Center for Hypertension and Personalized Medicine

CORE FACILITIES

PHYSIOLOGICAL CORE

The physiological core is well equipped with various instruments to provide technically advanced physiological evaluation in rodents.
Cardiac and vascular functional assessments: Two highly sophisticated 4-channel multi myograph systems available to measure vascular reactivity (Multi wire myograph system - 620M, Danish myotechnology, Denmark); A Millar pressure-volume catheter and its recording system, to measure PV-loops and dP/dT for diastology and cardiac function; Acuson Sequoia™ C512 Ultrasound system for echocardiography from SIEMENS (This item is available through the University core laboratory facility); Mouse Monitor S heated platform with pulse oximeter module and ultrasound cable to sync to Asucon sequoia C512 for ECG and pulse oximetry from Indus Instruments.

Blood Pressure measurements: This aspect of the Physiological Core is operated and maintained by the Core Facility Manager, Blair Mell, BS. The Center provides access to two IITC equipment for semi-automated tail cuff blood pressure measurement in rats and mice, two CODA tail-cuff blood pressure system from Kent scientific and apparatus for direct blood pressure measurements of 24 animals concurrently by telemetry (Data Sciences International). An implantable Stellar telemetry system (TSE) that allows 24 hour blood pressure monitoring of 16 animals at once with just one wireless receiver.  This allows for animals to be co-housed and have normal social interaction since the animals do not need to be single housed and placed on their own platform receiver.

Surgical equipment: Schott ACE I goose neck fiber-optic light source for visualization during surgical and other procedures; Kent Scientific SurgiSuite Heated surgical platform with LED light and magnetic retractor sets for mouse and rat; Kent Scientific mouse/rat intubation kit and stand; Harvard Apparatus MiniVent type 845 rat/mouse ventilator; Olympus SZX7 Dissecting microscope with Olympus DF PLAPO lens and a boom stand; Dage MTI color HD camera with connections for recording pictures and video.

Renal function measurements: Two metabolic cage units to collect urine samples from 72 animals.  NanoDrop 3300 Fluorimeter from Thermo Scientific for FITC-inulin based measurement of whole animal and single kidney glomerular filtration rate (GFR).

Aerobic running capacity tests: Two rodent treadmills to measure the aerobic running performance of the rats from Columbus Instruments (Model Exer-4; Columbus, OH).

GENETIC/GENOMIC CORE
The genomic core contains equipment required for genotyping, functional assays, mutation detection and positional cloning: StepOnePlus™ 96-well Real-Time PCR System from AB-bio system; digital camera for recording agarose electrophoretograms from Gel logic- 100 imaging system, Kodak. Protean II Xi 2-D Electrophoresis from Bio-Rad; Omega Lum G chemiluminescence/UV-VIS gel and membrane documentation system from Aplegen; Blotcycler automated membrane processor from Precision Biosystems; Applied Biosystems (ABI) 7500Fast qPCR machine; Qiacube from Qiagen-for extraction of RNA, DNA and Protein; TissueLyser LT with 12 tube adaptor from Qiagen; Agilent 2100 Bioanalyzer.                                  

Microbiome Core:
The microbiome core is equipped with an Illumina MiSeq next generation sequencer that can generate 15 Giga bases and enables pooling of 96 samples in a library for metagenomics analysis. The core provides 16S metagenomics services for internal and external users, including DNA extraction, library preparation, sequencing and data analysis from a variety of biological samples (feces, saliva, oral swabs, tissues) of rodent, fish and human origin. After sequencing, data (FASTQ files) is processed and provided to the user in a compressed folder that includes operational taxonomic unit (OUT) summary, diversity analysis, taxa summary, enriched taxa, predicted functional pathways and statistical analyses.  The microbiome core also performs whole genome sequencing for cultured bacteria using Illumina Nextera XT library kit, with as little as 10ng of DNA. For pricing and more information click here: Microbiota/Microbial Community Services.

Other Institutional Resources:

The following resources are available through the George Isaac Laboratory for Cancer Research (GILCR). This laboratory was established following generous funding from the George Isaac family. Under the direction of Dr. Willey, this laboratory harvests expertise and resources from the UT-Promedica community to advance collaborative translational lung cancer research. Major equipment available at the GILCR are: an Ion Torrent PGM System for next generation sequencing, three thermal cyclers for PCR (one of which is an ABI Fast 7500 realtime instrument), three Agilent 2100 Bioanalyzers for microfluidic capillary electrophoresis and analysis of nucleic acids and proteins, six agarose gel electrophoresis units with power supplies, two microcentrifuges, two tissue culture laminar flow hoods, two tissue culture incubators, one fume hood, an inverted microscope with digital camera, balances, a refrigerated tissue culture centrifuge, a Nanodrop spectrophotometer, two refrigerators, two - 30 degree C freezers and one -80 degree C freezer. A Fluidigm Access Array system is available on loan from Fluidigm in the P.I.’s laboratory and a MinION MkI nanopore next generation sequencing device has been delivered to the University of Toledo as a beta test device, and is accessible for this proposed project. Shared resources include FACSAria IIU and FACSCalibur flow cytometers, Abbott m2000 and Life Technologies StepOnePlus real-time PCR instruments, a refrigerated high-speed centrifuge, autoclaves, walk-in cold room, and a dark room with an automated processor.

BIOINFORMATICS CORE

The CHPM Bioinformatics Core is operated and maintained by Dr. Xi Cheng. This core provides the infrastructure for the analysis and visualization of large datasets, with an emphasis on various sequencing data and promotes individual researchers to tap the ever-growing data generated by new research technologies. CHPM has power tools for the analysis and visualization of RNA-Seq, ChIP-Seq, DNA-Seq, and Methyl-Seq data using Strand-NGS software package (V.2.5.1). Strand NGS supports an extensive workflow. The workflow includes various features including standard differential expression analysis, differential splicing analysis, differentially methylated cytosines across samples/target genomic segment, detecting variants (SNPs, MNPs and short InDels), copy number variations, identifying transcription factor binding sites, and identifying histone modification sites using the PICS and MACS peak detection algorithms as well as. It also supports for novel discovery including identifying novel genes and exons and novel splice junctions. It includes the ability to detect variants in the transcriptome, and the ability to detect gene fusion events. Further downstream analysis such as GO, pathway analysis, etc can be performed on the set of interesting genes.

Additional bioinformatic resources are available through the UT Health Science Campus Bioinformatics Computer Lab,  which was developed for both teaching and research purposes. This computer laboratory contains a dual 2.0 GHz G5 processor Macintosh running Mac OS X Tiger, and a 3.0 GHz, 2.5 GB RAM Dell computer running Windows XP. In addition, the lab recently acquired 18 Intel core duo 2.66 GHz iMacs, with 4 GB of RAM, and running a dual-boot OS with Windows XP and Mac OS X Leopard. They are fully networked and thus can be used as a UNIX cluster during off-peak hours. In addition, there are two Linux workstations (16 cores with 2.8 Ghz processors; 128 GB of RAM; 2 TB hard drive) and six modern computers with Internet2 access via the College’s gigabit Ethernet backbone, and has an assortment of software for managing, analyzing and graphically representing data. All the computers are equipped with SAS, SPSS, R, and n-Query program. These computers have access to the Ohio state-wide grid of supercomputer clusters from Ohio Supercomputer Center (OSC), Columbus, OH, and support from the personnel for parallelization of large-scale computations. OSC’s HP-built, Intel® Xeon® processor-based supercomputer, dubbed the Oakley Cluster, can achieve 88 teraflops or, with acceleration from NVIDIA® Tesla™ graphic processing units (GPUs), a total peak performance of 154 teraflops.

VASCULAR PATHOLOGY CORE
The laboratory of vascular pathology consists of a dedicated area (~100 sq. ft.) of laboratory space fully equipped for animal surgery, dissection, necropsy and cryosectioning. The pathology laboratory is adjacent to a cold room and refrigerators and freezers, and is equipped with a Zeiss Axiovert 40CL inverted microscope (bright field and fluorescence, with X-Cite 120Q Illuminator system) with Micropublisher 3.3 Megapixel Cooled CCD Color Digital Camera, coupled to NIS Elements D software for acquisition and analysis, including camera and Nikon Motorized Microscope Drivers and computer system; a HM550 Cryostat (Thermofisher) and dissection microscope with stroboscopic lights. A separate area within the pathology laboratory is dedicated to tissue and slide processing for immunohistochemistry and immunofluorescence. 
LIPIDOMICS CORE
The lipidomics core is operated and maintained by Dr. Levison, who is an expert in the use and operation of high end analytical instrumentation including various High Performance Liquid Chromatographs and Mass Spectrometers. The facility includes Single Quadrupole and Ion Trap GC/MS, High Resolution Q-TOF and Orbitraps, Triple Quadrupoles and Quadrupole Ion Traps. These LC/MS systems provide the necessary chromatographic resolution to optimize sensitivity and specificity for the identification of disease pertinent bio-markers and drug metabolites. Dr. Levison expertise in liquid chromatography specific to high throughput analyses includes online solid phase extraction, and multiplexed multichannel parallel HPLC.
BIOCHEMICAL CORE
The biochemical core contains all the standard equipment necessary for all biochemical analysis from tissue/cell culture samples. Polytron- PT3100D tissue homogenizer from Kinematica AG, temperature controlled Sorvall RC-5C Plus Superspeed Centrifuge, NanoDrop 2000 UV-Vis Spectrophotometer from Thermo scientific, SpectraMax spectrophotometric micro plate reader from Molecular Devices and GloMax-96 Microplate Luminometer from Promega. Two laminar flow hoods and two inverted microscope for cell and tissue culture from Leica. ELISA plate shaker; 96-well plate washer; ultracentrifuges; Environ Shaker from Lab-Line; Centrivap Concentrator from Labconco; Gel Dryer from Bio-Rad; WKL 230 Water Cooler from Brinkman; HM550 Cryostat from Thermofisher; Biological Safety Cabinet from Forma Scientific; Heracell 150i Tri-Gas cell culture incubator from Thermo Scientific; Bio-rad TC10 automatic cell counter; Hugo Sachs Elektronik Easy Cell Extraction System Type 803 for isolation of primary cardiac fibroblasts and myocytes via aortic perfusion of whole hearts from Harvard Apparatus. Odyssey Infrared protein detector system: this system provides a highly sensitive and accurate way to quantify immune-detected proteins on blotting membranes. It also has the capability for simultaneous detection and quantification of multiple proteins. 
IMAGING CORE
The core is equipped with a Leica TCS SP5 Laser Scanning Confocal Microscope with a Multi-photon Laser and is located within the University of Toledo's Advanced Microscopy & Imaging Center.  Specifically, the Leica TCS SP5 is equipped with both conventional and high-speed resonance scanners. The Multi-photon laser is attached to an inverted microscope and allows deeper penetration into tissue with less photo-bleaching/damage. Five lasers plus multi-photon excitations are available, producing the following laser excitation lines:  458, 488, 514, 561, 633, and 710-990nm (from the tunable Ti-Sapphire MP laser).  The system is capable of collecting up to 7 colors simultaneously for quantitative confocal image analysis, 3D reconstruction, FRAP and FRET, animation, stereo imaging, single layer projection, time lapse collection, and co-localization analysis.
Last Updated: 8/18/17