NSF Grant To Launch World's First Open-Source Genetic Parts Production Facility

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NSF Grant To Launch World's First Open-Source Genetic Parts Production Facility

http://www.medicalnewstoday.com/articles/176749.php

With seed money from the National Science Foundation (NSF), bioengineers from

the University of California, Berkeley, and Stanford University are ramping up

efforts to characterize the thousands of control elements 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.

Today, a single designer microbe can take years to create and cost tens of

millions of dollars, since each control element - a promoter or transcription

factor - has to be identified, characterized and tweaked in order to be reused.

One UC Berkeley project to engineer microbes to produce the anti-malarial drug

artemisinin took 10 years to get out of the lab into small-scale production, at

a cost of $25 million.

The new effort, called the BIOFAB: International Open Facility Advancing

Biotechnology (BIOFAB), aims to produce thousands of free, standardized DNA

parts to shorten the development time and lower the cost of synthetic biology

for academic or biotech laboratories. The BIOFAB has received two years of

funding from the NSF and matching support from founding partners Lawrence

Berkeley National Laboratory (LBNL) and the BioBricks Foundation (BBF), a

non-profit organization that supports and promotes the use of synthetic biology.

" 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 founding BIOFAB director Drew Endy, an

assistant professor in Stanford's Bioengineering Department and president of the

BioBricks Foundation.

" 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, UC

Berkeley professor of bioengineering and head of Synthetic Biology for LBNL's

Physical Biosciences Division.

The BIOFAB takes its name from the fabrication, or Fab, that 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. With computer-aided design (CAD) software,

rapid-prototyping equipment and clean labs, Fab Labs could quickly produce

innovative devices not yet ready for mass production.

" 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, 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. "

Keasling, who chairs the BIOFAB executive committee, led the project to

biosynthesize artemisinin. He is now director in Emeryville, Calif., of the

Department of Energy's Joint BioEnergy Institute (JBEI), which focuses on

developing commercially viable biofuels.

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, " said Endy,

while today, such parts are widely used by college students as part of the

International Genetically Engineered Machine competition (iGEM), catalogued by

institutions such as MIT and JBEI, and used daily in synthetic biology labs

around the world.

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.

" What exists today is not a professional parts catalog, " Arkin said. " But the

parts we have, while not perfect, are better than nothing, and they are helping

researchers all over the world. "

" We now need to move beyond Lego™ metaphors and genetic toys to professional

technologies, " Endy added.

Operating in partnership with the UC Berkeley-led, NSF-supported Synthetic

Biology Engineering Research Center (SynBERC) directed by Keasling, the 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 will be

applied to parts collections in other microbes and used to assemble engineered

biological systems.

" Even though we will be building parts and making systems, we are still in the

foundational research stage, " Arkin cautioned. " But in starting BIOFAB, we will

accumulate the specialized know-how and the community of researchers necessary

to become a resource for production and training in synthetic biology. "

The 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.

" The BIOFAB promises not just to deliver needed foundational technologies, but

do so in support of open innovation and collaboration in biotechnology, " said

Grewal, a Harvard Fellow and BioBricks director.

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, security and communities 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 ,

doctor of theology and head of BIOFAB Human Practices.