were several safety considerations that related to our project

1. General laboratory safety (Researcher safety)

Given that any laboratory can be a hazardous environment if the correct safety protocols are not adhered to, all team members who worked in the wetlab were briefed on laboratory safety. A departmental laboratory safety manual was provided and each person was expected to familiarise themselves with the contents of the manual as well as any specific safety rules pertaining to the laboratory which they were working in.

A copy of the Departmental Safety Manual can be found here.

2. Working with bacteria (Researcher safety)

The initial cloning steps used construct the machine were all conducted using laboratory adapted strains of E.coli such as DH5α and XL1-Blue, which when handled, stored and disposed of in the correct pose no safety risks. The final constructs were electroporated into a model Gram-positive organism (Bacillus subtilis). Some work was also done on the final intended chassis (L.gasseri ADH). Both of these organisms are considered safe to handle and pose no risk to the researcher, although care was taken to handle, store and dispose of the bacteria in a safe and sterile way.

3. Manipulating gene expression using quorum sensing (Environmental and public safety)

Our project deals with quorum sensing mechanisms in Gram-positive organisms. We have designed a fusion peptide which directly upregulates gene expression when it binds to its cognate promoter. It has been suggested that our peptide can activate expression of 20 different genes. The synthetic fusion peptide is also expected to be much more effective at increasing gene expression than the natural quorum peptides it is derived from. There are several safety issues regarding this Biobrick:

Firstly the quorum peptide we have selected activates virulence in Bacillus thuriengiensis and Bacillus anthracis. B.t is a soil bacterium which is pathogenic to insects and b,a is a human pathogen. It is possible that unintended exposure to our enhanced quorum peptide could increase virulence in these organisms. It is also possible that the peptide could activate gene expression by binding to promoters other than the one we intended it to, causing off target effects in lgasseri or other gram positives in the vaginal mucosa. Although the work done to test this mechanism thus far has not posed a safety risk, as no invivo work was conducted, and there was no possibility of the quorum peptide encountering any bacteria any than those we exposed it to in a sterile in vitro environment. However, if this work was to be developed further, the implications of this Biobrick part and how to ensure that it acts only on its intended target need to be carefully considered.

Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes, o did you document these issues in the Registry? o how did you manage to handle the safety issue? o How could other teams learn from your experience?

The plCR-PapR quorum peptide is the only part which could raise a potential safety risk. It only poses a safety risk if it comes into contact with other Gram-positive organisms. The full potential risks were documented on this part’s page on the Registry. This safety risk was only theoretical due to the fact that we only worked with it in a very contained lab environment thus no special precautions needed to be taken.

It is important to consider all the possible effects of a Biobrick part. Many transcriptional activators or regulators have off-target effects. It is important to build in regulatory mechanisms that can limit or control such effects, or to keep these possibilities in mind if any testing is to be undertaken outside of a controlled and sterile setting. Is there a local biosafety group, committee, or review board at your institution? Yes. We informed them of our project in its current form as well as the possible next steps that could be undertaken and they responded thus: The safety aspects pertaining to an engineered commensal bacterium would depend on what is being inserted into the bacterium (as the commensals themselves are safe for use) – presumably in this case a expression casette producing a colour reagent upon stimulus. One would question the possible toxicity of such a colour product if it is not one that has been tested for human use (many dyes of often used in patients to detect various disorders etc – so many are considered safe for in vivo use). Some dyes may perhaps cause allergic reactions in some individuals. I would hardly think mere manipulation of the commensal would turn the “good guy” into a pathogenic organism – there are many published articles that show very positive use of genetically engineered commensals so would support that this would be a highly unlikely event.

This project is a proof-of-principle design therefore would need to be demonstrated as a workable in an in vitro system. If promising as a concept then issues pertaining to safety would become relevant. Then either further preclinical work could be done in an animal model to test for safety and efficacy in a cervical cancer/HPV challenge model; phase 1 safety trial in humans and so on.

I think this is a great concept that should not to my mind present any major hurdles w.r.t. safety considerations; certainly at this early stage general safety rules of any basic laboratory would apply.

The normal flora of the vaginal mucosa would present no problem. However, under conditions of altered flora such as in sexually transmitted diseases, bacterial species can be very altered. I don’t think the species you mention are generally around even under pathogenic conditions, but can’t be sure. It should also be kept in mind that there are some very unusual sexual practices (herbal, additives to dry the vagina etc) where some unusual “creatures” may be introduced (and I don’t mean the sexual partner – although that may be another story).

Again, in terms of safety testing at a time of being introduced one would ideally first test in a normal healthy non-pathogenic setting; once safety shown this could then be tested in individuals with STDs or HIV-1 etc as these patient groups would be associated with distorted bacterial floras.

http://web.wits.ac.za/Academic/Research/Biosafety.htm 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? Although