UCSD Partners with Venter Institute
to Decipher Genetic Code of Marine Microbes

By Ioana Patringenaru I January 23, 2006

Officials announce a new initiative that will help researchers analyze the genetic code of ocean microbes in relation to many other pieces of information. From left to right: Chancellor Marye Anne Fox, UCSD alumnus J. Craig Venter, who will partner with UCSD, Larry Smarr, director of Calit2, which will lead the project, and John Orcutt, director of the Center for Earth Observations and Applications at the Scripps Institution of Oceanography.

Since 2003, Sorcerer II has crisscrossed the world’s oceans, dropping its anchor every 200 miles and harvesting samples of microbial life. The results of the project, financed by UCSD alumni J. Craig Venter and his research institute, have been staggering: the expedition uncovered up to 40,000 new species at some sites and discovered millions of new genes between Halifax and the Galapagos, with many more to come.

We are, it seems, surrounded by a sea of genes.

Other scientists are working on similar projects. But researchers have had trouble finding computer servers that could handle all that data. For a while, Venter’s institute even used computers that animated the movie Shrek 2.

An experiment in the Sea of Genes exhibit at the Birch Aquarium allows visitors to extract DNA.

A $24.5 million gift from the Gordon and Betty Moore Foundation lifted that obstacle. The J. Craig Venter Institute and UCSD will use the money to create the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA).

“This initiative puts UCSD at the forefront of a new discipline,” Chancellor Marye Anne Fox said at a press conference Jan. 17 at the Birch Aquarium.

Each computer in CAMERA’s server is about 200 times more powerful than a home PC, said John Wooley, Associate Vice Chancellor of Research and one of the investigators on the project. Researchers also will be able to access the server through connections that are 100 times faster than today’s Internet, he said. So scientists in Sweden could work with CAMERA as if they were in the next room on the UCSD campus.

“We’re bringing a whole new world together, 24/7,” Wooley said.

Another item in the exhibit shows a helix of DNA.

The database will allow researchers to analyze the genetic code of ocean microbes in relation to many pieces of information, including data about their environment and about other microbial species.

The California Institute for Telecommunications and Information Technology (Calit2) will lead the project in partnership with the J. Craig Venter Institute in Rockville, MD, and the Center for Earth Observations and Applications at Scripps Institution of Oceanography. Researchers also have ties to UCSD’s School of Medicine and School of Pharmacy. The partners hope to get other scientists involved. During the Jan. 17 press conference, they outlined their vision of CAMERA’s potential. Sorcerer II’s mission is raw discovery, Venter said. But by looking at microbes, scientists could get a better idea of how life evolved, he added. Venter led a successful effort to decode the human genetic code.

“We’re an ocean planet,” said Calit2 Director Larry Smarr. “To understand ourselves — after all we’re mostly water — we must understand our planet.”

So far, researchers have found genes in many species that also can be found in the human genetic code, Venter said. Scientists also could get a better handle of how life forms can survive higher carbon levels in their environment, he said. Some pharmaceutical companies also hope to find ingredients for new medicines in the ocean, Smarr said.

“This is an exciting day for UCSD,” Chancellor Fox said.