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GSAC Sashays into Savannah, Starts with Systems Biology

SAVANNAH, GA Sept. 22 (GenomeWeb News) - The likelihood of finding a genome sequencing conference in Savannah, Ga. would seem just as small as, say, that of seeing an armadillo crossing the city's magnolia-lined streets.


But in recent years, armadillos have in fact arrived in Savannah on produce trucks from Texas and become the latest fashion in east Georgia roadkill ---they call them possums on the halfshell, according to a local taxi driver. And last night, TIGR's 15 th annual Genome Sequencing and Annotation Conference opened here at the Savannah International Trade & Convention Center, along the shores of the Savannah river.


The reason that TIGR chose to hold the conference here has something to do with Savannah's proximity to Hilton Head, S.C., where the first GSAC conference was held, said Craig Venter, TIGR's president and the conference co-chair. More specifically, it was about size: just over 700 people have registered for the conference, Venter reported in his opening address to attendees.


While there has been whispering in the genomics community about the withering of GSAC attendance in the past few years, from a height of several thousand in the 2000 Miami conference, Venter said he wants it this way, and even hopes the conference would get small enough to go "down the road" again to Hilton Head some time soon. "Our goal has been to work toward a more intimate conference," in order to raise the level of discussion, said Venter.


However, he added, next year the conference will be held in the Ronald Reagan building in Washington, DC.


The reason, perhaps, for some of this schizophrenia about the future of the GSAC conference stems from the fact that genome sequencing has moved into a new, yet-to-be charted phase.


"It's become pretty trivial to get a genome sequenced,said Venter. "But it's not very trivial to understand what it means."   This task of making sense of all the sequence and fitting it back into biology, is what the conference is all about, he said.


In line with this theme, Leroy Hood, founder of the Institute for Systems Biology, headlined the opening plenary session.  Hood opened his talk with the observation that scientists in the genome world these days seem split into those that are technology-driven and those that are biology driven.  "What I am going to argue is that what is really fundamental is to have biology drive the science," he said.


For Hood, this 'biology' is of course systems biology. And, by systems biology, he said he means biology that is 1) hypothesis-driven; 2) uses global analysis; 3) is quantitative; 4) is integrative; 5) is iterative; and 6) examines the dynamics of life rather than looking at an organism in a static state-i.e. at one time point.


"At the heart of this is that biology is an information science and we now have the high-throughput tools to focus on biology as an information science," he said.  


Hood discussed some of the work that ISB scientists have been doing to try to put this paradigm into practice.


One collaboration with Stephen Quake and colleagues at Caltech involves the design of a systems biology-driven nanochip that allows users to interrogate the behavior of a live cell on a nanopore, and also use nanowire sensors to analyze gene and protein expression on the contents of cells, and use nanocantilevers to interrogate protein-protein and protein-DNA interactions. Hood said this sort of microfluidics technology will enable scientists to increase the throughput of information in systems biology research.


Another example of systems biology in practice that Hood cited was ISB researcher Andrea Weston's  on galactose metabolism in S. cerevisae , in which she departed from the steady-state experiment "to a dynamic experiment where you tickle a system" over a time course, inducing galactose genes, and looking at gene perturbations. Eventually, work like this can be mapped into a network architecture, he said-the kind of complex circuits that resemble more of a page from an engineering textbook than a traditional biology diagram.


Indeed, when Eric Davidson of CalTech followed later in the evening with a talk on sea urchin endomesoderm gene regulatory networks, he went so far as to show slides of feedback loops between cis regulatory elements, which he experimentally validated through repressing a repressor gene and then adding fluorescent reporters to show what the gene to be repressed did without repression in sea urchins. This type of process - forming a hypothesis, and pertubing the system in order to test out the hypothesis and see how the system works - is an approach that Davidson, Hood, and others emphasized as key to systems biology work.


Another concept at the center of Hood's talk was that of biomodules--small networks of interacting proteins and genes that then interact with each other, and then connect to other biomodules to form the larger network-or architecture-of the biological system.


But major challenges remain in the area of systems biology, Hood said. On the academic level, where centers for systems biology and integrative biology are being established, the biggest challenge, according to Hood, is integration. "How do you create a cross disciplinary faculty?," he asked. "How do you put together the high-throughput technology? How do you deal with salary scales of software engineers and engineers so you doint get funneled off to industry?"


And then, while the centers themselves have received abundant funding, there is the issue of how to fund the research. A major challenge remains in getting the funding agencies, especially at the level of study sections, to understand that systems biology is more than "a big fishing expedition.," Hood said. "But we are pushing to get that."


GSAC will run through Wednesday, Sept. 24.


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