Though it’s a relatively new area of biological research, synthetic biology may be the solution to learning more about how natural living systems work. The field, which combines science and engineering, focuses on the design and construction of new biological systems not found in everyday nature.
Researchers are already looking at how synthetic biology can be applied to detecting toxins acting as warfare agents or enabling point-of-care virus detection. Assistant Professor Douglas Densmore (ECE) is focusing on another area of interest in the field – formal specifications of DNA parts and devices.
To explore the ways living systems carry out specific tasks and exhibit modified behavior, researchers create and introduce specific DNA parts into living organisms (such as bacteria). Currently, the discipline is largely a trial-and-error process of specification, design, and assembly.
This area of research would greatly benefit from a more formalized process that includes more rigorous specifications of the desired system components as well as constraints on their composition. To solve that problem, Densmore has created a domain-specific language named Eugene to address the lack of formalization in this process.
Agilent Technologies recognizes the potential of such an approach and has awarded $56,520 over one year through their Applications and Core Technology University Research (ACT-UR) program for the proposal titled, “Augmenting and Extending the Eugene Domain Specific Language for Synthetic Biology.”
In addition to the funding, the program also connects Densmore with an Agilent mentor. Allan Kuchinsky, a principal project scientist in the Molecular Tools group, will fill that role.
Kuchinsky thinks that, like in large-scale integrated circuit design, creating clearly-defined policies will make the field more approachable to many as opposed to just a handful of experts.
“I believe that, in a similar way, the use of design rules and constraints, manifested in languages like Eugene, may be pivotal to making the practice of synthetic biology accessible to a new generation of designers and drive innovation in disease treatment, energy production, and manufacturing, ” said Kuchinsky.
“This is an excellent opportunity for us to extend Eugene’s capabilities to capture a richer set of biological behaviors,” added Densmore.
The collaboration will allow Densmore and his research team to use formalized, high level specifications to create derivations of initial designs quickly and efficiently. At the same time, the systems will be tied to automated assembly mechanisms so that the actual DNA designs can be produced with minimal designer effort, minimal cost, and maximum yield.
Eugene will allow for the definition of biological properties, parts, devices, and rules. It not only captures the data associated with biological building blocks but also their organization and relationships.
“Partnering with Agilent on this project speaks to the need for this technology and will also serve as a great example of industrial and academic collaboration, ” said Densmore.
-Rachel Harrington (firstname.lastname@example.org)