Participants gearing up for this year’s International Genetically Engineered Machines (iGEM) synthetic biology competition are using their knowledge of bioinformatics to help fight the unethical use of synthetic biology. They are developing algorithms that can be used to determine if synthetic cell parts or DNA are developed that mimic the components of biological weapons.
The iGEM team—comprised of students at the Virginia Bioinformatics Institute (VBI) at the Virginia Polytechnic Institute (Virginia Tech) and the engineering school INP- Grenoble Ensimag (France)—developed software called GenoTHREAT. It can be used to monitor the content of the DNA sequences uploaded onto GenoCAD, the VBI’s online protein design program, to ensure that the program is not used for illegitimate purposes. A similar approach could be used by iGEM to monitor the content of the Registry of Standard Biological Parts.
Synthetic biology is a rapidly expanding field and the demand for biological parts is rising. Research into disease progression, drug delivery, and synthetic life are just a few of the ways that biological components can be extremely beneficial to researchers. But synthetic biology could be used for more sinister purposes, like biological warfare, if genetic components are used to create deadly viruses or toxins.
“When biological weapons were cultures of anthrax or other select agents, it was possible to prevent the spread of biological weapons by restricting access to dangerous samples. Now anyone can obtain sequences that are potentially dangerous,” Jean Peccoud, associate professor at VBI and leader of Virginia Tech's iGEM initiatives, told BioTechniques. “So it is important to detect the possibility that people are using gene synthesis in an illegitimate way.”
According to Peccoud, a resurrection of 1918’s pandemic influenza virus is a good example of dangerous gene synthesis. “If someone were to order this sequence again, it would be important to detect it, and make sure that the person placing this order intends to use it for legitimate research,” said Peccoud. "The iGEM work will help gene synthesis companies and their customers ensure such research."
The algorithms designed by the students for the GenoTHREAT software are based on the Centers for Disease Control and Prevention (CDC) Select Agent and Toxin List. The CDC list is a comprehensive compilation of dangerous substances that could be weaponized. By basing the new software on the CDC list, the students are creating a program that is compatible with all the major substances that the government monitors. This makes it possible that the program could one day be used by the government for its own oversight duties. The students are creating a database of test cases so they can better estimate the performance of different screening strategies.
“The fact that undergraduate students are working on a biosecurity project and will talk to other undergrads about biosecurity is very significant,” said Peccould. “It's an indication that the community is taking this issue seriously and feels responsible for the safe practice of this new discipline.”
The final results of the VBI and INP-Grenoble Ensimag teams’ analyses will be presented in November at the 2010 iGEM competition. The Massachusetts Institute of Technology organizes the annual competition, which is intended to spark interest in the development of standardized parts for biological research.
“The students’ message is that everyone has a responsibility in preventing the [inappropriate] use of synthetic biology,” said Peccould. “It is not the exclusive responsibility of the government to ensure that synthetic biology remains safe. We can also do our share.”
