Researchers at NCRC using bioinformatics

Published 12:00 am Tuesday, December 1, 2009

By Emily Ford
Scientific research under way at the N.C. Research Campus generates so much biological information that no spreadsheet or computer file can contain it.
When scientists study biology at a molecular level, as they do in Kannapolis, they encounter problems so complex that a vast and relatively new scientific field is required to help find answers.
It’s called bioinformatics, and the University of North Carolina at Charlotte specializes in it.
Bioinformatics can help determine the exact point at which a new cancer drug should interact with a cell.
“Bioinformatics really began as a solution to a problem,” said Dr. Lawrence Mays, director for the UNC-Charlotte Bioinformatics Research Center. “The problem was a flood of data that was difficult to understand.”
Two decades later, the flood waters continue to rise. A genome that once took years to sequence now takes only weeks, thanks to high-throughput equipment like that at the Research Campus.
Instead of studying one gene at a time, scientists now can use gene chips for gene expression analysis.
“A single chip with an active site the size of your fingernail can be the equivalent of a couple million test tubes,” Mays said.
These mind-boggling amounts of data led to bioinformatics, or the discovery, development and application of new computational technologies to help solve biological problems.
“It’s forced people to think in a different way,” Mays said.
UNC-Charlotte researchers in Kannapolis will manage and analyze massive datasets using super computers, helping their colleagues from seven other universities on the $1.5 billion Research Campus better understand human health and nutrition.
Collaboration is prized in Kannapolis, where Dole Food Co. owner David Murdock is developing a 350-acre biotechnology hub on the ruins of an old textile mill he once owned. In that spirit, Mays said he’s hiring faculty for Kannapolis whose areas of expertise complement scientists already at the Research Campus.
“These are not primarily service providers,” Mays said. “These are people who will develop new techniques and bring real scientific innovation to the North Carolina Research Campus.”
Dr. Ann Loraine, a plant geneticist and plant biologist, has developed better procedures to understand plant genomes, a fundamental goal at the Research Campus.
Loraine’s lab has a National Science Foundation grant to create highly interactive software to display plant genomes.
Scientists in her lab are also working on Web-based tools to display data generated during a major collaboration with N.C. State University and the Murdock Research Institute to map the blueberry genome.
Understanding proteins, or the enzymes vital to metabolism, is another crucial component of the Research Campus.
Scientists studying proteins and metabolism use a technology called mass spectrometry. State-of-the-art mass spectrometers at the Research Campus generate large volumes of complex data.
UNC-Charlotte’s Dr. Xiuxia Du is developing new techniques for analyzing that data, specifically with nutrition research in mind.
“Her work goes way beyond computer analysis,” Mays said. “It will extract much more information from the instruments than you would normally get.”
UNC-Charlotte will provide bioinformatics support to universities and private companies in Kannapolis.
Dr. Wei Sha leads this effort. Thanks to her background in metabolomics, she has a collaboration underway with the UNC Nutrition Research Institute in Kannapolis to better understand metabolism.
UNC-Charlotte operates a $750,000 computer system located in the Core Laboratory at the Research Campus.
Super computers like these make bioinformatics possible.
“Your desktop might have two processing units in it. The cluster we have has over 500 processing units,” Mays said. “We can do things hundreds of times faster.”
Data files that come off the genetic sequencers in the Core Lab are hundreds of times larger than files on a typical computer.
That data immediately goes into the computer cluster for genome assembly, Mays said.
Eventually, UNC-Charlotte will have 3,500 square feet of suites and offices in the Core Lab Building. But the state budget crisis has prevented Mays from hiring additional faculty and staff or moving into the school’s permanent home.
“The funds have to be released,” he said. “We are limited as to what we can do.”
Mays anticipates hiring six more people with doctorates or master’s degrees. There will be opportunity for people with bachelor’s degrees, but not as much as with the other universities, he said.
In Charlotte, the university’s new Department of Bioinformatics and Genomics will move into a $35 million, 94,000-square-foot building this summer on the Millennial Campus with the Charlotte Research Institute.