Systems Biology Facility Core (SBFC)
Overview
The Systems Biology Facility Core (SFBC) brings together a wide array of advanced technologies available to CEHS researchers and provides the resources to assist investigators in the design and implementation of new studies to take maximal advantage of these powerful tools. The previous Biomarkers Facility Core facilitated access the modern "omics" technologies, and UNC has continued to support these efforts and committed extensive resources to insuring that state-of-the-art instrumentation is available in areas such as genomics, proteomics and metabolomics. These high-throughput methods have been extensively used by CEHS investigators to generate and test new hypotheses in the areas of environmental exposure and toxicology. To provide the most efficient access to UNC's expanded capabilities and integrate new resources in bioinformatics, the Biomarkers Facility Core is being upgraded to the SBFC, which will be closely integrated with the Biostatistics and Bioinformatics Facility Core (BBFC) and the Integrated Health Sciences Facility Core (IHFSC).
A systems biology investigation can generate a staggering amount of data. To address the need to analyze and integrate these data, the SBFC will work with the BBFC to develop the Computational Biology Resource (CBR). New investigators are easily overwhelmed by the rapidly advancing technologies in the systems biology world. To facilitate the translation of important biological questions into feasible systems biology research projects, the Systems Biology Research Network (SBRN) is being developed.
Goal and Specific Aims
The goal of the Systems Biology Facility Core is to provide easily accessible resources that enable CEHS investigators to unleash the power of advanced omics technologies for their research applications. The foundations of this goal are described in the following three specific aims.
Aim 1: Establish and Maintain the Systems Biology Sub-Core Facilities. CEHS investigators will have priority access to these six facilities, including reduced rates for services and support via pilot project grants.
- Genomics and Bioinformatics provides RNA measurements, gene expression analyses, micro RNA analyses and comparative genomic hybridization.
- DNA Damage provides DNA/protein extraction, abasic site assays and DNA response analysis using DT40 cell model systems.
- Biomarkers Mass Spectrometry provides highly specific and ultra-high sensitivity measurements of selected biomarkers including specific DNA and protein adducts. It also houses a QTOF mass spectrometer that will provide mass spectrometry-based metabolomic data.
- Proteomics performs identification of separated proteins and identification of proteins in 1 and 2D gels. Using mass spectrometric methods, molecular weight determination along with characterization of post-translational modifications such as phosphorylation and glycosylation are performed. Protein quantification is performed by differential gel electrophoresis using cy-dyes and 2D-PAGE along with differential isotope labeling.
- Metabolomics provides global and targeted metabolic profiling on a wide variety of biofluids along with cell and tissue extracts. Multivariate statistical analyses and pattern recognition tools are used to elucidate the critical metabolic perturbations. Analyses are performed using both NMR-based methods and MS-based methods in collaboration with the Biomarker Mass Spectrometry facility.
- Anatomic Pathology provides standard immunohistochemical staining assays along with more advanced quantitative tissue microarray analyses using digital imaging methods.
1. Data mining of high-throughput omics data
2. Generation of biochemical networks based on omics data
3. Mapping of altered genes, proteins and metabolites to metabolic pathways
The CBR will collaborate with RENCI scientists with expertise in advanced mathematics and extensive computing power to develop new tools for the visualization of data to facilitate biological interpretation and the generation of new hypotheses.
Aim 3. Develop the Systems Biology Research Network, with three main functions.
- Guide researchers toward the appropriate SBFC sub-core(s). The director of the SBRN will facilitate the interactions between the Research Navigator, Flexible Interdisciplinary Research Group (FIRG) investigators and the individual sub-core directors to rapidly develop research plans that make use of our extensive systems biology resources.
- Assist CEHS investigators by providing seamless interactions with the BBFC and the IHSFC, including the mammalian genotyping sub-core.
- Organize Systems Biology Group Meetings. The SBRN will organize a bi-weekly group meeting composed of research talks and journal club discussions to provide CEHS investigators with an informal training ground for advanced omics technologies. Sub-core directors will provide updates on facilities to encourage full utilization of the services offered.
Director, Members and Affiliates |
|
|---|---|
| SBFC Director: | Thomas M. O’Connell, PhD |
| Genomics Sub-core | |
Director: |
Michal Topal, Ph.D. |
Lab Manager: |
Yan Shi, Ph.D, |
| Technician |
Ling Li, MS, |
Technician |
Deying Zang, B.S. |
| DNA Damage Sub-core | |
Director: |
Jun Nakamura, D.V.M., Ph.D. |
| Biomarker Mass Spectrometry Facility Sub-core | |
Interim Director: |
Louise Ball, Ph.D. |
Research Analyst: |
Leonard Collins, BS, MBA, |
| Proteomics Sub-core | |
Director: |
Carol Parker, Ph.D. |
| Faculty Director: | Xian Chen, Ph.D. |
| Associate Director: | Maria Warren, Ph.D. |
| Metabolomics Sub-core | |
| Director: | Thomas M. O’Connell, Ph.D. |
| Laboratory Manager: | John Grimes, MS |
| Post-doctoral researcher: | Wimal Pathmashiri |
| Anatomic Pathology Sub-core | |
| Director: | Ryan Miller, M.D., Ph.D. |
| Laboratory technician | Courtey Boyd |