BIDAC

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.

 

Cell Imaging

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.

 

Zebrafish (CZAR)

The CZAR is a 5,600 sq. ft. secure biometrically-controlled-access Core Facility housing 8,000 aquaria. CZAR staff members provide Zebrafish husbandry expertise, regulatory oversight and compliance, laboratory equipment maintenance, propagation and maintenance of wild type lines, and a 24/7 emergency response.

 1,100 sq. ft. is dedicated to researcher use with:

1) laboratory benches for breeding fish;

2) three experimental rooms outfitted with 8 stereomicroscopes and microinjection devices;

3) a microscope room with two dedicated fluorescent microscopes;

4) experimental bench space for genotyping;

5) a separate Quarantine Room that houses zebrafish imported from other laboratories;

6) a dedicated fume hood for treating animals with chemical mutagens, and

7) an Alternate Light Cycle (ALC) room shifted by 4 hours from the main fish rooms.

 

1,500 sq ft is dedicated to staff use with:

1) experimental space for cryopreservation of genetic lines and in vitro fertilization;

2) a kitchen for washing aquaria, etc., and for preparation of chemical solutions;

3) food preparation facilities, including growth of live foods for larvae and juveniles; and

4) office space for the permanent staff.

 CZAR Equipment    

  • M205 FA Leica Fluorescence Microscope
  • Zeiss Fluorescence Microscope with LED light source
  • Olympus Fluorescence Microscope
  • 8 microinjection stations with bright field stereomicroscopes
  • Analog camera and monitor to facilitate teaching microinjection in real time

The CZAR is approved and regularly inspected by the Institutional Animal Care and Use Committee (IACUC) and the University of Utah is fully accredited by the American Association for Accreditation of Laboratory Animal Care. All CZAR personnel have received animal care training and have been approved by the IACUC.

The University of Utah Crocker Biology Research Zebrafish (CBRZ)- Facility Description

CBRZ is a new 1200 tank Zebrafish facility, administered as a satellite of the School of Medicine CZAR facility, in a custom designed ~600 sq ft room in the basement of the Crocker Science Center.  A separate temperature controlled ~200 sq ft room is dedicated for embryo microinjection, with three Leica S9 microscopes equipped with Narashige injection setups.  A Leica M205 microscope with DFC7000T camera and SOLA SM365 light engine is also available for fluorescence screening and imaging.

CBRZ is approved and regularly inspected by the Institutional Animal Care and Use Committee (IACUC) and the University of Utah is fully accredited by the American Association for Accreditation of Laboratory Animal Care. All CBRZ personnel have received animal care training and have been approved by the IACUC.

 

DNA Peptide

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.

 

DNA Sequencing

The DNA Sequencing Core Facility is part of the Health Science Center at the University of Utah.  We provide DNA Sequencing services to the research community and off-campus researchers. We specialize in consulting with scientists to help plan and implement experiments in support of their research questions.  We helping users understand and troubleshoot their data and identify optimal data processing pipelines.  We employ the latest technologies to generate high quality data with a fast turnaround and competitive prices and are willing to push outside the standard limits of our instrumentation when users have novel approaches that they want to try.  We strive to provide as much personal attention as possible to our many users.

Facilities and Instrumentation and Services: In support of DNA Sequencing activities we utilize state-of-the-art DNA sequencers such as the Oxford Nanopore MinIon, as well as other established platforms such as the Ion Torrent Proton, the Qiagen Q24 Pyrosequencer (for probing the methalome), capillary sequencing and lab robotics including the Biomek FX for liquid handling needs. We also support single cell work through the 10x Genomics Chromium Controller located in our core.  We have the ability to accept Illumina based sequencing requests with turn-around time of approximately 3 weeks for university clients.

Data from standard DNA sequencing services are typically reported to customers same day in as little as 6 hours from receipt of the samples. Sample information is submitted online and sequencing data files are available online for download using a simple and secure interface immediately after the run completes. We are also willing to facilitate data analysis from runs we generate.  For example, runs completed on our Ion Torrent Proton are aligned, and variants called for no additional cost upon request from the user.  10x data pipelines similarly can be employed for very minimal cost on our server.

 

 Drug Discovery Core

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 uniqueness of the Drug Discovery Core is that it coordinates the cooperative efforts of individual research groups in a wide variety of different drug discovery stuides, ultimately leading to discover novel chemical probes and new pharmaceutical lead compounds. The most valuable assets at the facility are the private/proprietary chemical collections that could result in new intellectual property. These unique molecules of therapeutic potential offer the facility to assist in the translation of fundamental discoveries in biology into novel therapeutics and commercial opportunities. It’s anticipated that the discovery of candidate lead compounds from the facility will stimulate interest in commercial development of technology at the University of Utah through licensing agreements with pharmaceutical industry partners and the production of new start-up biotechnology companies.

  Facilities and Instrumentation and 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 (1300 sqf) is a centralized, staffed facility, and houses instrumentation and robotics required for high-throughput screening. The core is equipped with a high-throughput high-content immunofluorescence imaging system (Molecular Devices ImageXpress Micro XLS) and a high-throughput Bio-tek Neo2 Plate Reader with stacker: capable of high-throughput reading of fluorescence, luminescence and absorbance at any wavelengths. The core is also equipped with a variety of liquid handling instruments (Tecan EVO 96-well and Tecan EVO 384-well automated liquid handling systems with sterile enclosure). Additionally, the core has HP D300 Digital Dispenser which is 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. The laboratory space housing these systems includes laboratory benches and cell culture and chemistry hoods.

Electron Microscopy

 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.

 

Flow Cytometry

 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 5 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.

Facilities and Instrumentation and Services: In addition to these services, we also provide instrumentation that covers virtually any cytometric assay. First of all we offer 3 cell sorters ranging from 2 laser 4 colors all the way to 5 laser and 18 color capabilities. These sorters can sort into 96 or 384 well plates and have nozzles sizes from 130um to 70um for very gentle sorts or high throughput sorts. The facility has 8 traditional analyzers from both Becton Dickinson and Beckman Coulter. These range from 3 laser 8 color to 5 laser 18 colors. Most of these instruments also have high throughput samplers to accommodate 96 well plate runs. The Flow Core also has 2 instruments that are not traditional flow cytometers but serve tremendous need in the lab. First of all the lab has an Amnis Imagestream Imaging Flow Cytometer. This instrument is invaluable for any assays where the statistical reliability and multicolor potential of flow cytometry is crucial, but localization or imaging is also needed. We also have a 5 laser Cytek Aurora Spectral Analyzer with 64 detectors. This instrument is a workhorse for virtually any assay but excels when greater than 15 colors are needed in the same tube. Finally the lab has a number of ancillary equipment including Miltenyi GentleMac tissue dissociator, incubators, centrifuges, and biosafety hoods.

 

Genomics

 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

 The HSC Cores machine shop is a large facility specializing in the fabrication, development, and repair of medical, surgical, and research devices of all types.  Our staff has worked on the cutting edge of research devices for 30 years. Our shop handles all types of fabrication including welding of exotic materials, milling, drilling, lathe work, CNC controlled machines, plastic working equipment, and wood working tools.  We are known for our ability to take an idea from concept to working drawings, then to working products in a short period of time.  This service is a great aid to investigators requiring special devices to pursue their research work.

 

Mass Spectrometry and Proteomics Core

The Proteomics and Mass Spectrometry Core at the University of Utah is one of the longest serving cores at the University of Utah and provides proteomics and mass spectrometry services for the campus community, other academic institutions and biotech companies in the regional area. The Core is staffed by a Director, James Cox, and two PhD level research associates, one dedicated to sample analysis, the other providing bioinformatics services. While the emphasis of the facility 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.

Facilities and Instrumentation and Services: The Core provides a wide range of services with a focus on proteomics. Central to this is quantitative shotgun proteomics using stable isotope methods which include TMT, SILAC, and iTRAQ labelling. These assays are performed using Thermo QE-HF fit with nanoLC. For complex samples the Core provides off-line high pH MudPIT fractionation using a dedicated Agilent 1200 HPLC with an automated fraction collector. In addition to quantitative proteomics the Core also performs PTM analysis on digested peptides using various enrichment strategies. For top down intact protein analysis a Bruker Maxis HD II with ETD fit with both nano flow and capillary flow liquid chromatography is employed. For proteomics data analysis, the Core uses ProteoIQ-2, Proteome Discoverer 2.2, Compound Discover 2.1, Tracefinder 4.1, two high-end MASCOT servers, MASCOT Distiller, Sequest, and Skyline. For basic mass spectrometry services such as accurate mass determination of small molecules, peptides and polymers, a number of instruments are employed for this including a Bruker Ultrafextreme MALDI-ToF, the Bruker Maxis II and an Agilent 6545 UPLC-QToF. The Core is fully equipped to perform a wide array of mass spectrometry based analysis.

 

Metabolic Phenotyping

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.

 

Metabolomics

The Metabolomics Core at the University of Utah performs cutting edge low molecular discovery and quantitative “-omics” analysis. This includes profiling metabolites and/or lipids as well as tracing the metabolic fate of these using stable isotope tracers. Our services are conveyable and are available to researchers at the University of Utah as well as investigators nation and worldwide. The Core is staffed by the long serving Director, James Cox, and three other PhD level research associates including one individual dedicated to the development and implementation of software needed for data analysis of novel or difficult projects. What is most unique about this Core is the interpersonal relationships that we strive to develop between our staff and individual investigators to answer challenging scientific questions. This relationship building has proven to be very productive and has led to a number of high impact publications over the past 14 years.

Facilities and Instrumentation and Services: The Core employs a proven pipeline for metabolomics and lipidomics with the overarching theme of biomarker discovery using a non-biased discovery approach followed by validation using targeted quantitative mass spectrometry. This pipeline is enabled by our highly skilled staff and state of the art instrumentation. For metabolomics, instrumentation includes an Agilent 6545 UPLC-QToF for non-targeted discovery analysis and a Sciex 6500 QTRAP for biomarker validation. Lipidomics employs an Agilent 6530 UPLC-QToF for non-biased lipid biomarker discovery and a 6490 UPLC-QQQ instrument for quantification of altered lipids species. Bioinformatics employs both commercial and in-house developed software to identify altered metabolites in a biological system with metabolite identification and validation using authentic standards when available or through electronic libraries when not.

Fluxomics and isotope tracing are two other related and commonly performed services. The Core employs a targeted approach to these depending on the metabolites being traced. An Agilent 5977B GC-MS with High Efficiency Source is optimal for TCA cycle intermediates, most amino acids, and glycolytic intermediates. A targeted scanning method for the detection of low abundance isotopes is used making this an ideal instrument for these metabolites. For metabolites not amenable to GC-MS which includes urea cycle intermediates, nucleotides and lipids a Thermo QE-HF is employed. Data analysis software for this includes a variation on in house developed software and EI-Maven. In short, the Metabolomics Core at the University of Utah has the expertise and instrumentation to fully profile the metabolome, lipidome and the fluxome.

 

Mutation Generation & Detection Core

 The University of Utah Mutation Generation & Detection (MGD) Core Facility supports researchers by developing and optimizing the latest DNA nuclease reagents and protocols for targeted genome editing. Currently, the MGD core specializes in providing customized CRISPR reagents for gene editing in multiple model systems, including Drosophila, C. elegans, zebrafish, mammalian cells and mice. Additionally, the MGD core can and has developed specialized editing reagents for researchers who work in non-standard model organisms or require specialized reagents for their specific system. Beyond reagent development, the MGD core has established partnerships with the Drug Discovery Core, the Mouse Transgenic Facility and the Centralized Zebrafish Resource Center to create engineered cell lines, mouse models and zebrafish models, respectfully.

 Facilities and Instrumentation and Services: The MGD core has all the necessary resources and equipment to carry out the molecular techniques required to accomplish targeted gene editing and to identify animals or cells carrying the correct target genomic modification. Custom high-throughput genotyping services include traditional PCR methods for the identification of targeted insertions and high-resolution melt analysis (HRMA) for the identification of nuclease induced mutations. HRMA is a highly sensitive, high-throughput, closed tube assay for the identification of a wide range of sequence variations. In order to validate induced mutations and insertions, the MGD core offers targeted sequencing services. Lastly, the MGD core has specialized equpiment available for community use including a BioFire Defense LightScanner and a Lonza 4D Nucleofector. The MGD core provides training of lab personnel in the use of this equipment, the implementation of the DNA nuclease reagents and help in troubleshooting problems should they arise.

 

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.

 

Nuclear Engineering

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.

 

Pre-Clinical Imaging

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.

 

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.

 

Transgenic Mouse

The Transgenic and Gene Targeting Core is available to produce transgenic and gene targeted mice using pronuclear injection of DNA constructs or CRISPR reagents into embryos or using more traditional methods of targeting embryonic stem (ES) cells and injecting them into blastocyst stage embryos to produce germ line chimeras.  We have mastered alternative methods for generating CRISPR mice including zygote electroporation of nucleases (ZEN) and in vivo Genome editing via Oviductal Nucleic Acids Delivery (GONAD).  The TGTC offers related procedures including cryopreservation and storage of mouse sperm and embryos, rederivation of mouse lines from frozen embryos, in vitro fertilization (IVF) to reanimate frozen sperm, development of primary ES cell lines from targeted mouse lines, and karyotyping of ES clones.  We have experience with 8-cell injections, tetraploid and morula aggregation, laser assisted IVF, and early embryo manipulation. The TGTC utilizes the latest technology and strives to optimize the newest techniques to efficiently generate requested mice for researchers both on campus and throughout the world.  We attribute the success of our Core to the many years of expertise and vast knowledge of the highly qualified members of our team using our state of the art, highly sophisticated equipment.

Facilities and Instrumentation and Services:  Equipment includes three full microinjection stations (Nikon and Leica) and dissection microscopes with fluorescence imaging capabilities (Olympus, Leica and Zeiss), Femtojet injectors, Peizo drills, an XYClone laser, a NEPA21 ElectroKinetic system, BioRad electroporator, pipette pullers, microforges, a MINC IVF incubator, and a Thermo rate controlled embryo freezer.  The Core maintains the necessary mouse colonies for basic procedures as well as small colonies of commonly used deleter mice, as well as the basic strains of germline competent ES cells.

The Core is available for technical advice regarding injection procedures, cell culture techniques, vector design and construction, as well as guidance on analysis of ES cell clones and mice. The Core is amenable to new ideas and available to undertake new methods that researchers are interested in.

 

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.