Core facilities description:

Institutional Infrastructure

The School of Medicine operates a number of core facilities that offer both advanced technologies and equipment. These facilities include the following (see http://www.cores.utah.edu for more information):

Biostatistics Cell Imaging DNA Sequencing Electron Microscopy Flow Cytometry

Genomics Tissue Histology Knockout/Transgenic Mouse Mass Spectroscopy Microarray/Bioinformatics

Nuclear Magnetic Resonance Oligonucleotide/Peptide Synthesis Protein Interaction (Biacore) Small Animal Imaging

The Core Facilities operate under a central administration headed by Dr. Jerry Kaplan, Assistant Vice President for Basic Sciences at the Health Science Center and Dr. Janet Lindsley, Associate Director of the Core Resources. Drs. Kaplan and Lindsley are assisted by Ms. Janet Bassett and Ms. Lin Wrathall. The Core Facility office is responsible for personnel and financial affairs. All of the Core facilities operate on a charge-back basis, although the percent recovery of operating expenses for each facility varies greatly. For example, the DNA Sequencing Core recovers all expenses, while other Cores such as NMR, Cell Imaging and Knockout/Transgenic Mouse are heavily (50-90%) subsidized by institutional resources. The goal of the Cores is to make technology and expertise available to all faculty members and students. The institutional view is that supporting core facilities is the single best way that institutional funds can be used to promote the University’s research mission.

While Drs. Kaplan and Lindsley administer the core facilities, they are overseen by a faculty oversight committee. The committee is composed of members of various departments at the School of Medicine, and meets on average twice/year.

Table 1. Membership of Core Oversight Committee, with departmental affiliations

name	title	department
Janet Lindsley, Ph.D. Committee Chair	Associate Professor	Dept. of Biochemistry
Frank Fitzpatrick, Ph.D.	Professor	Dept. of Oncological Sciences, Huntsman Cancer Institute
Alejandro Sanchez Alvarado, Ph.D.	Associate Professor	Dept. of Neurobiology & Anatomy
David Stillman, Ph.D.	Professor	Dept. of Pathology
Wesley Sundquist, Ph.D.	Professor	Dept. of Biochemistry
David Virshup, M.D.	Professor	Dept. of Pediatrics, Oncological Sciences, Huntsman Cancer Institute
Robert Weiss, Ph.D.	Professor	Dept. of Human Genetics
Dennis Winge, Ph.D.	Professor	Division of Hematology, Dept. of Biochemistry

The function of the committee is to evaluate the quality of existing cores, and to recommend both the creation of new cores and the termination of outdated or ineffective cores. This is accomplished in part by periodic surveys of faculty needs. The most recent survey was conducted in January 2004. The oversight committee also provides a venue for discussion of the operation of particular cores, free of conflicts of interest. Recommendations from the oversight committee are transmitted to Dr. Lorris Betz, Vice President/Dean of the Health Science Center.

DESCRIPTIONS OF THE INDIVIDUAL CORES:

The Biostatistics facility offers Ph.D.-level consultation for grant proposals, manuscripts and other research activities requiring biostatistical input. The available services include sample size and power calculations, the development of study designs and analysis plans, interpretation of analysis results and advice regarding optimal statistical software for a project.

The Cell Imaging facility provides training and consultation on the use of confocal microscopy, widefield automated microscopy, and software analysis tools for the deconvolution and quantitative analysis of image data. Two Olympus confocal microscopes (one FVX and one FV300) can be used with live or fixed samples. Sophisticated image acquisition and analysis regimes are possible, including time-lapse, z-series, ratiometric analysis, and deconvolution.

The DNA Sequencing core has a new state-of-the-art 96-capillary high-throughput DNA sequencer. The facility has a standard turn-around time of 1-2 working days, and offers discounted rates for samples submitted in 96-well plates.

The Electron Microscopy core provides investigators with a variety of electron microscopy capabilities and image analysis (quantitative morphology). Technical services offered by the core include transmission and scanning electron microscopy, histochemistry and immunohistochemistry.

The Flow Cytometry facility offers cell sorting and quantitative fluorescent measurements. The facility has a Becton-Dickinson Vantage cell sorter, a Union Biometrica “worm sorter” to fractionate C. elegans based on developmental stage, viability and expression of fluorescent proteins, and two FACscans.

The Genomics facility provides full-service genotyping, from PCR set-up through data analysis, for genome-wide scans, fine mapping, allelic imbalance (LOH), microsatellite instability, and SNP detection. The facility also offers real-time quantitative PCR access on the Applied Biosystems 7900 platform. Researchers rent the instrument on a per run basis and the core provides training as well as a copy of the data analysis software.

Tissue Histology

The Knockout/Transgenic Mouse facility includes a micro-injection/surgery room, pathogen-free animal rooms, a tissue culture facility, and a molecular biology laboratory. The core offers technical assistance for blastocyst injection procedures and maintains all transgenic mouse colonies in an isolated section of the vivarium dedicated for this purpose. The core maintains a full complement of genomic libraries, selectable markers, bacterial and phage vectors required for gene modification in mouse embryonic stem cells, and other rodent and human cultured cell lines.

The Mass Spectroscopy & Proteomics facility provides mass spectrometry services and consultation for both small molecule and protein analysis. The facility has a triple-quad MS/MS instrument with electrospray (ESI) ionization, a MALDI-TOF, a ThermoQuest LCQ Deca ion trap for LC/MS/MS, and a Sciex API-III ESI quadrapole mass spectrometer for small molecule analysis. Molecular mass measurements are made with typical errors of +/- 0.25 Da at M_r 1,000, or +/- 2 Da at M_r 25 kDa.

The Microarray facility helps researchers perform cDNA-based microarray experiments while the associated Bioinformatics facility aids in the experimental design and analysis of results. The microarray system consists of an Amersham BioSciences GEN III Array Spotter and a GEN III Array Scanner. The facility has a very large inventory of cDNA clones (>80, 000) from human, mouse, Drosophila, yeast and planaria. The facility has a new experiment management database to provide easy access to results, and is assembling gene annotations and software tools to allow the integration of gene expression data with other biological databases.

The Nuclear Magnetic Resonance facility helps researchers determine the structure of proteins, nucleic acids and natural products. The instruments available in the facility include a Varian Unity 500 MHz NMR, a Varian Inova 600 MHz NMR and a Varian Mercury 400. The facility also has several Sun and SGI workstations for offline data processing and biomolecular structure determination.

The Oligonucleotide/Peptide Synthesis facility provides synthetic peptides and oligonucleotides, with specific modifications as needed. Additionally, the facility performs Edman sequencing of proteins/peptides, including the identification of phosphorylation sites using this methodology.

The Protein Interaction (Biacore) facility provides characterization of the assembly state, affinity, and kinetics of macromolecular binding interactions. Currently, the facility has 8 SPR-based biosensors including the BIACORE 3000, 2000 and S51 optical biosensors. These instruments can be used to study interactions between proteins, oligonucleotides, oligosaccharides and lipids.

The Small Animal Imaging facility has a small animal computed tomography (CT) scanner for use with sacrificed or live animals. Uses include embryonic and adult specimen anatomy, bone mineral density, bone mineral content, bodyfat content, and angiogenesis index.