Team:British Columbia/Safety

1. Would any of your project ideas raise safety issues?

Our project idea is to engineer a Staphylococcus aureus-specific phage that contains DspB, a biofilm matrix-degrading enzyme and is controlled by a S. aureus quorum-sensing system. In terms of human or animal safety, this engineered phage should not pose any biohazardous risk since it is specific to bacteria and can already be found in nature albeit without DspB. DspB is also found in nature and not harmful to organisms since it serves only to degrade extracellular carbohydrate polymer bonds in the biofilm matrix. Furthermore, the phage and DspB are expressed/triggered by elements of the S. aureus quorum-sensing system when a notable concentration or biofilm of S. aureus is present. Our project ideas should also not have any severe impact on the environment since the phage targets S. aureus biofilms.

The phage standard which we are introducing to the iGEM competition allows basic modification of bacteriophage genomes and must be treated with care. Due to a bacteriophage's higher potential for mutation (as high as 10^-6 mutations per base pair compared to eukaryotes at 10^-8 mutations per base pair) there is a greater chance of catastrophic mutations occurring. It should also be considered that if phage DNA mutates to be harmful in some way, the potential spread is greater because every phage is capable of up to 200 progeny. On the other hand, although phages have a 100 times greater chance of mutation per base pair, this is balanced partially by the refinement of their genome. Since phage genomes generally range from 15 kilo base pairs to 150 kilo base pairs so that the genome can physically fit inside the capsid, there is not a high percentage of junk DNA. In summary, the phage standard does not introduce any inherent risk that is not already present when dealing with phages.

If our phage mutates to become more promiscuous, we foresee that this engineered system might be employed to attack other bacterial biofilms. However, this is not uncommon in nature. Furthermore, the phage will still be under the control of the S. aureus quorum-sensing system, and it will unlikely be expressed/triggered in its new infected host. DspB is also only known to degrade S. aureus and Escherichia coli biofilms. Conversely, if the phage mutates to become unable to infect S. aureus, then that phage will probably end up at a dead end, being unable to infect or replicate. The probability of this happening is moderate.

If DspB mutates and gains the ability to degrade a greater variety of biofilms, it is again not uncommon in nature. In our case, it will still be contained within a phage specific to and only expressed in S. aureus. If DspB loses its function, then the phage will just have to work alone, but there will not be catastrophic consequences. The probability of this happening is moderate.

If the quorum-sensing promoters that control the expression of the phage and DspB mutate to become constitutive or incorrectly activated even without the presence of a biofilm, then the phage will simply lyse its host prematurely. If the promoters mutate to become inactivated, then the system will cease to function, but once again there will not be catastrophic consequences. The probability of this happening is moderate.

If we had to imagine the worst case scenario ever... a realistic one maybe that the phage manages to target various bacteria AND DspB also degrades various biofilms AND the quorum-sensing promoter becomes appropriate to various bacteria, resulting in widespread degradation of all types of biofilms without control. This would have some environmental ramifications since biofilms are found on most natural surfaces. But the probability of this happening is extremely low considering that most bacteria don't even recognize each other's promoters and have internal guard mechanisms to shut down expression of DNA from foreign species.

If we had to break through the bounds of imagination to imagine the absolute worst case apocalyptic scenario ever, maybe our phage will mutate into a human-specific virus AND DspB will become able to degrade various polymers in humans AND the quorum-sensing promoter will become a constitutive promoter so that our phage will wipe out the human race. But the probability of this happening is as low as that of our team producing a flying pig in time for this year's iGEM Jamboree.

2. Do the new BioBrick parts that you made this year raise safety issues?

Our new BioBrick part, DspB is a biofilm matrix-degrading enzyme and does not raise any significant safety issues. It has been sequenced and assayed for its enzymatic activity and found to be reliable. In the circumstance that a safety incident occurs, users will be able to contact us and we will update the Registry with their report.

3. Is there a local biosafety group at your institution?

The local biosafety group for our project is the Department of Health Safety and Environment (HSE) of UBC. Our laboratory space and equipment meets all safety requirements as per Canadian regulations and the regulations of the HSE. All members of our team have also taken the required Laboratory health safety course from our local biosafety group. Presently, our team has not embarked on research using pathogenic bacterial strains or phages. Our research also does not involve the transference of toxins or drug resistance that could compromise the use of the drug to control disease agents in humans, veterinary medicine, or agriculture.

4. Do you have ideas to deal with safety issues that could be useful for future iGEM competitions?

4.1. Biosafety engineering and design of a safer chassis
Current safety engineering tools such as Event Tree Analysis (ETA) and Fault Tree Analysis (FTA) have yet to be extensively incorporated into synthetic biology models. One large obstacle is the fact that organisms are complex and not everything is known about their inner processes and community interactions. So while synthetic biologists are able to make logical predictions regarding their designed part or system, the sphere of knowledge of the chassis is greatly limited. This reason also motivates the current search for a safer chassis-one that is understood inside and out. In order to engineer safety into our synthetic biology parts or systems, it is necessary to attain a good understanding of what it does in its natural setting, design safety elements based on this knowledge and its extrapolation, and then collect experimental data on its behavior and mutability in synthetic settings. Just as conventional safety engineering utilizes real engineering data and designs, biosafety engineering has to become a whole and unique field unto itself. Research in controlled system-destruction is growing, and there will probably be research in the mutability of different types of synthetic biological circuits. One field of research that is instrumental to biosafety engineering is that of the intelligent synthesis of whole genomes from scratch. This will no doubt provide valuable insights as to the workings of the organism in study and also lead to the production of synthetic chassis and systems that are much more manipulable, controllable and predictable.

4.2. Public perception of risks and safety issues
Through our human practices project, we are exploring different perspectives of synthetic biology by asking members of the public, as well as iGEM participants, to create art in the form of visual arts or stories conveying their perception of synthetic biology and its potential impact on the world. We hope that by stimulating the public to learn more about synthetic biology and hopefully engaging in a meaningful exchange of ideas, the public will gain a deeper and sounder understanding of what synthetic biology is and how synthetic biologists also seek to install the necessary safety infrastructure. By asking for public opinion, synthetic biologists also have the opportunity to address public concerns and lay a firmer foundation for future synthetic biology ventures and applications in the real world. Since the benefits and consequences of synthetic biology research are shared by both researchers and the public, the two must actively seek to listen, inform and negotiate. Scientific risk assessment may produce quantitative measures of potential damage, but this is only a model of what may happen in reality. In order to validate the assumptions, applicability and foresight of these risk assessment estimates, we need to receive the input of the public, who are representative of real-life data. As the term “human practices” suggests, synthetic biologists who endeavour to develop the human practices aspect of their research must consider the same things that society considers. Will the fruits of our research be accessible to the poor? Are people in charge trustworthy? Will there be potential consequences for future generations? Are there ways for us to control the applications of our research? In other words, our synthetic biology parts and systems are like children born into the world. Scientific risk assessment is careful planning. Engaging with society is the actual raising of synthetic biology children. There has to be an increase in public awareness of what synthetic biology is and what it can do. There also has to be an increase in dialogue (whether through public forums or through art and entertainment) not just within the scientific community but also with the public.