If a genetically or synthetically engineered organism is release into the environment, how will we know? How can we tell it apart from the millions of microorganisms that exist naturally in the wild? That’s the challenge being taking on by a multi-institution research team, including Eric Young; assistant professor of chemical engineering at Worcester Polytechnic Institute (WPI); that is developing a bio-security tool that can detect engineered microorganisms based on their unique DNA signatures.

Genetic engineering, in which genes are adding to the genomes of organisms, and synthetic biology; which focuses on understanding and designing better DNA sequences; are both using today to make a wide array of products, such as pharmaceuticals, like insulin, and agricultural crops. Genetic engineering also is using by biotechnology companies from start-ups to multinational corporations; to manufacture products like detergents, food ingredients, and biofuels.

For decades, the U.S. government has sponsored research on and development of engineered organisms; and better ways to design DNA, while the government and the synthetic biology community; have worked together to develop safety and ethical practices; to ensure the organisms that are make are safe and can be contained. For example, the government has sponsored the development of “kill switches”; that make it impossible for engineered organisms to survive outside the lab.

Better ways to design DNA

Recently, the U.S. government and research scientists have identified a need for new tools; that can identify engineered organisms when they are mix in with a myriad of naturally occurring microorganisms. These tools could eventually be deploy to detect engineered organisms in the environment. But they could be using to protect a company’s intellectual property should an organism; it designed accidentally escape the lab or to detect intentional releases of potentially harmful organisms.

However, this is the task being taking on by the multi-institutional team charge with developing such a tool. The project is fund by an 18-month award from the Finding Engineering Linked Indicators (FELIX) program; but Intelligence Advanced Research Projects Activity (IARPA); an organization within the Office of the Director of National Intelligence that funds research to address challenges facing the U.S. intelligence community.

The award has a second phase that could be renewed for an additional 24 months. Raytheon, a Massachusetts-based defense contractor, is the primary contractor; Young; but who has received a $377,746 award for his part of the project, is one of five subcontractors. The others are Johns Hopkins University, Princeton University, University of California at San Francisco; and Mission Bio, a San Francisco-based biotech company.

Engineering of bacteria

“We realize the power of engineering and bio-engineering, whose expertise is in synthetic biology; including the genetic engineering of bacteria, yeast, and fungi. We are excited about the promise of synthetic biology; but we also have an ethical responsibility to think about the potentially negative uses of the technologies we develop,” said Eric Young; Assistant Professor of Chemical Engineering, Worcester Polytechnic Institute

“My lab is developing engineered organisms to solve problems, and we use safety practices; beyond what we are required to use. Hopefully, this project will lead us to a low-cost tool that we can use to make sure everyone; but is working to prevent the release of organisms into the environment, from universities to manufacturing plants to DIY bio enthusiasts; in their garages,” said Young.

The antimalarial drug

Scientists create engineered microorganisms by introducing new genes into their genomes that enable them to produce valuable drugs, biofuels, or food products. A bacterium containing the human gene for producing insulin, or a yeast bearing multiple genes from several organisms to make the antimalarial drug artemisinin are examples. Because many of the genes in these engineered organisms exist in nature, telling them apart from non-engineered organisms in soil or water samples can be challenging. “It’s akin to finding the proverbial needle in a haystack,” Young said.

He added that the key to making that distinction will be identifying genetic signatures for each organism. By virtue of the way they are produced, the majority of genetically engineered organisms have one or more short sections of DNA that are unique to their genomes and make them different from their non-engineered cousins.