Safety

Experiments have been done to verify the algorithms used by FLAME. Concerns about biosafety simultaneously arises as we carried out the experiments. In this wiki page, we hope to demonstrate our responsibilities for biosafety, and what we have done already to ensure that we base our wetlab on biosafety rules. And the safety form of SYSU-Software is available on:

Safety Concerns about Designed Genetic Circuit

FLAME is a software for automatic design and simulation of genetic circuits. Our experiments aimed at verifying how well our algorithmic simulations can reflect the reality of real experimental data. Meanwhile, we should test the performance and safety of these designed circuits. So we had some of the genetic circuits designed by FLAME tested, and obtained experimental results. Then we compared the algorithmic simulations with experimental results.

Some of the genetic circuits have been reported in previous journal papers, so safety of these well-known genetic circuits are well tested, and FLAME adopts these circuits as frameworks for further design by users. In addition, FLAME can design new circuits with ordinary parts such as GFP, LacI, AraC, TetR and so on. These parts have been adopted by synthetic biologists as well as iGEM teams in circuit designs for years with little safety concerns.

Laboratory Safety

Our wetlab experiment works in Level 1 labs and use Risk Group 1 organisms; that is, we use Escherichia coli K-12 as model species. So, for the safety of experimenters’ sake, we abided by the laboratory safety rules of Sun Yat-sen University. We obeyed the safety rules during the whole process.

Before experiments, lab coats, gloves and closed toe shoes are required for entry to labs in Sun Yat-sen University (Figure 1, left). When performing the experiments,, we utilized E. coli as our model species which is harmless to both experimenters and the environment. At the end of our wetlab experiments, we cleaned the lab, appropriately sterilized the equipment with high temperature, carefully packed the wastes for safety disposal by company before discarding (Figure 2, right), and washed our hands.

These measures (of course formulated by safety rules of biology labs in SYSU) are crucial to guarantee that we stick to biosafety.

Figure 1 Jinyu Li, one of our team members, was doing experiments in Prof. Yongjun Lu’s lab. Left: lab coats, gloves and closed toe shoes are required in lab. Right: wastes were carefully packed for further disposal.

Public & Environmental Safety

It is already mentioned in the “Safety Concerns about Designed Genetic Circuit” section that our software as well as experiments utilize parts which are commonly used in synthetic biology, and there should be little safety concerns.

During our experimental process we produce little harmful wastes and gases. Moreover, appropriate disposal of wastes produced in the experiments further reduced the release of harmful wastes. Some detailed demonstrations of the methods that we adopted to dispose of wastes have already been provided in the “Researcher safety” section.

We paid much attention to experimenters’ laboratory habits because they make a difference to biosafety around the labs. So safety training was carried out for everyone participating the wetlab to make “dos and don’ts” in lab known to the experimenters. For instance, opening the door with used gloves on is severely prohibited.

In sum, our experiments made use of harmless parts, produced little harmful wastes which afterwards are appropriately disposed of, and required strict training to cultivate good habits in labs. All of theses are our practices for the goods of public and environmental safety in labs.