BIDAC is a health science core facility providing advanced image analysis, data science and scientific visualization services to research laboratories and private industry. Our areas of expertise include machine learning, deep learning (AI), medical computing, scientific visualization, data science, data analytics and data engineering. These application-oriented consulting services leverage the expertise of the Scientific Computing and Imaging (SCI) Institute, an internationally recognized leader in visualization, scientific computing and image analysis applied to a broad range of domains.
We have been developing and applying novel services, currently in use via multiple collaborations. By leveraging software and hardware infrastructure, this includes the creation of a big data engineering workflow for radiology imaging, enabling secured data transfer, database archiving and data management of large datasets. We also have expertise in artificial intelligence, applying, comparing and fine-tuning state-of-the-art neural networks to perform robust imaging data classification, regression and segmentation tasks. In addition, we also offer training and support for various innovative and robust software packages, developed at the SCI Institute and broadly available to the scientific community under open-source licensing.
By helping collaborators turn data into insights, BIDAC complements existing core services, enhancing health science research capabilities and fostering collaborative multidisciplinary activities.
The Fluorescence Microscopy Facility provides training and consultation on the use of confocal microscopy, widefield automated microscopy, and software analysis tools for quantitative analysis of image data. There are four convenient locations convenient to the School of Medicine (HSC), Huntsman Cancer Institute (HCI), Sorensen Molecular Biology and the Crocker Science Center (CSC). Three full time Ph.D. level staff and a technician are available for consultation, training and to maintain the equipment. Our annual user base spans >300 unique users who log >12,000 hours of usage and > 150 individual PIs at the Medical Center, Liberal Arts College and Engineering school.
Facilities and Instrumentation: These locations have 9 confocals between them, including; two Leica SP8s, two Nikon A1s, two Olympus FV1000s, two Bruker Ultima 2-Photon confocals and a Zeiss 880 Airyscan Confocal. Automated microscopes with stage incubators are available (C02, temp., humidity) in three locations, and are available for live cell imaging (Nikon Ti HSC, Nikon Ti HCI, Olympus IX81 CSC). Metamorph, Nikon Elements, Imaris, Leica, and Zeiss Zen software are available for 2D and 3D analysis of image data. Users can be trained in analysis and or custom Image processing using Matlab is also available.
As an integrated part of the Core Facilities Department, Fluorescence Microscopy can support current multidisciplinary research and facilitate the preliminary stages of new investigations. Since being established in 1999 the Fluorescence Microscopy facility has grown to support a broad range of research at the School of Medicine, College of Engineering, Pharmaceutics and Liberal Arts. Integrating equipment, training, education and expertise helps maximize the impact of capital equipment and facilities and ensures our users have the expertise to effectively leverage the resources that the core facilities provide.
Facility provides investigators with standard and specialty oligonulcleotides and peptides. Specialty modifications include chromophore labeling, functional group modifications, and modified bases/amino acids. These synthetic products are used in a wide range of biochemical, molecular, and clinical applications. For example, primers and probes necessary for Q-PCR and synthetic peptides serving as antigens in ELISPOT assays are important tools to monitor immune responses from blood samples.
Laboratory: The DNA Sequencing and Genomics Core laboratories are co-located in 2500 sq. ft. on the second floor of building 585. We have dedicated clean space for master mix preparation that contains one class II/A2 hood, a larger general lab area where all sample manipulations take place that precede any PCR steps, and a dedicated post PCR space where PCR occurs and any manipulation of amplicon (including running gels) occurs. This setup is to minimize any possibility of amplicon contamination in our molecular testing. The general lab area contains everything needed for general molecular biology needs. This includes various centrifuges (both tube and plate spinning versions) as well as water baths, dry baths, a liquid handling robotics system (BioMek FXp), as well as other various minor lab devices required in a standard molecular biology laboratory. The PCR area has numerous thermocyclers to support varying PCR experiments or Next Gen Sequencing (NGS) library building as well as array runs. This area contains all the typical equipment needed for molecular biology experiments including centrifuges, pipettes, and a class II/A2 hood for use when opening PCR plates to further help contain PCR amplicon contamination. There is also an Illumina iScan array reader and there are real-time PCR instrumentation to support labs needing to run their samples using this methodology as well as two computers dedicated to customer use for analysis and setup of such plates. The PCR space also contains the Applied Biosystems 3730xl that is used for Sanger sequencing as well as fragment analysis pipelines.
Major Equipment DNA Sequencing and Genomics :
- Applied Biosystems 3730xl DNA Analyzer. This instrument remains state of the art for capillary electrophoresis and is also very useful for fragment analysis with down to 1bp resolution. This instrument has been a workhorse in sequencing and genomics for approximately 30 years and doesn’t appear to be showing any signs losing its usefulness.
- Oxford Nanopore P2Solo (coming). This instrument has recently been acquired by the core. It is capable of running up to two full human genomes per run using long sequencing chemistries from Oxford Nanopore Technologies. The read lengths will vary depending on the DNA quality provided, but the longest single read on ONT platforms to date is 4.2 million bases in one read. The vast majority of runs target sizes more in the range of 10-50kb per read and therefore produce more reads per run. In addition to returning sequence of the sample, the instrument is also capable of providing methylation state of the DNA using a modified base caller available for the system.
- Oxford Nanopore MinIon. This instrument is a much smaller version of the ONT platform and is capable of running smaller runs such as plasmid sequencing, small genomes (bacterial for example) with all the same benefits of the larger P2Solo.
- Agilent Fragment Analyzer. This instrument is generally used for QC of NGS libraries or quality of DNA or RNA extractions including size distributions. Various kits are available that can cover from only a few hundred bases size range to around 50kb DNA fragments.
- Illumina iScan. This instrument has been in use running any Infinium arrays that Illumina produces for multiple years. Although sequencing is becoming cheaper over time, arrays are still frequently used for screening large numbers of samples that would be cost prohibitive using sequencing at this point in time. Arrays exist to cover things from GWAS studies to targeted panels focused on individual diseases.
- Applied Biosystems QuantStudio 12k Flex. These two instruments are the workhorses for real-time PCR runs in the core. In addition, with a simple block change, these instruments can also run Open Array (a smaller for of array testing owned by ThermoFisher that allows targeting of much smaller numbers of genes than available by the Illumina platform).
- Element Biosciences AVITI. This sequencer is the newest addition to our DNA Sequencing Core. This is a mid-sized sequencer capable of yielding up to 2-2.4 billion reads at once. It can be used to support any type of short read sequencing currently in use. The chemistry is distinct from the predominant Illumina chemistries and yields on average higher quality base calls. In addition it is able to maintain base quality even after repetitive regions (a known issue with Illumina chemistries). Cost/Gb is very similar to the Illumina NovaSeq 6000 S4 flow cells.
Shared equipment: We have access to an autoclave and ice maker for our building as well.
Drug Discovery Core
Laboratory: The Drug Discovery Core at the University of Utah provides University researchers access to small molecule libraries for screening, to equipment for automation, and to synthetic chemistry support for the characterization and validation of compounds for potential use as therapeutics, diagnostics and biological tools. The Core currently offer the following services: high-throughput screening; small molecule chemical libraries (230K compounds); CRISPR-Cas9 libraries; CRISPR gene editing service; Viral packaging service; assay development; consultation on target identification/validation, hit to lead optimization, PK/PD/Efficacy; chemical support for drug discovery; synthetic chemistry support; and follow-up assays on hits.
The Drug Discovery Core laboratory occupies 1020 sq. ft. on the third floor of the College of Pharmacy. It is a centralized, staffed facility, and houses instrumentation and robotics required for high-throughput screening. The laboratory contains all the equipment necessary to perform experiments for early stages in drug discovery process including bench top centrifuges, high speed centrifuge, sonication baths, heat blocks, -20°C freezers, 4°C refrigerators, and a chemical hood. The laboratory also has a separated, certified BSL-2 plus cell culture room, which has a cell culture incubator, cell culture biohood, water bath, and a fluorescence microscope.
Automated Sample Handling Stations:
- Tecan EVO100/MCA96 Liquid Handler with sterile bio-hoods
- Tecan EVO100/MCA384 Liquid Handler with sterile bio-hoods
- HP D300 Digital Dispenser – capable of generating dose response curves which eliminates serial dilution by offering picoliter to microliter non-contact dispensing of small molecules in DMSO directly into assay plate.
- KingFisher Duo Prime System – Automated DNA/RNA Extraction and Protein/Cell Purification
Automated Detection Systems:
- ImageXpress XLS Automated High-Content System: capable of providing automated cellular imaging in fluorescent modes for fixed- or live-cell assays
- Bio-tek Plate Reader with stacker: capable of high-throughput reading of fluorescence, luminescence and absorbance at any wavelengths.
University of Utah Electron Microscopy (EM) Core Laboratory prepares and images specimens by transmission or scanning EM and can also do two- and three-dimensional image processing. The lab specializes in biological EM, but has also worked with non-biological samples. The EM Core Lab also trains users in sample preparation, microscope use, and image analysis.
Facilities and Instrumentation and Services: The EM Core Laboratory is well equipped with six transmission electron microscopes, one scanning electron microscope, and preparation equipment. The Sorenson Molecular Biotechnology Building houses two transmission electron microscopes (TEMs): one JEOL JEM1400-Plus (120 kV) and one ThermoFisher Tecnai 12 (120 kV). A Hitachi H-7100 TEM (125 kV) is housed in the Radiobiology Laboratory Building, and another Hitachi H-7100 TEM is housed in the Biology Building. Gatan Orius or Ultra Scan cameras are found on the Hitachi, JEOL, and T12 microscopes. A ThermoFisher Tecnai F20 TEM (200kV) and a ThermoFisher Titan Krios TEM (300 kV) are located in the Crocker Science Center. The Tecnai F20 is equipped with a Gatan K2 Summit direct electron detector. The Titan Krios is equipped with an autoloading stage, Gatan energy filter, phase plates, and Gatan K3 direct electron detector. A Zeiss GeminiSEM 300 is available in the Crocker Science Center. The EM Core Lab is equipped for cryogenic TEM. All three ThermoFisher TEMs are equipped for cryo-TEM. Three Gatan 626 cryoholders are available for the Tecnai 12 and TF20 microscopes. An FEI Vitrobot vitrification robot is located in the Sorenson building. The lab has six ultramicrotomes for thin-sectioning work: one Leica UC7, three Leica UC6, one Leica UCT, and one Reichert-Jung Ultracut E. A sample preparation lab is housed in the Sorenson Building and contains equipment for preparing plastic-embedded, negatively stained, or cryogenic specimens. Other specimen-preparation equipment includes Baltec and Leica high-pressure freezing devices, a Pelco microwave oven, a critical-point dryer, a rotary microtome, a freeze-substitution machine, a glow-discharger, a sputter coater, and vacuum evaporator. Other general lab equipment is available. Common EM procedures done in the lab include thin-sectioning, negative staining, metal shadowing (for scanning EM), cryogenic EM, immuno-EM, 2D image classification, and 3D image reconstruction (freestanding-particle and tomographic).
Six personnel are available to do EM, help with experiments, or train users. David Timm and David Belnap are available to assist users with cryogenic or negative-stain specimens and image analysis.
Laboratory: The HSC Flow Cytometry Core Facility is a full service, state of the art lab. We offer the complete spectrum of cytometric solutions from consultation to report generation. We are currently staffed with 4 full time employees. This level of staffing allows us to accommodate training and sample prep services in an extremely timely manner. Whereas many Flow Cores simply provide access to instrumentation, our facility has a long history of supporting any level of drop off services that generally include panel design, sample prep, data acquisition and report generation. In addition to the major equipment listed below, the Flow Core also has a variety of ancillary equipment including: biological safety cabinet, incubator, centrifuges, Miltenyi Gentlemacs tissue dissociator, analysis computers, and a vacuum manifold for cytokine bead arrays.
Major Equipment Flow Cytometry
- 5 Laser BD FACSAria Cell Sorter
- 4 Laser BD FACSAria Cell Sorter
- 5 Laser Cytek Aurora Cell Sorter
- 2 Laser Propel Labs Avalon Cell Sorter
Analyzers (Conventional, Spectral, Imaging)
- 5 Laser BD Fortessa Analyzer
- 4 Laser BD FACSCanto
- 3 Laser BD FACSCanto
- 5 Laser Cytek Aurora Spectral Analyzer
- 4 Laser Beckman Coulter Cytoflex LX
- 4 Laser Beckman Coulter Cytoflex S
- 3 Laser Beckman Coulter Cytoflex
- 4 Laser Amnis Imagestream
The Genomics Core Facility at the University of Utah provides a variety of cost-effective genotyping services to researchers on campus and around the world. SNP (single nucleotide polymorphism) genotyping and microsatellite (short tandem repeat) genotyping are the primary methods that our facility employs to provide genotyping analysis. Several platforms for both SNP genotyping and microsatellite genotyping are available to meet individual project needs, allowing cost effective results for projects ranging in scale from single sites to whole genomes. In addition to genotyping, these platforms can be used for copy number variation and whole genome methylation analysis. The Genomics Core Facility also offers training and real time PCR instrument access for researches interested in performing gene expression studies ranging from single targets to hundreds of genes.
Any researcher performing studies involving SNP genotyping, microsatellite STR genotyping, copy number variation, methylation, or gene expression is encouraged to contact the Genomics Core Facility to discuss the most appropriate and cost-effective platform to achieve their study goals.
Iron & Heme
The Iron and Heme Core is part of the NIDDK sponsored, Center for Iron and Heme Disorders. The Iron and Heme Core provides analysis of metals, precursor porphyrins and heme; all from a variety of biological samples. The core specializes in the UPLC quantification of heme and porphyrin levels, and the measurement of activity of enzymes responsible for heme biosynthesis. The Core has a PhD level scientist as well as a specialist with a MS degree, and with more than 20 years of heme analysis experience, dedicated to complex assays needed to quantify iron, heme and the analysis of biosynthetic intermediates.
Facilities and Instrumentation and Services: The Core is equipped with both highly trained personnel and instruments needed for state-of-the-art measurement of metals and metabolic intermediates. This facility is equipped with an Agilent 7900-ICP mass spectrometer with a SPS4 autosampler, for metal analysis. Porphyrin analysis, is performed with a Waters Acquity ultra-high pressure liquid chromatography (UPLC) system equipped with a reverse-phase C18 column and tandem high sensitivity photodiode array and fluorescence detectors, an HPLC Waters Alliance HT HPLC system. Facilities include a dark room, two fume hoods and a deoxygenation system. It is equipped with refrigeration and freezer space, a spectrophotometer, centrifuges, cell disruptors, hot blocks, sample dryers and a lyophylizer, as well as a variety of miscellaneous small equipment needed to prepare and process samples.
Machine Shop and Hybrid Manufacturing Center
The HSC Cores School of Medicine Machine Shop serves the University of Utah’s entire campus as well as outside medical manufactures and researchers. The machine shop is composed of Journeyman level machinists skilled in CNC machining, Fusion 360 CAD software, prototyping, plastic and metal fabrication as well as mechanical and manufacturing design consultation. Our specialty is in rapid prototypes, hybridized manufacturing, CNC machining, computer aided design (CAD) and computer aided manufacturing (CAM). The machine shop specializes in machine and equipment repair, surgery tools modification and replication work, reverse engineering current or obsolete parts or just bringing a Student, Professor or Researchers experiment to life. A fundamental function of our shop is to use our core competency to assist researchers, students, doctors, and professors in achieving better designs and more efficient manufacturing solutions as well as providing cost effective research device designs. Our technical skills enable departments with limited budgets, grant money or resources to achieve their research goals in an affordable and timely fashion.
- 3 Axis Tree CNC milling machine.
- 2 axis Tormach 15L SlantPro CNC lathe with 8 tool turrets.
- Shapeoko Pro CNC router with 33”x33” bed and 25,000 rpm spindle to cut carbon fiber, plastics and other composite materials accurately and efficiently. The Router uses Vectric V carve software in addition to Fusion 360 software CAM capabilities.
- Creality CR10 SmartPro 3d FDM printer capable of printing all types of 3d filament powered by a large spectrum of 3d filament types in our 3d print lab.
- MatterHackers Pulse XE 3D printer capable of printing carbon fiber reinforced nylon printer
- Epax E10-8k Mono LCD resin 3D printer with a whole onsite selection of popular resins.
- Omtech AF3555-130W C02 laser engraver cutting machine with thirty-five 55” working area, this excellent machine cuts acrylic to serve a lot of on campus custom designed animal habitat fabrication as well as laser engrave some smaller stainless-steel parts.
- 4 Manual lathes and 2 Manual mills with DRO readouts for precision machining.
- Manual machine shop also includes grinders, sanders, drill presses, punch press, arbor press, metal bending tools, sheet and box brake equipment, metal sheers for sheet or plate.
- Plastics fabrication lab with Commercial grade, table saw, routers, miter saws, chop saws, bandsaws, and associated tooling as well as in shop stock for fast turnaround.
- Welding and fabrication equipment includes Miller Electric 220-volt MIG and Tig welders as well as spot welders, Oxy-Acetylene torch, silver soldering equipment and heat treatment equipment. The shop also has bending tools and slip rollers, and metal post processing equipment. Welding tables are modular with tooling for clamping and accurately positioning welding fabrication projects.
- Fusion 360 CAD, CAM software for modern efficient manufacturing design.
- Sheet metal design work, waterjet and laser jet manufacturing design consultation and fabrication experience. We team up with local laser and waterjet services to serve many of our projects and enhance value and turn around on many projects.
- Basic Metrology equipment for sufficient reverse engineering.
- Stainless steel passivation services.
University of Utah Metabolic Phenotyping Core (MPC) is a comprehensive resource that provides access to state-of-the-art instruments and experimental metabolic testing services. Our goal is to expand the scope of techniques available to investigators to expedite completion research focused on human metabolic disorders such as (diabetes, obesity and cardiovascular diseases), cancer, infectious diseases and aging.
Facilities and Instrumentation and Services: Quantitative measures of in vivo and ex vivo energy metabolism, insulin sensitivity, beta-cell function, mechanisms of body mass regulation (feeding, exercise and energy expenditure). Tests to assess the impact of genetic, dietary and pharmacologic manipulations on insulin sensitivity, whole body energy metabolism and body mass in mice. The tests to determine whole body insulin sensitivity and energy metabolism include oral and intraperitoneal glucose tolerance test, intraperitoneal insulin tolerance test, and hyperinsulinemic-euglycemic clamp. A Bruker NMR machine is used to determine body composition on rodents. CLAMS metabolic chambers are available for energy balance (food intake, energy expenditure and locomotor activity) at multiple ambient temperatures.
Cellular energy metabolism and mitochondrial bioenergetics are available with either the Seahorse XFe96 or XF24 analyzers. These analyzers measure energy metabolism rates of glycolysis and oxidative phosphorylation in real-time, and non-invasively in cell lines and tissues isolated from animals. These assays measure multiple mitochondrial bioenergetics parameters such as basal mitochondrial oxygen consumption rate (OCR), ATP synthesis linked OCR, proton leak, maximal respiratory capacity and mitochondrial reserved respiratory capacity. Since the Seahorse XFe96 simultaneously measures OCR and extracellular acidification rate (ECAR), which is mainly the result of glycolysis, it can determine if there is metabolic switch between oxidative phosphorylation and glycolysis in the cells. Other assays performed on XF analyzers are to determine substrate utilization by mitochondria including the metabolism of pyruvate/glucose, glutamine and fatty acid. In addition to the Seahorse assays described above.
The MPC also offers several radiometric metabolic assays for determination of glucose transport and its metabolism including glycogen synthesis, lipogenesis and glucose/fatty acid oxidation in cultured cells and isolated metabolic tissue samples such as skeletal muscle, fat cells and hepatocytes. The Bioanalytical section of measures hormones, growth factors, fuel substrates, neurotransmitters and cytokines/chemokines derived from animal studies using MagPix and Vitros 350 multiplex analyzers. Apart from providing expert help with these phenotyping services, the director of UofU-MPC director provides individualized guidance to investigators for designing and implementing these services in their research.
Laboratory: The Metabolomics Core laboratory occupies 2500 sq. ft. in the basement of the modern Emma Eccles Jones Biomedical Research Building and 500 sq. ft. on the second floor of Eccles Institute of Human Genetics. We have dedicated space for sample preparation including two chemical hoods. The laboratory contains all the equipment necessary to perform sample preparation for analysis including bench top centrifuges, high speed bead-ruptor mills, scales, sonication baths, heat blocks, -80°C and -20°C freezers, 4°C refrigerators, incubator-shakers, a UV spectrophotometer and all ancillary the equipment to be a self-sustaining metabolomics laboratory. Computer: In addition to the computers needed to operate the listed major equipment (see below) the Core maintains five separate data analysis computers. For data analysis the Core uses MassLynx, MarkerLynx, QuanLynx (Waters), AMDIS (NIST) and Mass Profiler Professional (Agilent) to perform metabolomics analysis on GC-MS data. For LC-MS data analysis the Core uses QualHunter, QuanHunter, Prodinder, Mass Profiler Professional (Agilent) and Analyst (Applied Biosystems). For metabolite identification the Core uses NIST, METLIN, Fiehn, Dictionary of Natural Products and Wiley databases.
MAJOR EQUIPMENT METABOLOMICS:
All mass spectrometers are housed within Core in room A306
- Agilent 7200 GC-QTOF with EI and CI capabilities. This state of the art gas chromatograph-mass spectrometer is a high resolution/high mass accuracy quadrupole time-of-flight instrument. It is fitted with a Gerstel MPS auto sampler that automates sample preparation for high throughput sample analysis. This workhorse instrument is primary used for the analysis of the low molecular weight metabolome and for flux analysis.
- Two Agilent 5977B gas chromatograph-mass spectrometers. These single quadrupole mass spectrometer are used for targeted quantification of metabolites using stable isotope labeled standards in single ion monitoring mode.
- Agilent 6545B QTOF. This high mass accuracy, high resolution instrument is fitted with an Agilent 1290 UPLC LC system that consists of two binary pumps, an autosampler, and a column compartment with switching valves for two columns. This workhorse instrument is primarily used for non-targeted polar metabolomics.
- Agilent 6545A QTOF. This high mass accuracy, high resolution instrument is fitted with an Agilent 1290 UPLC LC system that consists of two binary pumps, an autosampler, and a column compartment with switching valves for two columns. This workhorse instrument is primarily used to profile the lipidome.
- Agilent 6490 triple-quadrupole mass spectrometer. This instrument is fitted with an Agilent 1290 liquid chromatograph and auto sampler. Targeted quantitative analysis of metabolites and peptides is performed using this platform.
- Sciex 6500 QTRAP triple-quadrupole mass spectrometer. This instrument is fitted with an Sciex Exion UHPLC liquid chromatograph and auto sampler. Targeted quantitative analysis of lipids is performed using this platform.
- Sciex 7600 QTOF. This state of the art, high resolution instrument is unique with the abiltiy to perform EAD fragmentation which is highly advantageous for the identifiation of the posistion of double bonds in lipids and other molecules. In addition it is used for SWATH based lipidomics and metabolomics. It is fit with an Agilent 1290 UPLC.
- Thermo QExactive QE+ with Vanquish UHPLC for isotope tracer and flux analysis studies.
Other: The Core Director has access to the shared facilities of the Department of Biochemistry. These include dedicated large scale shaker-incubators, centrifuges, autoclaves and ice machines.
Mutation Generation & Detection Core
Laboratory: The University of Utah Mutation Generation and Detection (MGD) Core occupies 670 square feet of dual lab/office space in the Eccles Institute of Human Genetics building in room 7470. The MGD core contains all the equipment necessary for the standard molecular biology techniqiues required to generate gene editing reagents and detect target edits including PCR machines, bench-top centrifuges, floor centrifuges, water baths, heat blocks, -80°C and -20°C freezers, 4°C refrigerators, incubator-shakers, nano-drop UV spectrophotometer, gel electrophoresis systems and a chemical hood. Specialized equpiment available for community use includes a BioFire Defense LightScanner, Eppendorf Mastercycler Pro S Thermocyclers, a Lonza 4D Nucleofector and a cell culture hood. Data for MGD core computers is backed up routinely on a secure server, stored off site.
MGD Core Major Equipment:
- BioFire LightScanner HR I 96: used to perform DNA high resolution melting analyses.
- Three Eppendorf Mastercycler ProS PCR thermocyclers
- Eppendorf centrifuge 5430
- Two Eppendorf 5424 microcentrifuges
- Innova 43 bacterial shaker
- Innova 42 bacterial shaker
- Lonza 4D Nucleofector system: used to electroporate DNA and RNA into cells with high efficiency.
- 4D-Nucleofector Core Unit
- 4D-Nucleofector X Unit
- 4D-Nucleofector Y Unit
- 4D-Nucleofector 96-well Shuttle
- CCI biological safety cabinet
- Sorvall RT 6300 centrifuge
Other: The Core Director has access to the shared facilities of the Department of Human Genetics. These include access to common lab solutions, a shared TC room, a Biorad Gel Doc XR imaging system, floor centrifuges, autoclaves and ice machines.
National Center for Veterans Studies
Within the University of Utah, the National Center for Veterans Studies (NCVS) is charged with engaging in research in order to improve the lives of veterans, and is located in the Gardner Building on the south campus. The NCVS includes over 2000 square feet of office and laboratory space, including one large conference room with video teleconference capabilities, multiple computers with statistical software and Ethernet connections, and expanding financial resources to purchase additional state-of-the-art equipment. The NCVS is supported by faculty members who are principal investigators or co-investigators on several federal grants and contracts in excess of $10M, to include two DoD-funded randomized clinical trial currently underway at Fort Carson, Colorado, and a longitudinal health surveillance study with Air Force Special Operations Forces personnel. The Training Institute at the NCVS has trained over 1,000 mental health providers across the country and the world. The NCVS Training Institute employs three full-time psychologist lead trainers and five additional trainers. The goal of the training institute is to provide evidenced-based treatments for suicide prevention and treatment, PTSD, and depression.
Utah Nuclear Engineering Facility (UNEF) staff can assist in grant proposal development, experiment modeling, production of radioisotopes for experiment, measuring radioisotopes for biological studies, environmental sample analysis, elemental analysis, and sample sterilization.
Facilities and Instrumentation and Services: we have a 100 kW TRIGA Mark-1 nuclear reactor and state-of-the-art laboratories used for alpha, beta, gamma and neutron radiation detection. The TRIGA reactor is capable of irradiating samples to study nuclear materials, fiber optic sensors, nuclear instrumentation, electronic hardness testing, neutron and gamma irradiation, and isotope production for research, biological studies, and medicine. UNEF is the only Neutron Activation Analysis (NAA) facility in Utah, which provides a highly sensitive technique for identification and quantification of major, minor, and trace elements and isotopes in a material sample that is non-destructive by irradiating samples in the TRIGA reactor. NAA can analyze industrial samples, agricultural, biological, environmental, and geological samples. UNEF also provides fission track analysis for determining trace amounts of actinides in biological or other samples.
UNEF’s counting laboratories contain three High Purity Germanium (HPGe) gamma detectors, sodium iodide detector, cadmium delluride detector, liquid scintillation counting, and alpha spectrometry system capable of analyzing any radiation type. The HPGe detectors provide high-resolution gamma-ray spectroscopy for the detection and measurement of gamma rays from radioactive isotopes for environmental sample analysis, NAA, waste disposal, or biological samples. Alpha spectroscopy can determine actinide concentrations in environmental and biological samples.
Nuclear Magnetic Resonance
NMR spectroscopy is a powerful analytical technique for determining structures of proteins carbohydrates, nucleic acids and their complexes in solution and is highly complementary to X-ray crystallography. NMR is equally powerful for determining structures and stereochemistry of synthetic and natural products. Aside from high-resolution structure determination, NMR is also especially suited for screening and characterizing protein constructs for structural study, optimizing minimal protein domains and motifs and their corresponding complexes, assessing protein stability and homogeneity over a wide range of solution conditions, and mapping the protein-protein binding interface using chemical shift perturbation approaches. NMR titration and dynamical NMR approaches can be used to determine binding stoichiometry and binding parameters (kon, koff, Kd). Finally, NMR spin relaxation and chemical exchange can provide unique dynamical information, at atomic resolution, on the time frame of ps-ns (sidechain motions / rotational diffusion) to µs-ms (domain and loop motions) to minutes-days (protein folding-unfolding).
Facilities and Instrumentation: The NMR facility has access to 400, 500, 600, 800, and 900 MHz spectrometers, three of which are equipped with HCN cryoprobes (600, 800, and 900). The 400, 500, and 600 are located in the Univ. of Utah Health Sciences NMR Core Facility; measurement time is readily available on all instruments. The 800 and 900 are located in Colorado at the Regional Rocky Mountain and Keck Centers of which Univ. of Utah is a vested member (Sundquist and Davis groups) and owns 30% measurement time on the 800 and is guaranteed 10% share on the 900. NMR Core director Dr. Jack Skalicky assists with all aspects of sample preparation, NMR experimental setup, data processing and analysis, and structure calculation. The NMR facility owns substantial computing resources and has full membership in the SBGrid consortium.
This full-service imaging facility specializes in imaging small animals and specimens for preclinical and basic science research. It features a state-of-the-art Bruker Biospec 7.0 T horizontal-bore MRI and a Siemens Inveon CT scanner. The MRI scanner, which is equipped with multiple sets of high-performance gradient sets, upgraded power supplies, specialty RF coils and latest pulse sequences, is suited for a wide range of experiments, ranging from morphological quantification of up to 50 µm resolution, to tissue-microstructure assessment and functional MRI. The CT instrument is capable of scanning bony structures or stained soft tissues at up to 10 µm resolution, and has tunable source energy suitable for scanning biological tissues, many materials and even fossils. The facility has dedicated machine and RF coil shop, image processing and visualization workstations, animal surgery and specimen preparation rooms, and a full array of animal support and monitoring equipment for in vivo imaging. The Facility is staffed with full-time imaging and animal handling technicians. Consultation is available for experimental design and image visualization and analysis. As part of the University Core Facilities, scans performed at the facility are assessed a nominal hourly chargeback fee.
Laboratory: The Proteomics Core laboratory occupies 1500 sq. ft. in the basement of the modern Emma Eccles Jones Biomedical Research Building. The Core has dedicated space for sample preparation including two chemical hoods and a clean hood. The laboratory contains all the equipment necessary to perform sample preparation for analysis including bench top centrifuges, high speed bead-ruptor mills, scales, sonication baths, heat blocks, -80°C and -20°C freezers, 4°C refrigerators, incubator-shakers, a UV spectrophotometer and all ancillary the equipment to be a self-sustaining proteomics laboratory. Computer: In addition to the computers needed to operate the listed major equipment (see below) the Core maintains five separate data analysis computers. The Core staff is proficient in the use of multiple data analysis platforms including ThermoFisher Scientific Proteome Discoverer 3.0 software, Bruker PaSER version 2023, FragPipe v19.1, MASCOT Distiller, Scaffold 4.2, ProteinProspector v6.4.5, EncyclopeDIA and Skyline v21.2 software. In addition, the core has developed multiple new data analysis python scripts via PyCharm version 2022.2.2. All published data is made publicly available in accordance with the ProteomeXchange Consortium.
MAJOR EQUIPMENT PROTOEMICS:
- Agilent 1260 preparative HPLC system with diode array and fraction collector. This system is used for off line peptide fractionation and multiple affinity removal of 14 interfering high-abundant proteins from human and mouse serum and plasma samples. Both techniques allow for better identifiaction of proteins expaning the dynamic range of each analysis.
- Thermo QExactive HF with Dionex Ultimate 3000 nanoLC for high resolution targeted and untargeted proteomics and TMT-labeled quantification of proteins.
- Bruker Maxis II ETD paired with an Ekspert nanoLC 400 liquid chromatography system and electrospray ionization source is optimal for providing high mass accuracy of intact protein and biomolecule analysis.
- Bruker timsTOF Pro2 coupled to a Bruker nanoElute 2 LC system for high throughput identification and label free quantifiation of proteins.
Other: The Core Director has access to the shared facilities of the Department of Biochemistry. These include dedicated large scale shaker-incubators, centrifuges, autoclaves and ice machines.
Small Animal Ultrasound
Ultrasound has long been an extremely important tool in the practice of clinical medicine because it offers real-time imaging providing understanding of anatomy and physiology, is non-invasive and can be repeated serially. The small animal ultrasound core laboratory has the capability to extend ultrasound imaging to mouse, rat, and other animal models with excellent spatial and temporal resolution.
Facilities and Instrumentation: The facility has two state-of-the-art VisualSonics 2100 ultrasound machines, and probes that cover the spectrum from 9-70 MHz (standard human clinical ultrasound covers the spectrum from 2.5-12 MHz). These machines are capable of real-time 2D imaging as well as a full spectrum of Doppler techniques (pulsed-wave, color, tissue, power). One of the two machines is also capable of 3D imaging and contrast imaging (both targeted and non-targeted). Software is available for advanced image analysis of cardiac mechanics with speckle tracking that allows analysis of strain and strain rate. These tools allow near histologic resolution imaging of live animals, and are well suited to challenging applications such as the resolving the rapid heart rates of mice, or the microscopic size and function of early and mid-gestation embryos, and everything in between.
The core has capability for anesthesia and monitoring of mice and rats, and will support training your laboratory personnel in the design of protocols and the use of the equipment for acquiring images. An off-line image analysis station is also available for later review and analysis of studies.
Laboratory: The University of Utah Transgenic and Gene Targeting (TG) Mouse Core facility occupies 900 square feet of dual lab/office space with a separated tissue culture area in the Wintrobe building. This space contains all the equipment necessary to be a self sustaining laboratory including thermal cyclers, bench top centrifuges, heat blocks, water baths, -80°C and -20°C freezers, a 4°C refrigerator, incubators, shakers and all the essential equipment required to generate, rederive and preserve genetically modified mouse research models. The TG Mouse core has dedicated space in the OCM animal care facility, including a mouse suite with 356 square feet of animal housing space, 88 square feet of prepartory space and a separate 110 square foot surgery room that contains all the equipment required to perform mouse microsurgery to implant embryos. In addition, the TG Mouse core has access to shared procedure rooms and supplementary mouse housing space in an in/out room in the OCM facility. Data for TG Mouse core computers is backed up routinely on a secure server, stored off site.
TG Mouse Core Major Equipment:
- Nikon Eclipse Ti2 microinjection station, with fluorescence, CO2, heating/cooling stage used to perform pronuclear injection of 1-cell and 2-cell mouse embryos.
- Two Leica Dmi8 microinjection stations used to perform pronuclear injection of 1-cell mouse embryos.
- Eppendorf Transferman NK2 micromanipulators
- Eppendorf Femtojet microinjectors
- Eppendorf Piezo drill for handling of mouse embryos
- TMC vibration isolation tables
- Narashige MF-900 microforge for processing microneedle tips
- Sutter P-97 pipette puller
- Two Leica S9i stereomicroscopes
- Zeiss Stemi508 stereomicroscope
- Two Olympus SZX16 dissection microscopes, one with fluorescence
- Nikon Eclipse TS100 inverted microscopes
- ESCO, Forma, New Brunswick CO2 incubators
- MINC IVF benchtop embryo incubator
- Thermo Cryomed controlled rate embryo freezer for embryo cryopreservation.
- Brinkman benchtop autoclave
- Forma cell culture hood
- BioRad Gene Pulser Xcell electroporator for introducing DNA and RNA into mouse embryos and embryonic stem cells.
- NepaGene21 Electroporator system with concave electrodes for in vivo (oviduct) embryo electroporation, and with a glass slide electrode for ex vivo embryo electroporation.
- Two 96-well VeritiPro PCR thermal cyclers
- ProFlex 3 x 32-well PCR system
- Two 340L Thermo Scientific CryoPlus liquid nitrogen storage systems
USTAR Center for Genetic Discovery
The UCGD Core helps investigate the genetic basis for human disease by providing whole exome and genome sequence analyses for research and clinical projects. We specialize in variant calling and disease-gene discovery research.
Facilities and Instrumentation and Services: Computing infrastructure is housed and maintained at the University of Utah Center for High Performance Computing (CHPC), an organization of professional faculty and staff dedicated to providing access to high performance computing for research and education. The CHPC provides space, infrastructure, and systems support for large-scale computing and advanced networking systems. Computing equipment is housed in a newly renovated state-of-the-art 74,000 sq. ft. facility with 24-hour staff support, security, and high-efficiency cooling and energy supply systems. The CHPC cluster uses a Portable Batch System (PBS) job submission queue that facilitates large-scale analysis jobs. The University cluster also supports the OpenMPI message-passing interface, which allows for development and testing of scalable genome arithmetic software. All resources are HIPAA compliant.
Alignment and variant calling (including structural variant calling) for NGS datasets, variant interpretation, joint genotyping, disease gene discovery in cohorts and families, and ad hoc research analyses as dictated by the project. In total, the UCGD has available 2340 CPU cores and 3.25 PB of disc storage, plus access to additional shared resources. Total capacity for variant calling is approximately ~200,000 genomes annually via a combination of in-house and cloud-based processing. The UCGD Core has cloud computing expertise for massively scalable data access, processing and sharing, and maintains a web-based data portal for data access and collaborative analysis.
In addition to bioinformatics infrastructure and routine data analysis and management services, the UCGD Core provides a world-class team of professional software developers and scientists, and a collaborative environment for new investigators and those without significant bioinformatics experience. Scientific oversight for our core comes from internationally recognized computational genomics leaders Mark Yandell, PhD; Gabor Marth, DSc; and Aaron Quinlan, PhD. Core personnel are embedded within a dynamic network of over 50 computational genomics researchers, software developers, and analysts with the shared goal of integrating genome sequence information into health care.