RESEARCH CORE FACILITIES

Analytical Ultracentrifuge Core

Animal Behavior Core

Animal Facilities (Comparative Research, Center for)

Animal Imaging Core (Cancer Institute)

Assay and Analytical Core

Biobank, UMMC

Biomedical Materials Science, Department of

Clinical Research Support Program

Confocal Microscopy Core

Data Science Core (Cancer Institute)

Data Science, Department of

Drug Discovery Core (Cancer Institute)

Equipment Repair Facility

Flow Cytometry Core (Cancer Institute)

Geographical Information Systems and Remote Sensing Core

Histology Core

Library Services

Mass Spectrometry Core

Molecular and Genomics Core

Neuroimaging Core

Postmortem Brain Core

Transgenic Core

Add a Research Core

Analytical Ultracentrifuge Core

The Analytical Ultracentrifuge Facility is located in the Department of Cell and Molecular Biology in the Guyton Research Building. The services are available to faculty at UMMC and other education and research institutions on a fee-for-service basis.

Equipment Beckman XLA Analytical Ultracentrifuge equipped with absorption optics AVIV FDS system for fluorescence detection Anton Paar DMA 5000 for density measurements Anton Paar AMVm micro viscometer

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Animal Behavior Core The Center for Psychiatric Neuroscience Animal Behavior Core conducts state-of-the-art rodent behavioral testing for investigators at UMMC and other nearby institutions on a fee-for-service basis. The core facility is equipped to perform a comprehensive battery of behavioral tests to thoroughly phenotype overall motor and sensory function of rats and mice as well as specific behaviors of interest to specific investigators (learning and memory, operant behavior, motor function and gait, place/fear conditioning, pain/analgesia, depression and anxiety related behaviors). The core is equipped to assist in all aspects of rodent behavioral testing including design and execution of behavioral tasks as well as data analysis and interpretation. Services

• Behavioral and neurological phenotyping including neurological assessment (righting, reflex response, arousal, startle, seizure activity), activity balance/coordination, simple pain/sensory testing aggression

• Testing relevant to affective disorders and antidepressant activity (acute – forced swim and tail suspension tests and chronic social defeat, chronic mild/unpredictable stress, learned helplessness)

• Testing relevant to fear and anxiety and anxiolytic activity (Plus maze, zero maze, marble burying)

• Learning and memory (active/passive avoidance, spontaneous alternation, water maze, Barnes maze)

• Assessing ultrasonic vocalization for pain, anxiety, stress and sexual and social behaviors

• Sleep and circadian rhythm monitoring and/or disruption

• Assistance with specialized/custom testing as needed (e.g. sexual behavior, maternal behavior, social interaction)

Equipment

Noldus Ethovision (movement tracking) Noldus Observer (complex analysis of individual and social behaviors) Metris Sonotrack (ultrasonic detection and analysis system) Automex activity monitors Plexiglass observation chambers Swim test cylinders + dividers Sound Meter T-Maze, Water Maze, Barnes Maze Active Avoidance/Conditioned Place Preference Operant Conditioning Chamber Sleep and circadian rhythm recording facilities Website

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Animal Facilities (Center for Comparative Research) The Center for Comparative Research (CCR) is a centrally administered facility responsible for the care and maintenance of laboratory animals used in research. Included in CCR environments are animal housing areas, animal husbandry support services, and veterinary medical support facilities. Other specialized environments include neuroscience study areas, aquatic facilities, surgical modeling, and areas for biohazard containments. The CCR provides the management and resources necessary to maintain full accreditation by the Association for Assessment and Accreditation of Laboratory Animal Care International. Efforts by the CCR are 100% service-based to UMMC’s animal-based research programs. Support functions include daily animal, husbandry requirements, animal quarantine and conditioning programs, animal surgical and anesthetic support, laboratory animal veterinary medical care programs, and regulatory support (IACUC, OLAW, USDA). The CCR operates five distinct animal environments on the medical center’s campus. Animal housing and support space for studies are located primarily in five areas on the UMMC campus:

1) The Arthur C. Guyton Laboratory Research Building 2) The Arthur C. Guyton Laboratory Research Center 3) David Pankratz Research Wing 4) James D. Hardy Clinical Sciences Building 5) Translational Research Center

Total animal housing and support areas are approximately 44,000 square feet.

Animal care & use: 19,200 Support space: 24,800

Arthur C. Guyton Research Building

Total gross sq. ft. = 11,604 Net sq. ft. animal housing space = 5,199

The Guyton Building laboratory animal facility serves as a conventional resource for animal housing and support. Adjacent to the animal facility is the central CCR Office. There are a total of 28 individual animal rooms; a large surgical suite (two operating rooms with prep and equipment areas and veterinary laboratory for supplies & equipment), a feed/bedding storage area, a cage sanitation facility (clean & dirty side), several ancillary storage spaces, and small office and employee break room. The surgical room has an Amsco gravity sterilizer.

Arthur C. Guyton Laboratory Research Complex

Total gross sq. ft. = 15,381 Net Sq. ft. animal housing space = 6407 Net Sq. ft. animal imaging core = 1,200

The Guyton Laboratory Research Complex is contiguous with the Guyton Research Building and serves as the primary rodent housing facility for the institution. Rats and mice are housed in ventilated microisolator housing in barrier or modified barrier areas. Several suites of rooms are found whereby closely associated studies are housed in the same relative environment. A total of 21 individual animal rooms are found, as well as an expansive cage sanitation and processing area, bulk sterilization equipment, and veterinary procedural laboratories. The CCR central administrative offices are located in this area. The facility includes an animal imaging area with an IVIS Spectrum in vivo imaging system. Additional space is available for expanded animal imaging equipment. David S. Pankratz Research Wing - 8th Floor Laboratory Animal Facilities

Total gross sq. ft. = 12,358 Net Sq. ft. animal housing space = 4,668

The 8th Floor facility is utilized for conventional housing, as well as the capability to maintain animals in ABSL-2 infectious disease studies. It is also used as a rodent barrier environment for the maintenance of immunocompromised animals. There are two office spaces for veterinary and facility management, a total of 37 individual animal rooms, a small barrier facility (with a positive pressure entry vestibule and 6 cubicle designs, and a biological safety cabinet which provides a work area), a hazardous material containment area (with negative pressurization and entry vestibule and necropsy room), a large surgical suite (operating room, prep areas, veterinary lab & patient ICU), a feed/bedding storage area, cage sanitation facility (clean & dirty side), several ancillary storage spaces, and an employee break area with shower/locker facilities. Steris/Amsco vacuum sterilizer is in the surgery area. James D. Hardy Clinical Sciences Building

Total gross sq. ft. = 1,432 Net Sq. ft. animal housing space = 287

Designated as a genetically altered mouse core facility, this area contains small space for animal housing, a cage sanitation area, and a laboratory space for genetic manipulations. Aquatic Animal Facility

Total gross Sq. ft. = 2,818 Net Sq. ft. = 2,681

This area serves as an aquatic housing environment. Rooms are designed to house and maintain fish species. It has design capabilities for flow-through water systems, raceways and infectious disease challenge. One adjacent room serves to maintain reagents, supplies and pharmaceuticals.

Anatomy Surgical Suite (Department of Anatomy participates with CCR in management of this room)

Total gross sq. ft. = 505 Net sq. ft. = 505

This facility serves as a neurosurgical operating room. Website

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Animal Imaging Core (Cancer Institute) The Cancer Animal Imaging Core offers advanced imaging technology to accurately monitor the size of tumors growing within animals and detailed insight into some of the molecular and biological events occurring inside the animal, providing more information from experiments than traditional tumor measurements. Equipment

IVIS Spectrum animal imager system (Caliper Life Sciences)

Proscan 2 Ti-U Microscope with time-lapse real-time video capacity (Nikon) Website

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Assay and Analytical Core The Assay and Analytical Laboratory, located on the fourth floor of the Arthur C. Guyton Research Center, is operated by the Department of Physiology and Biophysics. The core provides uniform methods of collection, labeling, transporting, storage and analysis of biological specimens. Supported by a knowledgeable staff, the facility provides support for various radioimmunoassays, enzyme-linked immunoassays (ELISA), molecular, and chemical analyses. These facilities and services are available to faculty at UMMC and other educational and research institutions on a fee-for-service basis.

Equipment VET AXCEL Chemistry Analyzer

Assays Available Enzyme-linked Immunosorbent Assay (ELISA) Radioimmunoassay (RIA) Website

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UMMC Biobank The UMMC Biobank supports translational and clinical research in addition to serving as the tissue bank core of the Cancer Institute. Previously known as the University Biospecimen Repository, the biobank began operations in November 2011 with a focus on cancer-related surgery specimens. In March 2013, blood collections were expanded to other areas, including the transplant, gastrointestinal, congenital heart disease and HIV clinics. To date, the biobank has over 3,500 participants.

The UMMC Biobank has dedicated biorepository specialists for consenting patients and specimen processing. Our consent allows access to historical and future clinical data through the electronic health record (EHR) to facilitate in-depth translational research. Samples collected include whole blood, serum, plasma, white blood cells, tumor and normal tissue, handled according to the International Society for Biological and Environmental Repositories (ISBER) Best Practices. All freezers are on a back-up power alarm system with 24-hour surveillance. Equipment

The facility houses -80° and -20° freezers, 4°C refrigerators, an automated liquid handler, BSL II safety cabinet, cold and ambient temperature centrifuges, and cryostats and is monitored with a temperature management system.

Services Biobank services include biospecimen processing, kit production, and shipping. Website

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Department of Biomedical Materials Science The Department of Biomedical Materials Science facilities occupy nearly 5,000 square feet within the School of Dentistry for the research and characterization of a diverse range of materials (metals, polymers, ceramics, composites), of a wide range of properties (physical, mechanical, electrochemical, biological, etc.), and at all levels of interest - from atomistic to macroscopic. Core laboratories include facilities for tissue engineering, histology, computer modeling, metallography, corrosion, wear, fast fracture, fatigue, and failure analysis. The services are available to faculty at UMMC and other education and research institutions on a fee-for-service basis. Equipment

NOTE: The list of equipment items is extensive. Please refer to the website. Website

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Clinical Research Support Program The Clinical Research Support Program (CRSP) building is located adjacent to the main campus and easily accessible by interstate and state highways. The 8,000-square-foot CRSP facility comprises a reception area, 18 examination rooms, two laboratories for phlebotomy and storage of supplies, two conference rooms, private offices/cubicle workstations, and free front-door parking for research participants. The following equipment is housed in the CRSP and is at the disposal of the project investigators: a Thermo Electron Revco -80oC upright freezer, a So-Low C85-5 -85oC ultra-low chest freezer, several centrifuges (Eppendorf 5702R, Fisher Scientific Centrific 228, Clay Adams Dynac), a biohazard refrigerator, several mercury sphygmomanometers, one Healthometer and one Detecto 350-lb. capacity balance scales, and a Seca stadiometer. The facility also provides secure storage of study records, a photocopier, paper shredder, fax machine, several networked laser printers, and desktop computers networked to the internet and to UMMC’s intranet. Website

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Confocal Microscopy Core The Confocal Microscopy Core, located on the second floor of the Arthur C. Guyton Research Building is primarily an equipment core requiring user training.

Equipment

Leica TCS-SP2 laser scanning confocal upright microscope equipped with three individual lasers (488/546/633 nm) capable of imaging standard fluorescence dyes within the visible spectra, including FITC/TRITC, CY2/CY3/CY5, green fluorescence protein variants (GFP/YFP/RFP/DsRed) and many different indicator dyes (i.e. Ca2+, pH, membrane potential, oxidative stress, etc.).

Leica TCS-SP8 multiphoton confocal microscope equipped with three individual lasers (488/561/633 nm) capable of imaging standard fluorescence dyes within the visible spectra. This system uses a light green laser (561) instead of the 546 green laser. The 561 laser can still be used with standard CY3 and TRITC dyes, but Alexa 555 dyes are ideal. The multiphoton capability is provided by a Coherent sapphire laser. This system includes an inverted microscope with a Luden environmental chamber for temperature control.

Features

• Objectives: 63X glycerol, 1.37 NA, 40X oil 1.25 NA, 20X dry 0.7 NA, 10X dry

• 10X, 20X, 40X, 40X oil, 60X oil and 100X oil objectives

• Both SP2 and SP8 include motorized stages

• Super Z galvo stage

• Stage adaptable for slides, dishes up to 35mm, 25mm glass cover slip in an atto chamber

• Epifluorescence provided by a mercury lamp (SP2) or halogen lamp (SP8)

• Line scan and Z-scan modes

• High speed resonant scanner

• Transmitted light detection

• Tunable collection filter

• Time lapse

• Standard confocal microscopy with simultaneous or sequential image collection

• Inverted orientation permits fixed or live cell/tissue imaging.

• High resolution imaging

• Image enhancement

• 6PMTS: 3 color imaging (includes 2 high sensitivity hybrid detector, standard PMT), 1 transmitted light PMT, 2 non-descanned light detectors

• Multiphoton imaging (deep tissue imaging, dark/dense tissue far red imaging)

• FRET/FRAP (Fluorescence resonance excitation transfer/ Fluorescence recovery after photo bleaching)

• Quantitation, 3D reconstruct

• Quantitation and co-localization

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Data Science Core (Cancer Institute) The Cancer Data Science Core provides cutting-edge analytics in biostatistics, data science and populomics to cancer-related basic science, clinical and translational researchers. This core develops and applies statistically rigorous solutions for study design, analysis and information mining of "omics" and other biological data for the discovery of clinically actionable biomarkers, integration of these data with clinical information, and translation of genomic discoveries to the bedside to accelerate precision medicine in the cancer field.

Services

• Study design • Grant preparation • Data monitoring • Methods development • Data analytics and translation • Report/manuscript preparation • Lectures, workshops and courses on biostatistical methodology

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Department of Data Science The Department of Data Science provides biostatistical and information science expertise to researchers at UMMC and other academic health centers, pharmaceutical companies, medical research organizations, managed care providers, nonprofit organizations and government agencies, such as the NIH and the state health department. With an interdisciplinary approach that combines aspects of statistics, computer science, data mining, applied mathematics, predictive analytics and visualization, the department assists collaborators by turning vast amounts of data into actionable evidence. Department members collaborate with investigators on all statistical aspects of research studies, including study design, sample-size analysis, data analysis, interpretation, translation and manuscript writing. Pre-study consultation helps define objectives and endpoints, select an appropriate design, devise a blinding and randomization scheme, compute an adequate sample size, specify the statistical methods, and estimate the time required to accrue the total patient population.

The Department provides guidance and preliminary analysis throughout the project, completes final analysis and supports manuscript development at the end of the project. In addition to providing statistical support, the Department also provides data services, which includes support for capturing, cleaning, managing, and distributing data. Website

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Drug Discovery Core (Cancer Institute) The Cancer Drug Discovery Core laboratories are located within the National Center for Natural Products Research on the second and third floors of the Thad Cochran Research Center at the University of Mississippi campus in Oxford. The core houses cell culture facilities and instrumentation to support various assay modalities employing in vitro propagated human cancer cell lines. Natural product chemistry laboratories within the Core support fractionation, isolation and identification of anti-cancer compounds from various types of natural products. Capabilities • Support bio-assay guided fractionation of crude natural product extracts leading to the isolation and

identification of active compounds

• Identify signal transduction pathways targeted by crude extracts or pure compounds

• Provide active principles for more detailed follow-up in more clinically relevant tumor cell lines and in animal models

• Guide structural optimization of lead candidates identified in primary screening

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Equipment Repair Facility Phoenix Technical Services (PTS), a locally owned company, works with the UMMC to provide on-site integrated repair and preventative maintenance services. A technician is present at the Medical Center every Tuesday, and the company is available on an on-call basis other days of the week. PTS is capable of working on a variety of different instruments including large systems and refrigeration components and also provide limited custom fabrication and modification services. Back to Top

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Flow Cytometry Core (Cancer Institute) The UMMC Cancer Flow Cytometry Core, located on the 6th floor of the Research wing, provides state-of-the-art flow cytometry analysis and related services to the UMMC research community and affiliated institutions. We provide flow cytometry analysis and sorting, as well as consultation for experimental design and data interpretation. A trained operator is available to assist with instrument set-up as well as running and analysis of your samples. Prior to scheduling their first appointment, investigators must meet with the facility staff to discuss experiment plans to avoid potential pitfalls and optimize the time spent on the machine(s). In addition, a training course consisting of individual help sessions tailored to your specific needs is available upon request. Equipment

Gallios flow cytometer Moflo XDP cell sorter Website Back to Top

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Geographical Information Systems and Remote Sensing Core The Geographic Information System (GIS) and Remote Sensing (RS) program was established at UMMC in December 2000 and was the first GIS and RS program on an academic medical center in the country. Since UMMC is the only academic health science campus in Mississippi, its GIS/RS program is unique - not duplicating, but complementing GIS/RS-related activities of health studies at other universities across the state. The GIS/RS core facilities include the GIS laboratory, GIS conference room, and three offices with access to additional large conference rooms, computer closet/room, computer networking equipment and connections, and a dedicated full-time LAN administrator. Services

Two-day customized hands-on training

Hardware High-end workstations Dedicated servers GPS data loggers Meteorological data loggers Burkard mold spore and pollen traps Software The following GIS and image processing software can be obtained for research and teaching purposes at UMMC when licenses are available from IHL:

ESRI ArcGIS – ESRI

ENVI - Exelis Visual Information Solutions

ERDAS IMAGINE - Hexagon Geospatial Website

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Histology Core The Histology Core offers a variety of services including general histology, specialized histological staining, immunohistochemistry, light microscopy, vibrotome for gelatin sections, and general training. The services are available to UMMC and other education and research institutions on a fee-for-service basis. Website

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Library Services Rowland Medical Library supports the clinical care, research, and education missions at UMMC with electronic and print resources that offer depth and breadth in as many subject areas as necessary. The scope of the collection includes the core biomedical sciences, related sciences, selected social sciences and humanities to support the medical center programs in education, research, and health care services. Rowland’s collection numbers slightly more than 250,000 print books and bound periodicals and users have access to more than 23,500 e-journals, over 12,500 e-books, and approximately 80 databases in health sciences. Users are able to request books and journals not owned through interlibrary loan services. Rowland serves as a Resource Library within the National Network of Libraries of Medicine for the Southeastern/Atlantic region and is a member of various consortia for services and purchasing. Rowland Medical Library is located in the second and third floors of the Verner Smith Holmes Learning Resources Center on the main campus. Occupied in July 1982, the library has 55,612 square feet and provides seating for over 500 patrons with group and individual study areas, tables and chairs. The first floor houses a classroom for library-led classes, and the Collaborative Learning Center (CLC) with four Media:Scape units and booth seating for group study. The library provides wireless network access for individual study and research. Rowland houses an Archives division on the library’s second floor equipped for the preservation and restoration of documents, monographs, photos, films and other formats. The Division of Public Affairs and the Office of Academic Affairs also house materials related to the Medical Center in the Archives. An off-site facility of 9,000 square feet stores pre-1990 publications, and materials are retrieved when requested. Website

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Mass Spectrometry Core The Mass Spectrometry Core occupies approximately 1800 square feet of laboratory and office space in the David S. Pankratz Research Wing and the Arthur C. Guyton Research Complex. The core provides lipidomics, quantitative peptidomics/proteomics and metabolomics capabilities to researchers at UMMC as well as to other researchers from intrastate as well as interstate locales. The MSC provides expertise in LC/MS/MS, HPLC, sample preparation, method/assay development and data analysis and interpretation. The LC/MS/MS systems are very robust and allow not only targeted analyte quantitation but also Discovery "Omics" when the biomolecules of interest are enriched (IP's, Off-line fractionation/enrichment, gel bands).

Methods/Assays Available

Eicosanoids

Prostaglandins /Isoprostanes

Creatinine

LysoPhosphatidic acid

Cortisol

Erythromycin

Serotonin

Vitamin D3

Vincristine-Noscapine

Angiotensin Peptides

Protein Quant (MRMs)

Lipid Quant/Lipidomics

Proteomics on IP pulldowns and Gel Bands

Equipment

2 ABSCIEX QTRAP mass spectrometers (Models 4000 and 5500, ABSCIEX, Foster City, CA) with TurboV Electrospray Ion (ESI) sources each coupled to Dionex Ultimate 3000 HPLC systems under the control of Analyst 1.5.2 software. They have been optimized specifically for quantitative measurement of many physiologically relevant analytes at very low limits of detection.

2 HPLC systems (an Agilent 1100 series and one Dionex Ultimate system) equipped with UV, fluorescence, radioactive and light scattering detectors allow measurement of more abundant analytes and provide sample prep, cleanup, and enrichment capability prior to LC/MS/MS analysis. Website

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Molecular and Genomics Core The Molecular and Genomics Facility occupies approximately 1,100 square feet of laboratory space on the 6th floor of the Arthur C. Guyton Research Center. The Core supports genetic-based research initiatives at UMMC and across the region. The Core is well-equipped to perform genetic and genomic analysis on human and several model organisms, including rat and mouse. The Molecular and Genomics Core provides various genomics services, including sample processing, genotyping, sequencing, gene expression and early stage bioinformatics analysis. The Core also provides training and mentoring in genomic technologies. Equipment

NanoDrop 1000

Agilent Bioanalyzer 2100

Affymetrix GeneChip

Beckman CEQ 8000XL GeXP Genetic Analysis System

Strategene Real-Time PCR

Experion Bioanalyzer

Gradient Thermocyclers

Agilent High-Resolution Scanner

Bio-Rad MyiQ and iQ5

Table-top Microfuge (Eppendorf 1524)

Bench-top Centrifuge (Eppendorf 5810R)

Sonicator

Homogenizer Website

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Neuroimaging Core The Center for Psychiatric Neuroscience Imaging Core gives UMMC investigators access to state-of-the-art, sophisticated microscope and related equipment with advanced capabilities in the visualization, quantification and interpretation of neuronal systems at the cellular level.

Services

• instruction in the general use of the microscopic imaging equipment and further

• highly specialized expertise in the technical parameters relevant to the design, application and interpretation of quantitative morphological and neurochemical studies (technical parameters include Western blotting, tissue sectioning and histological staining of human postmortem and animal brain tissues)

• application of 3-dimensional cell counting techniques to different types of staining procedures

• determination of optimal conditions for immunohistochemistry

• guidance in the anatomical localization of the specific brain regions being studied Equipment

Nikon C1 confocal scanning microscope MCID image analysis systems Nikon 600 Light microscopes Nikon Light microscopes with MBF stereoinvestigator and neurolucida software Leica stereomicroscope Fluorescent microscope Leica cryostat Website

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Postmortem Brain Core The Postmortem Brain Core is organized in collaboration between the UMMC Department of Psychiatry and Human Behavior and the Departments of Psychiatry and Psychology, Case Western Reserve University, Cleveland, OH, and the Cuyahoga County Coroner Office, Cleveland. Investigators are provided with high-quality postmortem human brain samples meeting inclusion criteria for their research aims involving psychiatric illnesses, as well as the critical supporting information for the brain tissue. Equipment

Leica Cryostat CM3050S

Laser Capture Microdissection

-80º freezers

Microm HM400E Website

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Transgenic Core Services

• design of PCR primers for genotyping of transgenic or gene-targeted mice

• protocols and reagents for the isolation of DNA from mouse tails for genotyping

• mouse embryo freezing services for the research community including appropriate hormone treatment of mice, collection of fertilized mouse embryos, embryo freezing and storage

• consultation services for the generation of transgenic and gene-targeted mice

• assistance in obtaining already existing models, whether through commercial or academic sources

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