Agilent Renews Funding for Densmore’s Synthetic Biology Research

in Awards, Faculty, Graduate Programs, Graduate Student Opportunities, Graduate Students, Grants, News-CE, Recognition, Research, Research-CE, Students
January 3rd, 2013

Using a library of genetic parts like those from DNA sequences and a set of rules (i.e. constraints about the composition), Eugene generates user-defined composite DNA sequences automatically.

Using a library of genetic parts like those from DNA sequences and a set of rules (i.e. constraints about the composition), Eugene generates user-defined composite DNA sequences automatically.

Synthetic biology is still a relatively new research field, but we already know that in the future, it might be used to complete tasks too risky for the average human such as explosives detection or oil cleanup.

To make these plans a reality, synthetic biologists typically introduce specific DNA into living organisms like bacteria in order to instruct them to carry out certain jobs. Often, doing so can be a trial-and-error process.

To help create a more systematic approach, Assistant Professor Douglas Densmore (ECE) and his research group designed Eugene, a human and machine readable specification language that can be used to formalize and improve the efficiency.

“Imagine knowing English but not knowing how to put the words together,” said Densmore. “We’re essentially creating rules to make the sentences only instead, we’re working with DNA.”

Eugene is integrated into an eco-system of software tools that help automate the physical construction of the composite DNA sequences (for example, by using liquid handling robotics). Observing the DNA's behavior using technology like flow cytometry will lead to the discovery of novel constraints in composing parts of DNA sequences.

Eugene is integrated into an eco-system of software tools that help automate the physical construction of the composite DNA sequences (for example, by using liquid handling robotics). Observing the DNA's behavior using technology like flow cytometry will lead to the discovery of novel constraints in composing parts of DNA sequences.

In 2011, Agilent Technologies awarded Densmore over $50,000 for this research. In addition to funding, Agilent also connected Densmore to a mentor in their company, Allan Kuchinsky, a principal project scientist in the Molecular Tools group. To continue their partnership, Agilent recently awarded Densmore another $40,000 to further his work.

Much of this funding has and will help support Ernst Oberortner, a postdoctoral associate in the Department of Electrical & Computer Engineering who has assisted Densmore in his research over the last year.

“When Ernst came, Eugene existed, but he took it back to the basics in order to get better results,” said Densmore.

As a Ph.D. student at the Vienna University of Technology, Ernst Oberortner had already completed a lot of work on domain-specific languages (DSL) and programming languages used in software development.

“During my first year on the project, I was learning synthetic biology and extending Eugene’s functionalities,” said Oberortner. “Now I’d like to augment the Eugene language to move it to the next level.”

Densmore chose to work with Oberortner because of his extensive skills in computer science.

“He’s a good example of how computer science and biology can come together,” said Densmore. “Ernst didn’t have a background in synthetic biology but he was able to apply his experience and move our research forward.”

New funding will be awarded at the start of 2013.

-Rachel Harrington (rachelah@bu.edu)

Related links:
June 7, 2011 – “Agilent Funds Synthetic Biology Research by Densmore”