Revision as of 03:15, 12 October 2016

Safety

Safety is, of course, the one of the foremost concerns when designing a sythetic biology system. Addressed here is a wide range of points on the safety of the Michigan Synthetic Biology Team's project in the laboratory and beyond.

Would any of your project idea raise safety issues in terms of public saftey or environmental safety?

Our project is designed to function entirely on a piece of paper; no organism (besides the user) is required to make it work. Our cell-free design is made up mostly of DNA and other components necessary for protein synthesis. Some form of these components exists in every cell of every species, from E. coli to elephants. The in vitro nature of our final product would remove several potential hazards associated with a device utilizing live cells. There is no chassis organism in the final product which can escape into the environment.

The DNA used in our design is unlikely to be taken up and expressed by a naturally occurring microorganism because all DNA segments are linear and the T7 promoter driving expression is not transcribed by healthy bacteria. This greatly reduces the risks of using our recombinant DNA outside the lab. Even if the recombinant DNA used in our project were taken up by a natural microorganism, it codes for two fragments of beta galactosidase, an enzyme which is classified as a non-hazardous substance by GHS and HCS (4). The antibiotic resistance plasmids that are used for cloning should never leave a laboratory setting and would not be a part of the final product. Although these precautions alleviate some common concerns regarding the use of recombinant DNA outside the lab, it is important to remember that the project does still utilize recombinant DNA and therefore requires diligent consideration of possible unforeseen environmental effects.

The primary safety considerations of the project relate to its use as a diagnostic device. When developing such a device, false negatives and false positives are a major source of concern, and the potential damage of misdiagnosis must be carefully weighed against the benefits of diagnosing the disease correctly and quickly. Although accuracy and reliability have a large effect on a device’s safety, it is difficult to predict these parameters at such an early stage of development. Another potential danger would be the requirement of working with a small quantity of bodily fluid to operate the device. Any bodily fluid must be treated as a potential source of disease transfer between the patient and others.

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

The LacZ omega fragment Biobrick that we submitted is a commonly used reporter in synthetic biology. It encodes a version of beta galactosidase which is only functional when paired with the beta galactosidase alpha fragment. The full beta galactosidase enzyme is classified as a non-hazardous substance under GHS and HCS standards (4).

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?

There is no body specifically focused on overseeing biosafety hazards. The University of Michigan’s Department of Occupational Safety and Environmental Health reviewed the team’s laboratory and practices multiple times, and found that our lab space met their requirements for safety. Before our team started doing lab work, all our members were trained in laboratory safety and instrument handling in accordance with University of Michigan requirements.

How could parts, devices and systems be made even safer through biosafety engineering? Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions?

With a mass produced product that is based on exposed synthetic genes, there is a small chance of natural transformation by environmental bacteria. The products that would come from these genes’ expression are harmless, but to prevent mutation and spreading of these genes a simple failsafe was designed. Inspired by The Chinese University of Hong Kong’s 2012 project that featured a safety component that targets DNA using CRISPR (1). Our design is more simplistic; it relies on the weak expression of DNase I. University Oxford’s 2015 project included a part for DNase I and the necessary chaperone peptide (DbsA) (2). Using a weak promoter to slowly build up the enzymes concentration should not destroy the main template until after it has finished expression. The University of California, Berkeley 2006 iGEM documented a list of promoters and their relative strength and submitted them as parts (3). If it is decided to use this system, several different promoters could be tested with the DNase part in order to find the right level of expression.

A DNase-based suicide gene has applications with any cell-free synthetic gene network. It is almost every organism that comes in contact with it, and bacterial the do transform the suicide gene into itself will not survive long enough to spread gene further. It will also efficiently wipe away any DNA that was used and leave only short oligonucleotides behind.