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.
Nuclear Magnetic Resonance Facility -- Jack Skalicky, Ph.D., Director
Mass Spectrometry & Proteomics Facility -- Chad Nelson, Ph.D., Director
Cell Fluorescent Imaging Facility -- Chris Rodesch, Ph.D., Director
Bioinformatics Facility -- Brett Milash & David Nix, Co-Directors
Microarray Facility -- Brian Dalley, Director
Genomics Facility -- Mike Klein, Manager
DNA Sequencing Facility -- Derek Warner, Director
DNA and Peptide Facility -- Robert Schackmann, Ph.D., Director
Electron Microscopy Facility -- Kurt Albertine, Ph.D., Director
Flow Cytometry Facility -- Wayne Green, Ph.D., Director
Protein Interaction Facility -- David Myszka, Ph.D., Director
The Metabolomics Core Facility -- James Cox, Ph.D., Director
Transgenic and Knockout Mouse Facility -- Susan Tamowski, Director
Centralized Zebrafish Animal Resource (CZAR) Facility -- Gretchen King, Ph.D., Director
Nuclear Magnetic Resonance Facility
Jack Skalicky, Ph.D., Director
This facility 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
This facility 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
This 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.
Bioinformatics Facility
Brett Milash & David Nix, Co-Directors
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.
Microarray Facility
Brian Dalley, Director
This facility provides researchers with access to the Affymetrix and Agilent Technologies microarray platforms and to Illumina Solexa sequencing technology. Combining support for Affymetrix and Agilent microarrays enables the facility to offer a diverse set of microarray tools for applications that include measurements of gene, exon, or miRNA expression, SNP identification, DNA copy number (aCGH), location analysis of DNA binding proteins (ChIP-on-chip), and DNA methylation status. The supported microarray platforms offer product lines with catalog arrays representing a wide variety of organisms and include options for the printing of custom microarrays. The facility also offers services for massively parallel DNA sequencing using Illumina Solexa technology. The Illumina instrumentation enables the facility to offer applications that include sequencing of genomic DNA, targeted areas of genomic DNA, ChIP DNA, digital gene expression, and small RNAs. This Facility is able to provide experimental handling of all aspects of the microarray and Illumina Solexa sequencing process. These services include evaluation of nucleic acid quality on an Agilent BioAnalyzer, labeling of samples with modified nucleotides (Cy dyes or biotin), microarray hybridization, microarray scanning, feature extraction and annotation of scanned images, Illumina library preparation, and sequencing of libraries on an Illumina Genome Analyzer. Services at the Microarray Facility complement those at the Genomics Facility below.
Genomics Facility
Mike Klein, Manager
This 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. Services at the Genomics Facility complement those at the Microarray Facility above.
DNA Sequencing Facility
Derek Warner, Director
This facility uses state-of-the-art capillary instrumentation to provide high volume, 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.
DNA and Peptide Facility
Robert Schackmann, Ph.D., Director
This facility 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.
Electron Microscopy Facility
Kurt Albertine, Ph.D., Director
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.
Flow Cytometry Facility
Wayne Green, Ph.D., Director
This 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.
Protein Interaction Facility
David Myszka, Ph.D., Director
This 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.
The Metabolomics Core Facility
James Cox, Ph.D., Director
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.
Transgenic and Knockout Mouse Facility
Susan Tamowski, Director
This facility is available to make transgenic mice using pronuclear injection of embryos as well as gene-targeting of ES cells and blastocyst injection. The Transgenic and Gene-targeting Core offers related procedures including sperm freezing, embryo freezing, rederivation of mouse lines, IVF, karyotyping, and has added new services including ICSI (intracytoplasmic sperm injection) and development of ES cell lines from your mouse line. We have successfully provided genetically altered mice to University of Utah researchers via frozen sperm and frozen embryos shipped from all over the world. The Core is available for technical advice regarding injection procedures, cell culture techniques, vector design and construction; and we are open to new ideas and available to try new methods that you are interested in. The Core maintains the necessary mouse colonies for basic procedures, including a colony of flp mice and EYFP mice. We maintain 129 ES cells as well as 129/C57Bl6 hybrid ES cells for gene-targeting.
Centralized Zebrafish Animal Resource (CZAR) Facility
Gretchen King, Ph.D., Director
This 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.
