ACADEMIA

Important discoveries about the effects of global climate change on ocean life are coming to light through a collaboration between scientists and National Center for Genome Analysis Support (NCGAS) at Indiana University.

Researchers from the Pacific Biosciences Research Center at the University of Hawaii Mānoa and Ohio University commissioned NCGAS to provide bioinformatics skills and computational resources to study the transcriptome of zooplankton, the small, multicellular organisms that form the basis of the marine food chain. (The transcriptome is the set of RNA molecules produced in a population of cells.)

In recent years, scientists have seen a corresponding decrease in zooplankton along with cod fisheries in the North Atlantic Ocean. Theorizing that global climate change might be to blame, the scientists needed data to fully understand the phenomenon. Deciphering the messages or “transcripts” that the organisms’ cells produced allows researchers to pinpoint the causes of population changes. Their findings were published in the paper “De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda)” in the February 2014 issue of the journal PLOS ONE.

"It is critical to understand the effects of global climate change on ocean life — particularly on fisheries and other economically important marine animals," said Richard LeDuc, NCGAS manager. "For example, the paper mentions the collapse of North Sea cod fisheries and the role of these zooplankton. Apparently the zooplankton are unable to complete their life cycle, which results in less plankton, and thus less cod. This paper addresses fundamental questions about molecular changes in the zooplankton over their life cycle."

For the project, NCGAS technologists leveraged their prior expertise in optimizing Trinity software and took the lead in moving the data, running the key analyses, and transporting the results back to the researchers.

Trinity was developed by researchers at the Broad Institute of MIT and Hebrew University. It produces high-quality RNA sequence assemblies used by scientists studying gene expression. These RNA sequence assemblies allow scientists to know which genes are active within a living creature.

For LeDuc, the zooplankton findings are just one more way that NCGAS helps scientists concentrate on their work, not on data management. "Our center exists to provide both specialized computational resources and the skills to use them – thus allowing the life scientists to focus on issues within their expertise," he said.