General Safety and Bio-Safety

Would any of your project ideas raise safety issues in terms of: researcher safety, public safety, or environmental safety?

All experiments performed in our lab are supervised by either PhDs or professors that are currently working at the Inferfaculty Institute of Biochemistry. Their expertise reaches from genetics over molecular biology to structural biology. In case of questions concerning the handling of chemicals, devices, or biosafety the supervisors were always available. The procedures used in our lab were conducted based on protocols that are well-established throughout the scientific world and were performed in a biosafety level 1 laboratory, as requested by German law ("Gesetz zur Regelung der Gentechnik (GenTG)" [law for the regulation of genetic engineering]). In order to enable replicability and to avoid repetitive errors, all experiments done in the lab are documented in a common lab notebook that was handed to Professor Dr. Ralf-Peter Jansen at the end of each week.
Joining regular briefings concerning lab safety is an essential element of our education at the University of Tuebingen. In addition, Professor Dr. Jansen gave a special talk about biosafety to all members of our team.

Since the E. coli strains used within our project were specifically optimized to not carry out any pathogenic, toxicogenic, or colonising activities and due to the harmless nature of our parts we do not foresee any security concerns in the event of the realization of our project. Furthermore, a main part of the experiments done in our lab is based on the use of purified proteins, thereby minimizing the risk of any contaminations with genetically modified organisms. There is no reported harmful activity of the proteins used in our studies, namely the a-N-Acetylgalactosaminidase, a-Galactosidase and the Endo-ß-Galactosidase. These proteins originate from the organisms Elizabethkingia meningoseptica, Bacterioides fragilis and Clostridium perfringens, respectively. Since synthesized sequences were used for cloning of all of the proteins, aspects of biosafety regarding the original organisms did not have to be considered for our work.
Although the product of our application is thought to be used in public, the procedure of antigen-hydrolyzation will be carried out in a laboratory environment.

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

The organisms our parts originate from are classified as risk group 2 organisms, but we used gene synthesis to acquire the parts of our interest and did not handle the organisms themselves. Furthermore, our lab work was mainly based on purified proteins, thereby minimizing the risk of any contaminations with genetically modified organisms.
All of the parts we use are not known to have any harmful effect on humans or other organisms.

Which specific biosafety rules or guidelines do you have to consider in your country?

In Germany any work with genetically modified organisms is regulated by the "Gentechnikgesetz". There are different biosafety levels ranging from 1 to 4. Our lab has been registered as biosafety level 1. Our work matches the definition of level 1 since based on our current understanding we see no threats on human health or the environment originating from our work. Genetically modified organisms are allowed to be released into nature only after permission of the Umweltministerium (Department of the Environment) and once freed they need to be monitored constantly.

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?

Parts that are able to induce apoptosis or autolyis could be expressed under promoters that are activated in the context of specific environmental effectors. A huge amount of examples for these so-called kill-switches was designed by the iGem community and is now available in the registry (see for example 2011's team of UCL London and the 2013 BGU Israel's iGEM-team). By using a standard vector for the chromosomal integration of biobricked parts into E. coli as previously described (Zucca, Susanna, et al. "A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli." Journal of biological engineering 7.1 (2013): 12.) a new iGem-generated strain of bacteria could be designed that stably expresses a kill-switch mechanism.