Core Facilities
The School of Medicine and the Huntsman Cancer Institute have provided the support to develop a number of shared Core Facilities. These facilities provide a variety of advanced technologies and capabilities to researchers affiliated with the Program in Molecular Biology. A list of the Core Facilities presently in operation and a summary of their specific capabilities follows.
Transgenic and Knockout Mouse Facility
Protein Interaction Facility
Biostatistical Resource Facility
Cell Fluorescent Imaging Facility
Centralized Zebrafish Animal Resource (CZAR) Facility
DNA/Peptide Synthesis Facility
DNA Sequencing Facility
Genomics Facility
Electron Microscopy Facility
Flow Cytometry Facility
Metabolomics Core Facility
Microarray Bioinformatics Facility
Microarray Facility
Nuclear Magnetic Resonance Facility
Small Animal MRI Imaging & Computed Tomography (CT) Scanner Facility
Mass Spectrometry & Proteomics Facility
DNA/Peptide Synthesis Facility
Robert Schackmann, Ph.D., Director, bob.schackmann@cores.utah.edu
This core offers investigators synthetic peptides for use in generating antibodies; and it also provides oligonucleotide synthesis services for use as primers in PCR experiments, hybridization studies, and for DNA sequencing. This core also offers Edman protein/peptide sequencing.
Flow Cytometry Facility
Wayne Green, Ph.D., Director, wayne.green@cores.utah.edu
The Flow Cytometry Facility offers quantitative, multiparameter florescent analysis and cell sorting services to the research community. Two modified Becton-Dickinson FACScans (two laser, 5 color) and a FACSCanto II (three laser 8 color) analyzers are available for user operation or core-operated service. A FACScans is located in a satellite lab on the 3rd floor of the Huntsman Cancer Institute, bench 3-O. Trained users may access the analyzers in the Core Facility after hours and on weekends with their university ID card. Cell sorting services are provided by the core staff on a FACSVantage SE Turbo high speed cell sorter which has three excitation lasers (UV, 488nm and 635nm) and 7 fluorescence detectors. Sorted cells may be collected in bulk (tubes) or deposited in defined numbers of cells/well in a microtiter or other culture plate. Flow cytometry specific data analysis software (FCS Express 3 by De Novo Software) is available on-line for the analysis of data files in addition to off-line software (WinList, ModFit and QuantiCalc by Verity Software) located on a workstation in room 603 of the Facility.
Nuclear Magnetic Resonance Facility
Jack Shalicky, Ph.D., Director, shalicky@biochem.utah.edu
The Biomolecular NMR Center exists to facilitate the determination of protein, nucleic acid, and natural product structures and to provide analytical NMR services to the Health Sciences community. Instrumentation includes a Varian Mercury 400, Inova 500, and Inova 600 NMR spectrometers. The Inova 600 is equipped with a triple resonance cryogenic probe. The NMR center also has several SGI and Dell Linux workstations for offline data processing, analysis, and structure calculations. Instrument schedules, rates, detailed instructions for using the facility are available on the website.
Mass Spectrometry & Proteomics Facility
Chad Nelson, Ph.D., Director, cnelson@genetics.utah.edu
This core provides mass spectrometry services and consultation for the campus community, as well as other academic institutions and biotech companies in the regional area. While the primary emphasis of the core is geared toward proteomics research, the facility continues to provide basic support for a broad range of research and sample types, such as natural products, small synthetic molecules, and large intact biopolymers. The facility is equipped with several high-performance mass spectrometers, including a new state-of-the-art FTMS (LTQ-FT, ThermoElectron), with both ESI and Maldi ionization capabilities. Of particular importance for proteomics applications, the FTMS instrument provides high sensitivity (sub-femtomole), high resolution (>500,000), and high mass accuracy (<2ppm), affording greater sequence information and high confidence for protein ID. The FTMS is well equipped, with CID, IRMPD, and ECD fragmentation techniques for mapping modifications. LC/MS/MS instruments have nano-LC, for ultimate sensitivity and chromatographic performance. A range of Proteomics services include: protein ID from in-gel or solution digests by LC/MS/MS, FTMS, or Maldi/ToF; Complex protein sample ID; post-translational modifications; and in-house custom Mascot and Sequest database searching; FTMS and ESI/MS for accurate intact protein measurements to 150kDa MW.
Cell Fluorescent Imaging Facility
Chris Rodesch, Ph.D., Director, crodesch@cores.utah.edu
The Cell Imaging Facility provides training and consultation on the use of confocal microscopy, widefield automated microscopy, and software analysis tools for quantitative analysis of image data. The facility has two Olympus FV1000 Spectral confocals, two FV300 confocals a BD Pathway Confocal Bioimager and a custom 2-Photon confocal. We have also added a new Nikon AR1 fast scanning confocal for live cell imaging. Automated microscopes with on of five different stage incubators are available(C02, temp., humidity) are also available for live cell imaging. Metamorph, Imaris and Volocity software are available for 2D and 3D analysis of image data. Custom Image processing using Matlab is also available. Webpage:cellimaging.org
DNA Sequencing Facility
TBN, Director, dna@cores.utah.edu
The DNA Sequencing Facility uses state-of-the-art capillary instrumentation to provide high throughput, low cost sequencing services to the University community. The facility offers custom sequencing of plasmid DNA, PCR products and large insert templates such as cosmids and BACs. The facility also offers complete single or double strand coverage of cloned DNA by primer walking and contig assembly. By utilizing a specialized laboratory information management system, the core offers electronic sample submission and data distribution, usually within 48 to 72 hours of sample submission.
Genomics Facility
Mike Klein, Manager, dna@cores.utah.edu
The Genomics Facility provides a cost effective, high throughput genotyping and fragment analysis service to the University community. The facility utilizes fluorescent PCR technology and state-of-the-art capillary instrumentation to collect and analyze genotypes from human and mouse DNA samples. Technical services include genome scans, fine mapping, microsatellite instability (replication error), allelic imbalance (loss of heterozygosity) and single nucleotide polymorphism detection. Capillary runs are available for labs with fluorescently labeled PCR products. The facility has two high throughput real-time PCR instruments in 96-well and 384-well formats available for all researchers studying gene expression. The instruments can also perform SNP genotyping using TaqMan assays. Medium throughput SNP genotyping is available using Illumina’s Golden Gate Assays and the BeadXpress platform and is cost effective for genotyping hundreds of samples and hundreds of SNPs. Mutation detection services are available for those screening samples for SNPs, insertions, and deletions.
Transgenic and Knockout Mouse Facility
Susan Tamowski, Director, tamowski@genetics.utah.edu
The facility is available to make transgenic mice using both pronuclear injection of embryos and gene-targeting of ES cells and blastocyst injection. A new tissue culture/electroporation lab has recently been built to complement the existing microinjection/surgery room and animal room that are currently located in HCI. The core offers technical advice regarding injection procedures, cell culture techniques, vector design and construction; and maintains the necessary mouse colonies for these basic procedures. The Transgenic and Gene-targeting Core also offers related procedures including sperm-freezing, rederivation of mouse lines, IVF, and karyotyping.
Protein Interaction Facility
David Myszka, Ph.D., Director, dmyszka@cores.utah.edu
The Protein Interaction Facility provides easy access to advanced technologies used in characterizing binding interactions. Currently BIACORE 3000, 2000 and S51 optical biosensors are used to define the assembly state, affinity, and kinetics of an interaction. The advantage of optical biosensors is that they allow real-time analysis of molecular interactions without labeling requirements. This makes the technology applicable to the study of a wide variety of biological molecules including proteins, oligonucleotides, oligosaccharides and lipids.
Electron Microscopy Facility
Kurt Albertine, Ph.D., Director, kurt.albertine@hsc.utah.edu
This facility provides a variety of microscopy services to the basic science and clinical communities. Services and technical capabilities include preparation of specimens for light and electron microscopy, specimen observation and image capture for light microscopy (brightfield, fluorescence, differential interference contrast, etc.), and specimen observation and image capture for transmission and scanning electron microscopy. Other specialized techniques that are available are quantitative morphology (image analysis), histo/cytochemistry, and immunohisto/cytochemistry at the light and electron microscope levels.
Microarray Facility
Brian Dalley, Director, brian.dalley@hci.utah.edu
The Microarray Core Facility provides a comprehensive tool for microarray analysis through access to the Agilent platform. Agilent arrays have a maximal density of 244,000 features per slide. Features consist of a 60-mer oligonucleotide sequence, synthesized in situ on a chemically modified glass substrate using an ink jet printing process. The Agilent platform provides catalog gene expression, cgh, and/or ChIP-on-chip arrays for many organisms including human, mouse, rat, canine, C.elegans, zebrafish, Xenopus, Chick, monkey, yeast, and Arabidopsis. The flexibility offered by inkjet technology enables Agilent to print custom designed microarrays with no additional set up charges.
The Microarray Facility provides experimental handling of all aspects of the microarray process. Services include evaluation of nucleic acid quality on an Agilent BioAnalyzer, labeling of samples with Cy dyes, microarray hybridization, microarray scanning, and feature extraction/annotation of scanned images. The facility has acquired key pieces of instrumentation for performing this process including an Agilent Bioanalyzer, a Nanodrop spectrophotometer, Agilent hybridization systems, an Agilent scanner, and Agilent Feature Extraction software.
Bioinformatics Facility
Brett Milash, Director, brett.milash@hci.utah.edu
This facility can assist you with microarray experiment design, next-generation sequencing analysis, data analysis methods selection, data visualization, and choice of analysis software. A variety of analysis software tools is available through this facility, including GeneSpring, GeneSifter, Spotfire, Agilent CGH Analytics, T2, IGB, and Bioconductor. The facility’s staff can also assist with the design of custom microarrays, annotation of custom or commercial arrays, grant support, and access to public microarray databases.
Biostatistical Resource Facility
Rich Holubkuv, Ph.D., Director, rholubkuv@hrc.utah.edu
This facility offers consultation to the research community regarding biostatistical issues. Services include sample size and power calculations, development of study designs and analysis plans for research grant submissions, consultation regarding analysis of existing study data, interpretation of analysis results, and advice regarding optimal statistical software for a project.
Metabolomics Core Facility
James Cox, Ph.D., Director, jcox@cores.utah.edu
This facility is bridging the knowledge gap between phenotype and small metabolites. To perform this task the Core has purchased a MicroMass GCT Premier, a highly accurate time of flight mass spectrometer mated to a gas chromatograph (GC-MS). This instrument is able to analyze the small molecules involved in cellular metabolism in a qualitative fashion and is primarily used in the discovery phase of metabolomic analysis. The Core recently purchased another GC-MS, a Thermo Trace gas chromatograph with a TSQ triple quadrupole mass spectrometer serving as the detector. This instrument will be used in the quantification of metabolites that were found in the discovery phase. For metabolomic profiling of biofluids by nuclear magnetic resonance (NMR) the Core has purchased the Chenomx software suite. This software allows for the identification and quantification of common metabolites found in biofluids. The Metabolomics Core Facility focuses solely on the analysis of small metabolites. Within this mission several types of services are provided including: experimental design, sample preparation; instrumental analysis, assistance in data analysis.
Centralized Zebrafish Animal Resource (CZAR) Facility
Gretchen King, Ph.D., Director, gking@cores.utah.edu
The CZAR Facility provides state-of-the-art systems for housing, breeding, and doing experiments with zebrafish, an emerging vertebrate model system. It comprises 6000 fish tanks and redundant circulating water systems, and houses a large number of wildtype and mutant fish strains. It allows large genetic screens carried out as collaborations between multiple laboratories, and can provide animals and training for laboratories wishing to try pilot zebrafish experiments.
Small Animal MRI Imaging & Computed Tomography (CT) Scanner Facility
Edward Hsu, Ph.D., Director, edward.hsu@utah.edu
The Small Animal Imaging Facility extends the benefits of modern diagnostic medical imaging systems to the studies of anatomy and physiology in small animals. The Facility currently features state-of-the-art Bruker BioSpec 7.1 T horizontal-bore MRI and General Electric EVS-RS9 micro-CT scanners, both equipped with supporting and monitoring hardware that allows a wide variety of imaging experiments to be performed on live animals and specimens. Imaging scientists and full-time imaging and animal support technicians are available for technical consultation and experimental assistance. Because of the complex nature of animal imaging and that new technologies are continually being developed, potential users are asked to first contact the Facility Director for most up-to-date scanner capabilities and an assessment of experimental feasibility.
The Small Animal Computed Tomography (CT) Core has a scanner for use with sacrificed or live animals. This scanner can be used to differentiate bone from tissue/water from fat from air. Scanned areas of 88 x 88 x 43 mm can be reconstructed into 2- or 3- dimensional images at resolutions of 27 – 93 micron resolution (living animals are scanned at 46+ microns). With use of enteral (oral) barium or intravenous iodine contrast agents, other structures such as the gastrointestinal tract or the vascular system can be visualized. Without contrast, only skeletal structures can be seen with detail. Limitations include the inability to see texture in soft tissue, and the unavoidable delivery of small to moderate doses of radiation to the animal. Investigators can at this time have sacrificed animals scanned.
High Performance Computational Resources
Julio Facelli, Ph.D., Facility Supervisor
In addition to dedicated computational resources for biological chemistry research programs available in specific labs and departments, the Center for High Performance Computing (CHPC) provides training, software, and access to high performance computational resources or the larger campus community. Currently available hardware resources include an 8-node (32 processor) Compaq Sierra cluster with a QUADRIX switch and the Icebox cluster of ~303 nodes (388 processors) of Intel and AMD processors. Additional specialized servers are available for specific applications like large-scale statistics, molecular modeling, Genbank searches, etc. During the summer of 2003, a large NIH and University of Utah funded metacluster for bioinformatics ($2,000,000) came online. This includes a series of interconnected cluster computers including a high performance parallel cluster, a data-mining cluster, a visualization cluster, and a cycle farm. In addition, this metacluster integrates significant online storage capacity. In addition to hardware and software resources, the CHPC also provides advanced visualization capabilities including an AccessGrid node (allowing realtime video conferences to other AccessGrid nodes throughout the world) and training. For more information, see www.chpc.utah.edu.