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FEATURE: NASA Launches Into Genome Space from Silicon Valley

SAN FRANCISCO, Dec. 27 – The gray brick building that houses the Astrobiology and Life Sciences Laboratories looks out of place on the NASA Ames campus.

 

However, the building, situated between a monstrously large wooden 1930s dirigible hangar and a collection of curving white metal wind tunnel buildings that evokes the architecture in Woody Allen’s ‘Sleeper,’ represents the future vision of the facility: Think academia and biology—led by genomics—rather than wind tunnels and aircraft.

 

Perhaps this was an inevitable transformation for a research site that sits in biotech-rich Moffett Field, Calif. As James Kaysen, a senior research scientist at the NASA base, remarked: “Ames is in the middle of Silicon Valley. You can throw a rock and hit three gene chip companies.”

 

To be sure, “NASA is not a biology-oriented agency,” said Andrew Pohorille, director of the Center for Computational Astrobiology and Fundamental Biology, an interdisciplinary center established two years ago at Ames. But researchers there “are interested in biology” to answer specific questions: “Is there life out there [in space], and can we find it? Can we travel and live outside of life on Earth? These goals require biological research,” explained Pohorille.

 

“My view is that to really move forward in biology, you need to integrate different areas, including molecular modeling, conventional bioinformatics, and complex systems,” he said. “Only then will we get a full picture.”

 

NASA's genomics gambit

 

Taking advantage of its own broad computational technology and its proximity to genomics companies in the Bay Area, Ames is reaching out to biology at a time when organizational changes have transferred flight testing, once performed from its airstrips and in its wind tunnels, to other NASA sites.

 

The center is striving to become NASA’s fundamental biology research hub in part to help the computation and biology disciplines converge, but also for the budgets that accompany that goal, according to Ames scientists. These include $20 million per year for NASA’s Astrobiology Institute, based at Ames, though most of the money is currently distributed to 15 teams at other NASA sites, according to a NASA spokesperson.

 

Additionally, the Fundamental Biology program receives $30 million annually, though a large portion is used for research not taking place at Ames. NASA spends approximately $35 million to $40 million for consumables, technology, licenses, or expertise associated with genomics, including bioarrays, biochips, and gene sequencers, according to John Hines, senior technology program manager for the fundamental biology program at Ames. Hines said the genomics funding level is growing.

 

To beef up its internal genomics-oriented research projects, Ames researchers have been establishing working relationships with local genomics and proteomics companies and academic research centers. But the relationships are often lopsided: Some companies will offer deep discounts or give their technology to NASA for free in exchange for the visibility and prestige the association may offer, said Hines. Other firms provide licenses, technology, or expertise at industry pricing. Companies involved in some type of relationship with Ames include Aclara BioSciences, Affymetrix, Caliper Technologies, Cepheid, Clontech, and CombiMatrix, said Hines.

 

Caliper, for example, headquartered directly across Route 101 from Ames, sold the base an instrumentation platform, microfluidic chips, and technology as part of its applications-development program, said Michael Merion, vice president of sales and marketing at Caliper. Merion, who would not disclose what NASA paid for the system, said a typical applications package costs approximately $500,000 and that the company has an ongoing co-development agreement with the agency.

 

“NASA is trying to figure out conditions to speed up crystallization of proteins to get a 3-D view,” explained Merion. Caliper’s technology “enables researchers to explore what microfluidics can do for them. NASA feels protein crystallization will go better in a microgravity environment, none-the-less it is a manual process that takes place in months. We are trying to offer them an automated platform to more quickly get the crystallizations. NASA’s goal is to use it on the space station,” he said.

 

NASA Ames is also trying to bring genomics onto its base by encouraging an interdisciplinary approach to the research. With its location beside Route 101, Silicon Valley’s main artery, Ames said it plans to construct an educational and R&D campus intended to let NASA researchers and potential university and company tenants mingle.

Outer space via inner space

At the center of the computational-biology portion of this movement is the Life Sciences building, and within its grid of corridors and laboratories is Pohorille’s office, from which he oversees the Center for Computational Astrobiology and Fundamental Biology. The Center’s double-barreled name is a nod to the two NASA programs—astrobiology and fundamental biology—that funded the program when it was established to help researchers apply NASA’s intimidating computational know-how to the study of genomics and proteomics.

These challenges—determining if humans can travel and live away from Earth for extended periods, evaluating quantity and quality of life in space, and exploring the biological effects of microgravity on living organisms—are nicely suited to genomics, proteomics, and bioinformatics, scientists at the Center say.

“NASA has always been a technologically very cutting-edge agency,” said Pohorille. “[It was the] first to request miniature computers. Now biology will be one of the main technological drivers of the future [and NASA] doesn’t want to lose its edge.”

From his office, crammed with books and journals and dotted with coffee mugs and the odd piece of lab equipment, Pohorille coordinates a network of 40 scientists associated with the Center. This network includes theoretical physicists such as Pohorille, computer scientists, and biologists. The researchers remain under the auspices of their own programs at Ames and are free to delve as much or as little into Ames projects as they choose.

Those projects, of which Pohorille estimates 60 percent are focused on genomics, proteomics, and bioinformatics, include studying gene expression in microgravity, analyzing genomic data from space flights, flight simulation experiments, public data and data from partnership collaborations, and creating software to build models of gene regulation based on gene-expression data.

“Some people devote 100 percent of their time [to this research], some very little,” said Pohorille. “The idea is not to cut people off from their roots.”

The research is funded by a number of sources from a range of disciplines at Ames. These, together with a $1 million fund the Center receives each year from the astrobiology and fundamental biology program offices, help pay the scientists’ expenses. The researchers’ salaries are covered by the program offices where they are based. Researchers also get free access to 4,000 processors on Ames’ SGI supercomputers. This computer access is also an incentive for the Center’s other government agencies and academic institution partners, including the National Cancer Institute’s Advanced Biomedical Computing Center and Stanford University’s Center for Biomedical Computation, which established a partnership with NASA Ames in October, said Pohorille.

“My fond hope is that we forge strong ties with our local neighbors at NASA and thus produce an even more fertile environment for the big three goals of the Stanford Center,” said Russ Altman, director of Stanford’s CBMC. Altman says the goals entail partnering in research projects, pairing with NASA scientists in a mentor program in which Stanford students work on research projects at the NASA facility, and developing and using computational tools that includes large-scale analyses of microarray data, protein structures, and large-scale computations of molecular dynamics. These projects dovetail with the Ames Center’s goals, said Pohorille.

“We are a very good match,” he said. “Stanford may want to look at things for slightly different goals, like curing disease, but the techniques and strategy are the same.”

NASA is looking for a “very broad understanding of bioinformatics,” added Pohorille. “Not just data mining, but also protein structure and reconstructing metabolic and regulatory pathways from gene-expression and proteomic data. The connection between the genome and functional physiology is very complex. There are many techniques that need to be done and integrated. That’s the idea of the Center."

“It is very fun to be involved in work with NASA because of their romantic mission,” Altman said in explaining how the partnership is particularly attractive to the Stanford students working at CBMC. This pull also applies to private companies, though perhaps for less romantic reasons: a NASA partnership is like a celebrity endorsement. Adding the NASA insignia and name to a press release or product description—as Caliper, CombiMatrix, and other companies have done—is a marketer’s dream.

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