NC State Receives $6.5 Million from NIEHS to Study Effect of Environment on Human Health

Researchers from North Carolina State University’s Center for Human Health and the Environment (CHHE) have received a five-year, $6.5 million grant from the National Institute of Environmental Health Sciences (NIEHS) to investigate the effects of environmental factors on human health.

The primary mission of the CHHE is to understand how human health, of both individuals and populations, is affected by environmental factors and to use this knowledge to prevent or reduce negative environmental impacts on health. Through interdisciplinary research and collaboration, the CHHE wants to construct a complete picture of how environmental stressors interface with pathways, the genome and epigenome.

The grant will be used to further the CHHE’s work by advancing interdisciplinary research in the field of environmental health and supporting community outreach and engagement regarding environmental health issues.

The NIEHS grant will make the CHHE one of 22 centers across the U.S. dedicated to studying environmental health impacts. “Through the purposeful interfacing of different disciplines, CHHE will build on NC State’s unique research and community outreach strengths to make significant contributions to understand and prevent the adverse impacts of environmental factors on human health” says Rob Smart, William Neal Reynolds Distinguished Professor of Biological Science at NC State and director of the CHHE.

The CHHE was founded in 2011 and brings together 70 investigators from 13 departments and six colleges at NC State and as well as investigators from East Carolina University, Brody School of Medicine, North Carolina Central University, NC Department of Health and Human Services, and RTI NIH Eastern Regional Comprehensive Metabolomics Resource Core.

Cross-population Study Links Individuals’ Chemical Sensitivity, Genes

Researchers from North Carolina State University and across the U.S. conducted the first large-scale cell-based screening to test variations in environmental chemical sensitivity across a range of human populations and link those variations to genetic data. The data will improve risk assessment, and shed light on the ways in which our genes interact with certain chemicals.  Testing chemicals for potential human health hazards involves large-scale programs that test hundreds of chemicals in vitro – by exposing a cell culture to differing concentrations of a chemical and recording various responses in hundreds of assays. However, these cell-based tests are usually derived from either rodents or a small sample of humans.

Current NCSU Bioinformatics Research Center Director, Fred Wright and Texas A&M professor of veterinary integrative biosciences Ivan Rusyn, while both on faculty at UNC-Chapel Hill, partnered with the researchers at the National Institute of Environmental Health Sciences and National Center for the Advancement of Translational Sciences to conduct this large-scale experiment. They obtained cell lines from 1,086 individuals who had volunteered their genetic data as part of the 1,000 Genomes Project. The cell lines represented nine different genetic populations spread over five continents. They then exposed cells to 180 different chemicals at eight different concentrations each.

The data revealed that, for some chemicals, the range of sensitivity among individuals was greater than previously thought. The NC State team, including faculty members Alison Motsinger-Reif and Yi-Hui Zhou, was instrumental in discovering several genetic variations that correlated to chemical sensitivity. Most of the genes involved are associated with the way foreign substances get transported across cell membranes.

‘This broad, cross-disciplinary academic-governmental partnership is a model that will fuel important discoveries in environmental health and biomedical sciences,” Rusyn says. “We are very grateful to all who committed time, effort and resources to this important undertaking.”

“This is a great first step,” Wright says, “but ultimately we want to match other biological data and the chemical structures, to find out why genetic differences affect toxicity of some chemicals but not the others. In addition to giving us more personalized information about chemical dangers and helping us determine safe exposure levels for these substances, the data could help us design safer chemicals for everyday use.”

 

Spotlight on the Bioinformatics Consulting and Services Core: The UNC-NCSU Superfund Research Program

The Bioinformatics Consulting and Services Core (BCSC) has received a subcontract to partner with the UNC Superfund Research Program to provide assistance in biostatistics and bioinformatics, starting with the 2014-2015 grant year.  BCSC staff members Elizabeth Scholl, Ph.D., and Allison Dickey, Ph.D., provide consulting assistance to Superfund investigators at UNC-Chapel Hill and NCSU, under the direction of Superfund Bioinformatics leader Fred Wright, Ph.D.  “The BCSC provides important infrastructure to the Superfund Research Program, as well as a combination of expertise in biostatistics and bioinformatics,” says Wright.  Adds Dr. Alison Motsinger-Reif, Director of the BCSC, “this is the sort of partnership that benefits both NCSU and UNC, maximizing efficiency by combining our collective talents.”

The UNC Superfund Research Program (UNC SRP) seeks to understand the human health and environmental risks associated with exposure to toxic chemicals found at hazardous waste sites (sph.unc.edu/superfund-pages/srp/).  Research projects span biomedicine and engineering approaches in environmental sciences, with principal investigators across both institutions.

 

 

BRC investigators played an active part in the kickoff workshop for the Beyond Bioinformatics

BRC investigators played an active part in the kickoff workshop for the Beyond Bioinformatics [http://www.samsi.info/programs/2014-15-program-beyond-bioinformatics-statistical-and-mathematical-challenges-bioinformatic]

program organized by the Statistical and Applied Mathematical Sciences Institute (SAMSI), and will be playing key roles in the program throughout the 2014-2015 academic year. SAMSI, located in the Research Triangle Park, is the only research center funded by the National Science Foundation to advance the discipline of statistics.   The convergence of statistical and biological sciences, along with SAMSI activities, make this an especially intellectually rich time for bioinformatics at N.C. State.    The year-long program “Beyond Bioinformatics: Statistical and Mathematical Challenges” includes working groups on a variety of topics, including statistical issues that arise in evolutionary inference and analysis of Big Data.

The “Dependence in Evolutionary Models” working group includes N.C. State bioinformaticians Xiang Ji, Chris Nasrallah, Jeremy Ash, and Jeff Thorne.   Additional organizers include N.C. State mathematician Seth Sullivant, and Duke statistician Scott Schmidler. The working group has also brought in internationally acclaimed visitors, including Jotun Hein (Oxford University), David Pollock (University of Colorado Denver), Richard Goldstein (University College London), and Ziheng Yang (University College London).  Professors Hein, Yang, Sullivant, Schmidler, and Thorne are teaching a related graduate course on statistical molecular evolution at the SAMSI facility in Fall 2014. The evolution working group is concentrating on two questions: 1. How can evolutionary inferences be made when changes at one position in a DNA sequence influence the rate of changes at other positions?; and 2.  Which evolutionary scenarios can and cannot be disentangled by making inferences from DNA sequence data?

The “Multiple Hypothesis Testing and Simultaneous Inference” working group is organized by Yi-Hui Zhou and Fred Wright from the BRC, with graduate student fellow Ajay Kumar from the NCSU department of Statistics.  The working group is inspired by the critical need to perform false positive control in the presence of large numbers of statistical tests. Related problems are posed by the desire to perform inference on effect sizes for numerous parameters, such as effects of SNPs on disease risk, etc. This working group will consider current work on multiple testing and simultaneous inference, considering complicating situations posed by new technologies or special sampling situations.

BRC researchers play key role in new grant to improve sweet potatoes in sub-Saharan Africa

The Bill & Melinda Gates Foundation recently announced that it has awarded a $12.4 million grant to North Carolina State University to develop genomic tools for the improvement of the sweet potato, which is an important staple in several African countries. The grant provides funding for genomic and bioinformatics tool development, as well as new data to help improve drought and pest resistance. Led by principal investigator Dr. Craig Yencho in the NCSU Department of Horticulture, the NCSU team includes BRC researchers Drs. Zhao-Bang Zeng and Dahlia Nielsen, and other investigators at NCSU and several partner universities.

The grant draws on the wide range of expertise in statistical genetics and bioinformatics at NCSU. Dr. Zeng’s group will develop tools in for mapping important traits, while Dr. Nielsen will oversee transcriptomic assembly and related bioinformatics development.

See the full news release [http://news.ncsu.edu/2014/09/nc-state-receives-sweet-potato-grant/] for more details.

North Carolina State University’s Bioinformatics Research Center Launches New Website

North Carolina State University is very excited to announce the launch of our newly redesigned website for our Bioinformatics Research Center. Our new site was designed and built by TheeDesign Studio, a full service web design and internet marketing company in Raleigh, North Carolina. The new site is built on WordPress, a very user-friendly content management system. It allows our team to easily add and update content, image and video. It also allows us to add new pages and blog posts at any time without the help of a developer. Some of our favorite features on our new website are:

WordPress Website with Custom Design and User Friendly Interface

Our team at the NCSU Bioinformatics Center finds the WordPress platform to be intuitive and simple, making our new site easy to update and manage. Our homepage, research page, program information, and events pages are presented clearly for visitors to our site. Aside from the ease of the front end layout, WordPress features a back end that is just as easy and user friendly. Within just one hour of training, TheeDesign Studio taught our team how to update content, post blog entries, upload videos and photos, and manage job postings.

Responsive Web Design for User-Friendly Viewing on Mobile and Tablet Devices

The responsive design feature is one of our new and exciting features we’ve added. Responsive web design allows a site to respond and adapt to devices according to the orientation of our visitor’s screen size and resolution. This means that our visitors can view our website on various mobile platforms like their smartphones and tablets. This allows easier access to our website and information from anywhere for students, teachers, and prospects interested in our program.

Available Job Postings for Staff and Postdoctoral Positions

Our “Available Positions” page allows interested individuals to browse and apply for available positions at the staff and postdoctoral levels. Visitors to our site are able to see open positions as well as information about living in Raleigh and working at NC State University. The page allows quick and easy access to jobs in our Bioinformatics Research Center.

Onsite Bioinformatics Research Center Blog

Our newly designed website features an on-site blog, allowing our NCSU Bioinformatics team to show off all of their hard work done in the research center, while providing the Raleigh community with reliable information about the university’s department and programs. Our blog is easy and simple for our team to update and helps position our bioinformatics program as a valuable asset to the North Carolina community for research and education. We’re very excited about our newly designed site! We invite you to visit and see it for yourself. Don’t forget to check out our blog to see the latest news in our work and findings at NC State’s Bioinformatics Research Center and check out our graduate programs if you are interested in being a part of our team.

If you are interested in custom web design or internet marketing, please visit our friends at TheeDesign.com or call 919-341-8901.