Team:Valencia Biocampus/Safety

1. Do your project ideas raise biosafety issues?

Every project in Synthetic Biology should be assessed in terms of biosafety. It is important to evaluate all the risks the new projects could cause. In our project we additionally discussed a lot of ethical issues before we starting working. One of them, which was highly treatedaddressed, was the problem of mutations. Organisms can change and we cannot control all these changes, that means that when we design a modified organism with a specific target and a specific purpose, one cannot rule out that it can mutate and stop working as expected.

This topic has been analyzed through several discussions carried out in Bergen (Norway), Banyuls (France), Barcelona and Valencia (Spain) after showing our fantastic short—film. This film is part of our Human Practices project (available in our Ethical issues section: https://2012.igem.org/Team:Valencia_Biocampus/Ethics)

Public and environmental safety

We work with two kinds of organisms. Escherichia coli is a gram-negative bacterium that dwells naturally in the colon of some organisms, including humans. Some strains can cause serious food poisoning in humans, but laboratory ones are harmless due to some genetic restrictions. In addition, we are using ampicillin resistance genes in our plasmid as a selectable marker for bacterial transformations. Moreover, we also have special containers for biological material for storage and disposal.

In addition, we are using Saccharomyces cerevisiae. The strains we are using are disabled outside the laboratory because of amino acid deficiency. So, they are not expected to survive outside the laboratory.

All biologically-contaminated material, including Petri dishes, broth, inoculation plasticware and others were systematically destroyed by autoclaving.

None of our designs or parts are highly hazardous to the environment since they mainly involve environment-sensing genes and fluorescent proteins. In a hypothetical environmental release, they would have a disadvantage for overproducing useless metabolites such as GFP, so their competitiveness would decrease and they would not be able to survive for a long time. We have tested, with some values, how this metabolic charge affects their growing rate. Our results indicate that our genetically modifications decrease –rather than increase- biological fitness. We have not missed the possibility of horizontal gene transfer risks so we asked for non-conjugative plasmids which also required external inducers.

In conclusion, when we work, we are very concerned about the risk in public and environmental safety, and take the necessary measures needed to prevent damage.

Researcher safety

People who work in a laboratory should be taught properly about the risks. We had to verify the safety of our biological material, techniques and chemicals that we intended to use.

We have avoided using the most common hazardous chemicals and techniques in a laboratory. For example, we have used RedSafe® instead of ethidium bromide in our agarose gel. Ethidium bromide is an intercalating agent that distorts the structure of the DNA helix, it is both mutagen and carcinogen. In addition, we have followed the following points faithfully in order to develop our project with care and caution:

-Wear labcoats, as it prevents possible projections of chemicals from reaching the skin. Of course, it also avoids possible damage to your clothing.

-If you have long hair, it is advisable to put it into a pony tail.

-Use rubber gloves every time you can. However, it may be unsuitable to wear them when working close to a fire.

-Rinse your hands regularly when working with media and microorganisms.

-And last, but not least, remember that in the laboratory is strictly forbidden to smoke, eat or drink beverages.

In particular our project has a special consideration with UV-radiation in one of our constructions. In order to activate that construction it is necessary to irradiate with UV-light (254 nm), so we built a special machine to irradiate bacteria in a controlled and safe environment. This machine totally blocks UV irradiation towards researchers. The machine was called Tordeitor 3000. Here you can see a self-made video about it: http://www.youtube.com/watch?v=448MrmbAzdo.

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

Aside from general safety issues, none of the new BioBrick parts raises any particular safety issues; they are all well-known biological parts implemented in the best known (and safe) lab bacterium and budding yeast. That is because the different components of the constructions (promoters, protein products…) are highly used in molecular biology. Moreover, the protein obtained under the variety of conditions are not toxic, and they are widely known and commonly used in different types of studies (since the Green Fluorescent Protein was discovered the scientists have been improving it in order to get fluorescent proteins based in the original GFP but with better characteristics).

3. Is there a local biosafety group, committee, or review board at your institution?

There is not a specific biosafety group either committee at our Institute Cavanilles of València University to evaluate how safe our project is, but we have specific contacts in our iGEM team that are on bioethics and biosafety boards. For example, Manel Porcar, our main supervisor is in the national committee of biosafety. Moreover, among the audience of the projection of the short film in Norway there are members and ex-members of Norwegian and European ethics committees. In addition member of the ethical committee of the Clinical Hospital of València, took part in the debate. To read her letter, click here.

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?

Fortunately, whenever safety and security protocols are properly followed, environmental, researcher and public safety are well protected (unless, of course, the damage caused was impossible to predict by the current human knowledge). However, accidents may occur. This could carry undesired or even tragic consequences. Therefore, it is our responsibility as researchers to identify, describe and characterize all the biological and laboratory material we are working with, as well as the facilities and all the interactions between these elements in order to minimize the risk of any unwanted situation.

In order to reach this goal, we believe that communication is essential. This is one of the reasons behind our short movie “Talking Life”, one of the goals of which was to promote critical dialogue on the safety of synthetic organisms and mutants arising from them. Learning about the experiences experienced by other groups in security issues could also help preventing dangerous situations. If we know the existence of a new kind of hazard, the use of new ways to prevent accidents or how to react in case they occurred, we can help to develop new security measures or apply them if necessary.

During our experimental work, we detected certain cultures which weren't reacting as expected. We caracterized those cultures and identified a mutatuion as the reason of this malfunction. Thus we continued our experiments using aliquots of the original stock culture, avoiding any problem that could arise if we kept using the mutants. We want to highlight the importance of being on the alert and keeping a well preserved stock to turn to when things go wrong.

Characterization of biological material, is essential given the complexity of biological systems. The more we know about them, the safer we are. And it is important to know how well-studied those parts are. In particular, biobricks could be rated. The more tested and improved by other teams, the more trustworthy they are, so they could be better ranked. This could be added to the “Experience page” of each construction.