Duke University

Duke University is a private, academic research institution located in Durham, North Carolina. Duke enrolls approximately 6,600 undergraduate and 9,300 graduate students representing almost every state and many foreign countries.  The Duke Molecular Physiology Institute (DMPI) was founded in July 2013 as a consolidation of three pre-existing units: 1) the Sarah W. Stedman Nutrition and Metabolism Center located at the Duke Center for Living, 2) the Duke Center for Human Genetics, and 3) a group of clinical translational investigators. DMPI is organized into five functional areas that are based on its most prominent areas of expertise and competence: Basic Science Research; Metabolomics; Genomics and Epigenetics; Computational Biology; and Clinical Translation. Each section is primarily housed within the Carmichael Building, a state-of-the-art research facility created for Duke University Medical Center in 2013. 

Center for Living Overview

The Duke Center for Living hosts a number of health and wellness programs among five buildings located on a beautiful campus just two miles from nationally ranked Duke Hospital. Center for Living exercise facilities include a recently renovated 30,000 square-foot exercise facility with indoor saline pool, 1/12 mile indoor and 1/6 mile outdoor running tracks, private exercise studio, and over 100 pieces of exercise equipment. The Sarah W. Stedman Center for Nutritional Studies provides a space used for performing stable isotope infusion studies, euglycemic hyperinsulinemic clamps, IVGTTs, OGTTs, RMRs, BODPOD body composition assessments, muscle biopsies and other studies, as well as a Human Performance Laboratory with treadmills, an electronically braked cycle ergometer, ECG stress systems and metabolic carts (ParvoMedics). Led by Research Director William E. Kraus, MD, the Center for Living has been home to over a dozen moderate to large physiologic exercise training studies, screening 12,018, enrolling 1,444, and completing 1,045 participants in 14 detailed physiologic and exercise training interventions since 1999.

The Center for Living clinical facilities are staffed with physicians and over 50 staff that include exercise physiologists, nurses, physical therapists, physician assistants and nutritionists. The 14,000 square foot Sports Sciences Institute at the Duke Center for Living, has 18 patient examination rooms, a fully equipped nurses’ station (including emergency code team and defibrillator), X-ray room, and DXA scanner. An array of multidisciplinary Duke physicians hold clinic at the Center for Living to provide care related to: orthopedics and sports medicine, cardiology, neurology, general internal medicine, and other specialties. 

Carmichael Building Overview

The Carmichael Building is a two-story, 115,200 square foot, brick building, originally built in 1926 as a tobacco warehouse. Located approximately 2-3 miles from the main Duke campus, the interior of this historic building has been entirely remodeled as modern laboratory and office space. In addition to administrative space, freezer rooms, autoclaves, hazardous waste processing areas, and other utility space to support laboratory functions, approximately 76,000 square feet have been designated to serve eight defined research bays. Each research bay was constructed to provide contiguous laboratory and office space to meet the needs of a research team of approximately 25 individuals. Adjoining the open laboratory space in each research bay is approximately 2,200 square feet of specialized laboratory support rooms customized for the researchers in that bay (i.e. tissue culture rooms, cold rooms, fume hood rooms, instrumentation rooms, microscopy rooms, heavy equipment rooms, etc.). The remaining 4,100 square feet in each research bay contains the main connecting corridor for the building and an office suite typically composed of 5-6 private offices, cubicle space for 10-20 individuals, and a team meeting room. The Carmichael Building also houses a critical support unit for DMPI research operations known as the “freezer farm” – a specially designed 2,940 square foot air-conditioned space that contains two banks of upright 80°C freezers. Each freezer is monitored 24/7 by a wireless system allowing for the remote monitoring of critical parameters to ensure sample integrity. These freezers accommodate numerous precious biospecimens of great utility for musculoskeletal researchers such as serum, synovial fluid, and urine from well-characterized human cohorts, and waste tissues from joint replacement surgery and trauma consisting of cartilage, bone and synovial fluid samples. These freezers are used for the temporary storage of any project specimens during the period of their analysis.

DMPI Research Informatics

PEDIGENE® is a flexible, integrated system for managing the research informatics needs for hundreds of studies and includes large databases containing clinical, pedigree, molecular, and sample data. It is an internationally acclaimed computer data management system designed and licensed by Duke, utilizing a multi-layered security system to ensure participant confidentiality through all phases of a family and population study. The Oracle database server is housed in a FISMA compliant data center and study data are accessible only by study personnel at Duke as well as authorized collaborators outside of Duke. The system allows for the transfer of data to a wide variety of analysis program formats and then stores the analysis results. A data provenance solution, PEDIGENE® tracks all additions, deletions and changes of shared data along with the users making the changes and when. PEDIGENE® has already played a key role in localizing or mapping more than 50 genes involved in diseases and has been expanded to cover the research informatics needs of additional types of studies beyond just genomic.

Metabolomics Core Laboratory

The Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute have operated a purpose-built Metabolomics Core Lab for more than a decade that routinely participates in major clinical and basic science studies with DMPI, other Duke, and external-to-Duke scientists. The lab has five experienced, Ph.D.-level scientists working on method development, assay, and data analysis on a full-time basis.

DNA Bank

The Duke DNA Bank was originally created within the Duke Center for Human Genetics in the late 1980’s as a collaboration between several Duke investigators. The main function of the DNA Bank at that time was the immortalization and growth of lymphoblast cell lines from whole blood, and the extraction of DNA from those cell lines. Since then, the DNA Bank has grown into a facility that serves more than 50 principal investigators with active projects. There are several commercial BioBanks in the Durham area; however, such facilities provide sample storage only, and are not capable of many of the sample manipulations performed in the Duke DNA Bank. In addition to various sample storage options, the full range of services available through the Duke DNA Bank includes:

• Separation of plasma or serum from whole blood
  
  
• Storage of blood, bodily fluids, and tissue
  
  
• Extraction of DNA from blood, tissue, and saliva
  
  
• Extraction of RNA from PaxGene RNA tubes
  
  
• Quantization and quality testing of DNA and RNA
  
  
• Preparation of Guthrie blood cards
  
  
• Allocation of DNA and RNA, including normalization of concentration
  
  
• Custom robotic manipulation of DNA, RNA and other liquids
  
  

Molecular Genomics Core Facilities

Established in 1996, the Molecular Genomics Core (MGC) is a state of the art facility that offers a variety of experimental platforms to facilitate genomics research. The MGC has completed projects for more than 50 different investigators. The MGC primarily houses Applied Biosystems and Illumina instruments to perform genotyping, DNA re-sequencing, gene expression, methylation, and copy number variation experiments of all sizes.

A wide variety of assays are available in the MGC including the following:

• Focused uniplex SNP genotyping, real-time PCR, and High Resolution Melt analyses
  
  
• Focused multiplex SNP genotyping
  
  
• Genome Wide Association Studies (GWAS)
  
  
• Whole genome expression
  
  
• Whole genome copy number variation
  
  
• Focused DNA methylation profiling
  
  
• Whole genome DNA methylation profiling
  
  
• Next-generation sequencing applications