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NOAA makes novel use of pharma-based software
By Shelia Watson
Contributing Writer
The National Oceanic and Atmospheric Administration purchased a license for a sophisticated software system that is typically used in the pharmaceutical industry to conduct research at its Center for Coastal Environmental Health and Biomolecular Research, located on James Island.
The center carries out research and provides analytical services to evaluate the health effects of algal toxins on marine animals and humans.
The software, called Resolver, is made by Rosetta Biosoftware, a business unit of Rosetta Inpharmatics LLC, which is a wholly owned subsidiary of pharmaceutical giant Merck.
Fran VanDolah, a molecular biologist working on the project, said the software is used extensively in the pharmaceutical industry to screen candidate drugs for various uses as well as identify adverse effects of drugs.
“We’re the first organization using it for ocean sciences,” she said. “It’s very cutting-edge and a high through-put tool.”
The system is a versatile and reliable way to conduct toxicogenomics studies, determine biological mechanisms and identify biomarkers, said Yelena Shevelenko, vice president and general manager of Rosetta Biosoftware.
The system is a high-capacity data storage, retrieval and analysis solution for gene expression data. The system is ideal for life science research organizations that need to assess compound specificity or toxicity, identify new genes or therapeutic targets or compare and analyze large databases of expression profiles.
The center’s Marine Biotoxins Program will use the software to test the toxicogenomic response of animal models and protected marine species to marine biotoxins.
“The system will be a key element of our microarray facility,” said Jimmy Ryan, a molecular biologist who is leading the research. “It will help us characterize the global transcriptional response of human cell lines and other models to marine neurotoxins. These efforts are targeted toward alleviating the adverse effects that marine biotoxins have on people and the environment through functional genomic and toxicogenomic studies.”
Research in the Marine Biotoxins Program is targeted primarily at harmful algal blooms and the toxins produced by them. The blooms, which are proliferations of microscopic algae that occur on all coasts of the United States, produce potent neurotoxins that can cause mass mortalities of marine life, including protected marine mammals, and can accumulate in shellfish, causing closure of shellfishing industries and human health concerns, Ryan said.
The center does a lot of collaborative work with other organizations, VanDolah said, to research the impact of toxins on humans and marine mammals.
“For instance, whenever there’s an incident of mortality of several mammals somewhere, we go and research what killed them,” she said. “We have to determine whether it was the toxins that killed them or sonar that killed them or whatever is out there. Unfortunately, when the animals come to us, they’re no longer alive, but we can help find out what is going on to prevent other incidents.”
Ryan said the software is instrumental in such research.
“In using this software, we’re able to do a great deal of work that would take many staff persons a lot of time to accomplish,” he said.
The system uses high-performance algorithms to produce a comprehensive solution for rapid analysis of gene expression data and can accept and analyze data from a wide variety of formats, including DNA microarrays. The system applies error models to produce statistics for every gene expression measurement within the system.
Life science research organizations that have licensed the Rosetta Resolver system include top pharmaceutical companies as well as academic institutions.
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