Lab to be first 'open-source' for genetic parts

January 25th, 2010

(PhysOrg.com) -- Bioengineers from Stanford and UC-Berkeley are ramping up efforts to characterize thousands of molecular players and processes critical to the engineering of microbes.

With seed money from the National Science Foundation, bioengineers from Stanford and UC-Berkeley, are ramping up efforts to characterize thousands of molecular players and processes critical to the engineering of microbes, so that eventually researchers can mix and match these “DNA parts” in synthetic organisms to produce new drugs, fuels or chemicals. They’ll do this in a lab in Emeryville, Calif., called BIOFAB.

“Synthetic biology has the potential to make the engineering of biology much easier and more affordable. Via the BIOFAB we will help ensure that the public’s investments and interests in the next generation of biotechnology return the greatest benefits,” said co-director Drew Endy, PhD, an assistant professor in Stanford’s bioengineering department and president of the BioBricks Foundation.

Today, a single designer microbe can take years to create and cost tens of millions of dollars, since each control element—such as a transcriptional promoter that initiates the reading out of DNA to produce mRNA—has to be identified, characterized and tweaked to be reused. One UC Berkeley project to engineer microbes to produce the anti-malarial drug artemisinin took 10 years to go from lab to small-scale production, at a cost of $25 million.

To accelerate such bioengineering endeavors, Endy and his colleagues are launching the new lab (in long form it’s BIOFAB: International Open Facility Advancing Biotechnology) with two years of funding from NSF, and matching support from founding partners Lawrence Berkeley National Laboratory and the BioBricks Foundation.

The ultimate aim of BIOFAB is to produce thousands of free standardized DNA parts. Much as standardized parts made it much easier to construct products ranging from circuits to cars, standard DNA parts could also shorten the development time and lower the cost of synthetic biology for academic and biotech laboratories.

“This is an opportunity to build a framework that will allow us to set open standards for how we do biological design in the future, so that biological parts work reliably in everyone’s hands,” said BIOFAB co-director Adam Arkin, PhD, UC-Berkeley professor of bioengineering and head of Synthetic Biology for LBNL’s Physical Biosciences Division.

BIOFAB takes its name from the fabrication, or fab, service laboratories established in the early semiconductor industry to make it easier for academic and small industrial labs to design and manufacture small quantities of custom chips. Endy and Arkin proposed a similar fab lab for biology more than 10 years ago, but only now, Endy said, is the time ripe for an open and cooperative full-scale production facility.

“Besides Tom Knight [of the Massachusetts Institute of Technology], very few people were talking about standard biological parts 10 years ago,” he said, while today, such parts are used daily in synthetic biology labs around the world, and even by college students as part of the International Genetically Engineered Machine competition.

Nevertheless, of the estimated 3,500 critical control elements in an E. coli bacterium, fewer than 100 have been seriously studied and characterized. Of the 500-plus promoters listed in current registries, for example, fewer than 50 have been measured, Endy said.

BIOFAB is raising additional funds to hire 29 full-time staff who will systematically refine, standardize and characterize the activity of each genetic control element in E. coli, so that large-scale collections of genetic parts can be treated more like standardized components. What the researchers learn in working with E. coli, will then be applied to parts collections in other technologically useful microbes, such as yeast, and used to assemble engineered biological systems.

BIOFAB also will promulgate standards for technical and professional practice through application of resources such as the BioBrick Public Agreement, a new legal framework supporting open technology platforms in genetic engineering.

To best accomplish its goals, the BIOFAB is also fully integrating ethics research within its production planning and operations.

“Our task is to generate resources and help make decisions regarding ethical issues, including safety and security in genetic engineering, so that we can lead the development of open technology platforms in biotechnology that increase capacities and support human flourishing,” noted Gaymon Bennett, a doctoral student at the Graduate Theological Union in Berkeley and head of BIOFAB human practices.

With the proper ethical and scientific approach, BIOFAB’s founders say, the synthetic biology will flourish.

“The professionally staffed BIOFAB production facility will provide an essential resource that will allow many academic researchers and others to rapidly prototype, test and translate their foundational discoveries and ideas into practice,” said Jay Keasling, PhD, UC-Berkeley professor of chemical engineering and of bioengineering and senior faculty scientist and acting deputy director of LBNL. “By enabling everyone to better work together the BIOFAB will make the engineering of biology easier and more predictable.”

More information:
More information and announcements of open positions are available via http://www.biofab.org/ .

Provided by Stanford University Medical Center