Systems Biology Facility Core


Overview

The Systems Biology Facility Core (SBFC) 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. UNC continues to support access to the modern “omics” technologies and committs 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.

The SBFC provides the most efficient access to UNC’s expanded capabilities and integrate new resources in bioinformatics and is 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 (SBFC) 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.
  • Proteomics services include 1) identification of separated proteins from 1D and 2D gels, 2) molecular weight determination, 3) characterization of post-translational modifications such as phosphorylation, 4) identification of proteins in complex mixtures and 5) relative protein quantification of proteins in complex mixtures using stable isotope labels followed by 1D and 2D chromatography of peptides
  • 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.

Aim 2: Develop the Computational Biology Resource (CBR). The SBFC will coordinate with the BBFC to apply and develop advanced tools including:

  • Data mining of high-throughput omics data
  • Generation of biochemical networks based on omics data
  • 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 (SBRN), with three main functions.

  • Guide researchers toward the appropriate SBFC sub-core(s). The director of the SBRN will facilitate the interactions between the Director of Interdisciplinary Research, 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.

Personnel

Systems Biology Facility Core director:
Jeffrey M. Macdonald PhD; Department of Biomedical Engineering, UNC School of Medicine
Email: jeffrey_macdonald@med.unc.edu Phone: 843-1496
 
Genomics Sub-Core Director:
Michael Topal, PhD, Pathology and Lab Medicine; MED
Email: Michael_topal@med.unc.edu  Phone: 966-8208

Genomics Sub-Core Lab Manager:
Yan Shi, PhD, Comprehensive Cancer Center
Email: yan_shi@med.unc.edu  Phone: 843-7839

DNA Damage Sub-Core Director:
Jun Nakamura, DVM, PhD; DNA Repair Specialist
Email: ynakamur@email.unc.edu Phone: 966-6140
 
Biomarker Mass Spectrometry Facility Sub-Core Director:
Wanda Bodnar, PhD; Environmental Sciences and Engineering, SPH
Email: wanda_bodnar@unc.edu Phone: 966-2664

Biomarker Mass Spectrometry Facility Sub-Core Lab Manager:
Leonard Collins, Environmental Sciences and Engineering, SPH
Email: lbcollin@email.unc.edu Phone: 966-2664

Proteomics Sub-Core Director:
Lee Graves, PhD; Pharmacology, MED
Email: lmg@med.unc.edu Phone: 966-0915

Proteonomics Sub-Core Facility Director:
David Smalley, PhD; Pharmacology, MED
Email: dsmalley@med.unc.edu Phone: 966-8318

Metabolomics Sub-Core Director:
Jeff Macdonald, PhD; Biomedical Imaging, BME
Email: jmacdona@med.unc.edu Phone: 843-5154

Metabolomics Sub-Core Lab Manager:
Andrey Tikunov, PhD; Biomedical Engineering
Email: tikunov@email.unc.edu Phone: 260-7548

Anatomic Pathology Sub-Core Faculty Director:
C. Ryan Miller, MD, PhD; Pathology and Laboratory Medicine, MED
Email: Ryan_Miller@med.unc.edu Phone: 966-4333

Anatomic Pathology Sub-Core Facility Director: 
Nana Nikolaishvili-Feinberg, PhD; Lineberger Comprehensive Cancer Center
Email: nanan@med.unc.edu; Phone: (919) 966-9620
 
Funded by NIEHS Grant # P30 ES010126