Team:KAIST-Korea/Projects/report 52

E.Casso computer simulation

Modeling Approach

Assumption Made

From report 1: Quorum production by the Brush E.coli, we know that 56 quorum molecules are produced per minute. Although they are produced continuously in reality, we assumed that they appear altogether at the end of each minute for the purpose of simplifying the modeling procedure; it is difficult to capture the dynamics of a continuous production of quorum molecules in discrete, consecutive frames. To further simplify the procedure, we assumed that the frames are separated by a one minute time interval, which is compatible with the number of quorum molecules produced during the same time interval as determined in report 1.

We also assumed the petri dish as a two dimensional grid consisting of ordered squares of side length 1.1 micro-meter as this configuration approximates the micro-scale arrangement of E.coli with reasonable accuracy (report 2: Quorum Diffusion). The conclusions of this report also justify our assumption that quorum molecules diffuse sufficiently fast that we can assume that neighboring cells receive quorum at the end of each minute.

From report 3: Fluorescence production by the paint E.coli, we confirmed that fluorescent proteins are indeed produced by the paint E.coli upon receiving quorum.

In report 4: Fluorescence visibility justification, we observed that noticeable fluorescence builds up even if as little as only three out of a thousand adjacent cells are successfully induced by IPTG. From this result, we conclude that fluorescence is readily observable upon production of fluorescent proteins. Consequently, we assumed that each cell in our grid definitely displays colors in response to induction.

Public safety

Our project utilizes the random expression of four inducers and four subsequent reporter fluorescent proteins. These genes are not dangerous to the public. The cells used for engineering are harmless strains of E. coli. Thus, the engineered cells pose no evident danger to the public safety.

Environmental safety

To prevent the spread of our engineered E. coli and potential chemical leaks, chemicals, bacteria, and other potential biohazards were disposed as biohazard waste. Bacteria and media containing bacteria were bleached before disposal.

Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes, did you document these issues in the Registry? How did you manage to handle the safety issue? How could other teams learn from your experience?

Every component of our new biobricks came from the iGEM 2011 distribution kit. The components thereof are guaranteed to be safe.

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? If no, which specific biosafety rules or guidelines do you have to consider in your country?

Although there is no organization in Korea that specializes in the safety issue of synthetic biology, Korea Advanced Institute of Science and Technology has a Safety and Security Team which is in charge of making KAIST a safe environment for study and research. The Safetyand Security Team approves of research that abides by the safety regulations which it enforces.

Refer to the site: [http://safety.kaist.ac.kr/english/main/index.php KAIST Safety and Security Team]

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?

We think the best way to deal with safety issues is to encourage all iGEM teams to contribute in making one solid safety standard and make it official. This way, judges can grade the biosafety issues of the participating teams and perhaps give out awards to the teams that best meet this safety standard. Also, lectures related to safety issues can help ensure the enforcement of rules and requirements put forth by this official standard.