Emerging in the early 1980s, bioinformatics has evolved alongside advances in computational capabilities, the Internet and gene sequencing into a required tool box of methodologies to analyze data produced by gene sequencing and high-throughput screening technologies.
At the North Carolina Research Campus (NCRC) in Kannapolis, bioinformatics plays a more vital role than just data analysis. Located on campus, the UNC Charlotte Bioinformatics Services Division (BiSD) serves as a point of collaboration between the campus’ business and university partners that is accelerating scientific discovery in the areas of health, nutrition and agriculture.
Published in PLoS One in May 2012, BiSD contributed to the recent finding by the Appalachian State University Human Performance Lab and the Dole Foods Nutrition Research Laboratory, both at the NCRC, that bananas provide as much of an energy boost during exercise as sports drinks.
BiSD is also part of a multi-institutional consortium led by the North Carolina State University (NCSU) Plants for Human Health Institute, also on the NCRC, that is sequencing the blueberry genome. The Blueberry Genome Project, led by Allan Brown, PhD, assistant professor, molecular geneticist and faculty member of the NCSU Department of Horticultural Science, is identifying the genes linked to the berry’s health-promoting natural compounds and is expected to further discoveries with both medical and agricultural applications. Other consortium members include the NCRC’s David H. Murdock Research Institute (DHMRI) and researchers from Georgia Tech, Washington State University and the US Department of Agriculture-Agricultural Research Service.
Anne Loraine, PhD, associate professor in the UNC Charlotte Bioinformatics and Genomics at UNC Charlotte, has sequenced the entire blueberry transcriptome and submitted a paper for publication on new bioinformatics methodologies used in this research. The strong collaboration between NCSU, UNC Charlotte and DHMRI, the NCRC’s core laboratory, made the transcriptome work possible.
BiSD also manages industry contracts that range from statistical analysis of health surveys to sequencing breast cancer samples to find specific abnormalities. “Probably not surprising is the amount of cancer work coming in has really been increasing” said Cory Brouwer, PhD, director of BiSD and associate professor of Bioinformatics and Genomics at UNC Charlotte. “We are currently collaborating with two local biotech companies that are involved in cancer diagnostics and treatments in addition to discussions with several local academic researchers on various cancer studies and submitted grants. Hopefully, the research done on the NCRC and the network of those who are collaborating with this campus can be instrumental to understanding how we can prevent many types of cancer through healthier diets and nutrition.”
For Andrew G. Swick, PhD, director of the UNC Chapel Hill Nutrition Research Institute’s Obesity and Eating Disorders Research, which is located at the NCRC, the necessity of bioinformatics prompted him to partner with BiSD. They are collaborating on a study examining the metabolomic pathways that determine why some people respond to overeating with an increased metabolism and others by storing fat. Whole blood transcriptomic and metabolomic profiles, energy expenditure, metabolism, gene expression and other physiological changes that occur in response to over feeding in post-menopausal, obese women will be measured during the study.
“There’s a lot of physiologic data, and we really need the informatics to be able to sort through that and get some meaning out of it,” Swick said. “It’s always nice to be close to the people you work with (and) that is an advantage here on campus. Plus, they have a good infrastructure here in terms of the computational power.”
BiSD is powered by a 432-core processor Linux cluster with 8 GB RAM per core (3.4 TB total RAM). This increased memory is ideally suited for the high memory demands of biological data. Also part of the cluster are four high memory servers, one with 512 GB and 32 cores and three with 1TB of RAM and 24 cores. The system is expanded annually with additional computational nodes, disk space and memory to ensure that they are able to provide the bioinformatics support to any research partner, on or off campus.
To further enhance their capacity as a collaborative partner, BiSD has access to the resources of the Department of Bioinformatics and Genomics at UNC Charlotte’s main campus, less than 20 miles south of the NCRC, and supports research efforts there. This connection has led to several collaborations between NCRC researchers and researchers from the main campus of UNC Charlotte.
“Our whole focus is to be a service to this campus as well as the region and to help people with bioinformatics issues and challenges,” Brouwer said. “That’s why we are moving to building databases and doing programming to do more data integration and making more use of publicly available data so that we can go that next step in interpretation. We’re not just looking at the results of an experiment, but we’re able to look at the results in the context of what’s known in that domain. That’s the direction we’re going in.”
For more information, contact Cory R. Brouwer, director of the Bioinformatics Services Division and associate professor of Bioinformatics and Genomics at UNC Charlotte, at firstname.lastname@example.org.