Team:METU Turkey/Safety

Welcome!
We are Team METU_Turkey!

An importat issue: Safety!

All projects are being conducted in lab-safe strains of E.coli(dh5A) and Saccharomyces cerevisiae. All researchers have been trained in applicable lab safety to insure that no bacteria are inadvertently released into the environment. We have also been trained in proper handling of chemicals. In plastics projects, the actual organisms being engineered were maintained in lab conditions (cultures, bioreactors, etc.). None of the parts we made this year raise any particular safety issues that we can foresee. All of our major parts were either taken from pre-registered biobricks, None of our new parts would provide any foreseeable selective advantage in the wild. Thus, these parts would not increase bacterial survival in the case of accidental release.

Is there any possible situation against to our kill-switch mechanism?

Our kill switch mechanism is dependent to a cheap thickener (Xanthan gum), so our organism would die absence of it. Its basic logic is to addict the organism our wanted enviromental conditions, so it can be controlled.

Safety Questions & Answers

1.Would any of your project ideas raise safety issues in terms of:

RESEARCHER SAFETY?

There are no hazardous chemicals that we used in the laboratory except for EtBr that we used in a special room for gel visualization and some buffers used in commercially available kits.

PUBLIC SAFETY?

Since all the organisms used in the wetlab are destroyed after they are done working with they pose no danger for public safety. We use E.coli strain DH5alpha which is easy to kill and all the student members who work in the wetlab are very well trained to make sure there is no unwanted contamination. This year we are also working on a kill switch which, if works properly, will eliminate any bacteria whereas they will not be able to survive without Xanthan gum present.

ENVIRONMENTAL SAFETY?

As mentioned above a kill switch will be available in the organism which will initiate cell death when the cell is in an environment that does not contain enough Xanthan gum.

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

We have followed all the safety procedures during the isolation process from the cells we had and we successfully isolated the DNA without any problems that will raise safety issues.

3.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?

In our university we have a biosafety and ethical research center which monitors the safety of our projects. http://www.ueam.metu.edu.tr The members of METU Biology department are also members of National Biosafety Coordinating Committee. We are able to consult to them whenever it is necessary. Also biosafety is a very important subject for METU Department of Biology, whereas the student members are very well trained in the subject. Also the projects that we decided to work on are presented to many people in the area in order to see if they are of any concern for the biosafety regulations. All the procedures that are used in the lab are also approved procedures that are used by these people mentioned above.

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?

We believe using specific strains designed specifically for labwork will be safer. It is possible to genetically modify the organisms so that, they are not able to grow outside the lab environment. There probably is not a way to build some biobricks that can be modified in order to make them safer since their function will be the cause of safety issues.

More Safety Information!

Our organisms (Saccharomyces cerevisiae) are meant to live and die in foodstuffs so we will be testing them on food such as bread and cookies. Also, after cooking them in a 300 degree celsius oven, the yeast will die. Also, we are creating a kill switch mechanism which depends on a thickener (Xanthan gum, http://parts.igem.org/Part:BBa_K1606020 ).

We are using E. coli for all lab procedures. But our future prospective/future aim is to use it directly by Yeast.

Since we are using E.coli (DH5alpha), there are no extreme risks we should cope with. (We are also considering a kill switch mechanism.) However, we are using Safety Class II Cabinets, we work appropriate for aseptic conditions. We are using autoclave frequently. We are always sterilizing our waste and we give our waste to well equipped/trained biological waste assistants. We are wearing rubber gloves while we are not using flame.

Safe Shipment: Our DNA submissions always wait for the government inspections in USA. The inspections will be speed up by sending them a letterhead for multiple times by our principle investigator.

Kill Switch Mechanism

Kill Switch Circuit

Strong promoter without thickener of LuxR and antiholin sequence: For our kill switch model first we design a circuit that secrete antiholin LuxR gene to supress the activity of holin and endolysin enzymes for working under normal conditions by digesting gluten into its small particles. After this composite part we design a new circuit that our composite gene part secrete a thickener that dough doesn't lose its stability and viscose structure type for consumers' choice.

Lux promoter activated by thickener(Xanthan Gum) gene part of LuxR and it start to lyse the cell with holin and endolysin activity.

Xanthan Gum Structure

300°C Oven

After dough fermentation, dough is ready to bake under 300 °C, which kills all of the microorganism inside it(except sporulated bacteria). And also the enzyme will be denaturated.