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Team:Grenoble/Human Practice/BSS
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Revision as of 23:18, 26 September 2012
BioBrick Safety Sheet (BSS)
Design of the Biobrick Safety Sheet
Synthetic biology is a new and emerging discipline with a lot of potential but also with an important part of risk. But unlike other disciplines such as chemistry there is no standard and reliable way of assessing risk! Where does every component of our Biobrick come from? What was its initial function in nature? Should we fear a particular interaction with another component? Has a particular mutation been observed? These are the question that each biologist has asked himself at least once but could not find an answer because it is too complicated and exhausting! To release your pain the Grenoble Team proposed to include safety informations in the registry part. Thus every team and every biologist would be able to have access to these information and even add his own observations and experimental results to enlarge the database. To sum up, the Biobrick Safety Sheet includes mainly two sections:
- A section where we specify the biobrick, the origin and the initial function of each component in nature (promoter, rbs, coding sequence…), the intrinsic safety of each component and the other components it could interact with.
- A section that lists: the random interactions we observed during the construction, the results of at least one experiment that considers the environment in which the biobrick will evolve and other experiments we think it is important to consider in order to assess the biobrick risk level.
Other teams opinion about BSS
As we wanted the BSS structure to be clear and concise, we early contacted as many iGEM teams as possible. For this purpose we used the NTNU Trondheim matchmaker by posting a request. We have also sent an e-mail to all the European teams. You can find below the list of the teams that gave answers.
We have already had answers about the BSS from Virginia, Edinburgh, Groningen and Paris iGEM Teams A project linked with other iGEM Teams: collaboration
As far as the two last teams are concerned, we made a videoconferencing with iGEM Paris Bettencourt team. Thanks to the partnership with them, we had more information about the point of view of another iGEM Team. Moreover we discovered that our idea is complementary to their work. While they are trying to design tools to improve the safety and work on a way to quantify the biological risk, we are dealing with the information required to assess the risk. Our project is the base of the risk analysis. The structuring of the information would be great for their project because by designing tools, it is also important to know if they would be relevant. Thus our project is in accordance with what is currently done. Their feedbacks finally lead to a whole collaboration with Paris Bettencourt. Indeed, once the first skype session organized, we kept contact and could give them feedbacks about their own project. We also had the opportunity to move to Paris on Sunday the 16th and participate to the debate they organized about a possible regulation of GMOs use. You can find here more details about the event. But they advised us the same thing as the Edinburgh team, that is to say that we should put a link with what already exists. Because of these feedbacks we managed to revise our project. Indeed our goal is not to set up a concurrent system, but more to improve what already exists. We saw that it would be an utopia to have teams using directly the BSS. That is why we worked on a way to link our idea to the Registry of Standard Biological Parts. A way to do it would be to add another tab on BioBrick webpage that could be named Safety. In this part all the information about the way the BioBrick has been used environments in which it would evolve would be listed. In addition, drawbacks and bad effects that appeared would be explained. As it seemed practical, we decided to keep the sheet available for teams, if they need to communicate on what they are doing or using. Therefore other people and especially non biologists can have access to the information. The last feedback was send by the team of Virginia. To sum up they gave to us following advices.- Consider keyword tagging, so that experts in specific contexts can go to the registry and rapidly find a narrower list of parts of particular interest to review.
- Include links to a list of biosafety resources
- DIYBio list of biosafety resources (see for example Sandia National Laboratories - risk assessment framework
- Include compatibility with relevant safety regulations -- global biosafety consensus? NIH?
- Expand and standardize the symbol library on the sheet, at least to match the partsregistry
- Potentially look at protein interaction networks to predict non-intuitive implications
Why is this important ?
This approach is important because a lot of projects intend to use microorganisms outside laboratories. it is essential to make research on protection means. But it is even more necessary to know which hazards we should expect. Therefore having information on what would happen makes protections more efficient. Add to this, if we take a look at the number of iGEM teams that have competed since 2006, we notice that it is increasing steadilyand if the raise keeps the same we should have almost 350 teams in 2018.
Improvement of the project and of the BSS
What was underlined during the presentation of this BSS is that the main sheet is turned to the experiment aspect, whereas it is also important to focus on the theoretical aspect. Therefore we added a part in which it is asked to think about what possible interactions between BioBricks could occur. If this is correctly done, the perspective would probably lead the project to the creation of a software that would collect every possible interaction. for example, it is interesting to explain risks due to proteins, as:- its own toxicity (e.g. toxins)
- toxicity associated to a substrate (oxygenase) or product(peroxydase)
- its selectivity (adelylade cyclase)
- DNA biding specificity (activation or inhibition)(e.g. ompR)
- transcriptional factors specificity
