Fluidigm Technology to Help Pioneering Researchers Sustain Pacific Rim Salmon Populations
15 Oct 2007

What does every fisherman want? They want to be where the fish are and want a plentiful supply of fish. And what do conservationists want? They want to ensure that the wild salmon runs in Alaska, the Pacific Northwest, Japan and Siberia remain strong. A group of pioneering researchers has developed an innovative DNA profiling approach that helps grant both fishermen and conservationists their wish.

Through work done in Alaska, a pioneering group of researchers, led by the husband and wife team of Jim and Lisa Seeb -- formerly at the Alaska Department of Fish and Game and now members of the research faculty at the University of Washington -- have developed and proved a predictive DNA profiling program on one of Alaska’s most important fisheries.

While at Alaska’s Department of Fish and Game, the Seebs and their group spent years accumulating DNA profiling data of numerous critical spawning grounds, including those that feed into Bristol Bay. Through the sampling of tens-of-thousands of salmon and applying statistical analysis, the group could determine which streams, rivers and lakes would have an abundance of salmon and also pinpoint which fisheries would have weak returns and therefore should be protected. The Seebs work is now to be applied broadly across the Pacific Rim at the new International Center at the University of Washington’s School of Aquatic and Fishery Sciences.

“We use single nucleotide polymorphisms (SNPs) as genetic markers to survey different species of salmon that reside in the Arctic, Sub-Arctic and the Gulf of Alaska. SNPs are alternative forms of genes that vary by a single nucleotide base. These markers are used to manage the salmon fishing fleets for Alaska’s economic good while maintaining the salmon population,” said Dr. Jim Seeb. “The Seeb’s work blends cutting-edge biological research, ground-breaking natural resource management and advanced technology to identify which hatchery runs are abundant and where numbers of fish are great enough to keep Alaska’s salmon hatcheries healthy,” noted Gajus Worthington, Chief Executive Officer of Fluidigm.

From the age of 10 until age 23, Worthington spent his summers commercial fishing for salmon in Alaska, including the Cook Inlet. Like many Alaskan families, his depended on the sea for part of its livelihood. Worthington’s commercial fishing earnings helped pay for his education. He has first-hand experience of the delicate equilibrium fishermen face in operating a sustainable business and also keeping a critical natural resource in balance.

Salmon are anadromous: they are born in fresh water, migrate to the ocean, and return to fresh water to reproduce. After several years, depending upon the traits of each salmon species, the fish return to their original place of birth to start the lifecycle once again.

Exploding Demand
This predictive effort was so successful that demand to expand the group’s work was immediate, overwhelming the group’s existing infrastructure. They turned to breakthrough integrated fluidic circuit (IFC) technology from Fluidigm – called BioMark dynamic arrays. IFCs allowed the group to expand their work to conduct an ever-growing DNA profiling workload in record time and with minimal cost, thus addressing the fisheries management challenges of high-volume throughput and highly reliable results, while keeping costs low and maximizing limited manpower and resources to meet the needs in Alaska.

Now the Seebs are expanding their work internationally, having been appointed to the research faculty at the University of Washington where they intend to built a center to conduct similar work for fisheries in the Pacific Northwest, Japan and other parts of Asia.

“We had been using conventional micro-well plates but urgently needed to improve our efficiency to handle genotyping on a large scale. We studied every alternative technology but invariably ran up against unacceptable trade-offs between throughput, reagent costs, and call-rate accuracy. Fluidigm’s BioMark system is the only multiplex strategy that we consider viable,” Seeb added.

Integrated Fluidic Circuits (IFCs) contain a microscopic matrix of channels, valves and chambers on a silicone (not silicon) chip. Fluidigm’s IFCs automatically perform over two thousand experiments at a time-- 2,304 parallel, nano-volume reactions on each chip -- to be exact. Fluidigm estimates these IFCs provide six times greater throughput speed and a significant total cost reduction of 80 percent over traditional genotyping systems.

Alaska’s Department of Fish and Game currently samples approximately 100,000 individual fish per year. Instead of a room full of more than 15 expensive pieces of traditional equipment, it now uses a single Fluidigm machine and four throughput-enhancing systems to quickly complete all of its salmon DNA profiling for this program.

“I am incredibly proud Fluidigm’s technology is helping Alaska achieve its goals of protecting, maintaining, and improving the salmon resources of the state, and will help ensure Alaska’s unique fishing industry continues to thrive. We are happy to extend our technological contributions onto the world stage,” Worthington concluded.

This methodology has also been used in other Alaskan fisheries. For example, DNA analysis conducted using Fluidigm technology has been utilized to resolve treaty disputes between the U.S. and Canada over fish intercepted in coastal waters. DNA has also been used to profile King Salmon returning up the Yukon River. Scientists believe this research approach can be applied to help improve salmon fisheries throughout the Pacific and Atlantic rims and hope it is also applicable to helping other fisheries in danger, such as cod.

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