One of the strengths of the University of Vermont is the availability of well-managed core facilities for research that are accessible to all members of the research community. These core facilities feature state-of-the-art equipment for molecular cellular research. Training or service-for-a-fee is available at all facilities.

COBRE Neuroscience Imaging Core Facility

Director: Todd Clason

  •     Noran high speed scanning confocal microscope
  •     Deltavision Deconvolution Restoration System
  •     Biorad Multiphoton Microscope
  •     Calcium Imaging Microscope
  •     TIRF

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COBRE Neuroscience Molecular Cellular Core Facility

Director: Sheryl White

LiCor Odyssey Infrared Scanner

  •     ABI 7500 Fast Real Time PCR System
  •     PALM/Zeiss Laser Microdissection Microscope
  •     Ciphergen Protein Chip Biomarker System

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Microscopy Imaging Center

Director: Douglas J. Taatjes, PhD

TEM: Transmission Electron Microscopy: JEOL 1400 Transmission Electron Microscope.

  •     SEM: Scanning Electron Microscopy: JEOL JSM 6060 Scanning Electron Microscope with Oxford INCA EDS system.
  •     Confocal Laser Microscopy: Zeiss LSM 510 META Confocal Laser Scanning Imaging System.
  •     Super Resolution Miscroscopy: Nikon N-STORM Super-Resolution Microscope.
  •     AFM: Atomic Force Microscopy: Asylum Research MFP-3D BIO Atomic Force Microscope.
  •     Light Microscopy:
  •         Olympus BX50 Light Microscope with QImaging Retiga 2000R digital camera.
  •         Olympus IX70 Inverted Light Microscope with QImaging Retiga 2000R digital camera.
  •         Olympus SZX12 Dissecting Light Microscope with Optronics MagnaFire digital camera.
  •         Leica MZ16F Fluorescence Dissecting Light Microscope with Leica digital camera.
  •     ECIS: Electric Cell Substrate Impedance Sensing: Applied BioPhysics ECIS System.
  •     Cytometry: Compucyte Laser Scanning Cytometer.
  •     Microdissector: Arcturus XT-Ti Laser Capture Microdissector.
  •     Whole Animal Imager: Caliper LifeSciences IVIS Lumina II Whole Animal Imager.
  •     Image Analysis: Universal Imaging MetaMorph Workstation, Volocity and Stereo Investigator Workstation.

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Advanced Genome Technologies Core

Manager: Timothy Hunter

This core consists of three facilities: the DNA Analysis Facility, the Vermont Genetics Microarray Facility, and the Massively Parallel Sequencing Facility.  In addition, the core provides equipment, training, and education in basic molecular techniques such as RNA isolation, qPCR, western blotting, and molecular cloning.


  •     Automated DNA Sequencing

        -Cycle sequence reactions
        -Sequence runs

  •     Fragment Analysis

        -Genotyping, haplotyping, microsatellite markers
        -T-RFLP, AFLP

  •     Realtime QPCR

        -Quantitative PCR (absolute or relative)
        -Allelelic Discrimination Assays
        -SNP Detection (low or high-throughput)

  •     RNA and DNA extractions
  •     Nucleic Acid and Protein Quantification
  •     Molecular Imaging
  •     Consultation and Troubleshooting
  •     Computer workstation with DNA analysis software
  •     Instrumentation

        -ABI Prism 3100-Avant Genetic Analyzer (4 capillary)
        -ABI Prism 3130xl Genetic Analyzer (16 capillary)
        -ABI Prism 7900HT Sequence Detection System (Real-time qPCR)
        -AB 7500 Fast Real-time PCR System
        -ABI 6100 Nucleic Acid Prep Station
        -BioRad EXQuest Spot Cutter
        -BioRad Personal Molecular Imager FX
        -BioRad Molecular Imager FX (with external Laser)
        -BioRad Fluor-S MultiImager
        -DNA Engine 96-well gradient Thermal Cycler (2)
        -NanoDrop (2)

Computer Annex
The software accessible to users includes: GeneMapper, Autoassembler, Sequence Navigator, DNASTAR, Sequencher, Chromas, Edit View, BioEdit, Quantity One, Primer Express, Primer Select, and Dissociation Curve software.

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Microarray Core Facility

Manager: Tim Hunter

  •     Experimental design consultation (jointly with Bioinformatics Group)
  •     Assistance in RNA and DNA Extractions "LCM, Flow sorted, difficult tissues"
  •     RNA Quality/Quantity assessment
  •     Gene Expression Profiling
  •     DNA Mapping (SNP, LOH, CNV)
  •     Expression profiling using 3', Exon and Gene Arrays
  •     Hypothesis testing: gene or pathway-based
  •     Support letters for grant applications; text for publication
  •     Discounted pricing on many consumables and reagents through core facility negotiations

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MRI Center for Biomedical Imaging

Co-Directors: Joshua Nickerson, MD and Richard Watts, PhD

Supporting Biomedical Research
The UVM MRI Center was established in support of biomedical research at the College of Medicine, and around throughout the University. As a College of Medicine core facility, we concentrate on functional MRI (fMRI) and specialized neuro-imaging; however, our state-of-the-art 3T MRI scanner is fully equipped and we have the ability to image almost any anatomical structure. We have purchased custom made mouse and rat coils that allow us to obtain images with sub-millimeter (200μ) resolution.

During the fall 2013, the magnet was upgraded to Philips' most recent system platform. UVM became the first site in North America to operate the "d-Stream" MRI system, which supports unlimited coil channels and direct signal digitization at the receiver coil. The digitized signal results in improved signal-to-noise-ratio (SNR), which often translates into increased resolution.

The MRI Center is able to support various types of qualitative and quantitative imaging techniques, including:

  •     Cardiac
  •     Diffusion (Including DTI or DKI)
  •     Functional (fMRI)
  •     High-Resolution Anatomical Structural
  •     Perfusion (Also pCASL)
  •     Small Animal
  •     Spectroscopy (Molecular)
  •     T1 and T2 (Both qualitative and quantitative)
  •     T1ρ

Dr. Joshua Nickerson, M.D.-Co-Director and Neuroradiologist
Dr. Richard Watts, D.Phil-Co-Director (MRI Physicist)
Dr. Trevor Andrews, Ph.D-Assistant Professor (MRI Physicist)

Administrative/Technical Staff
Jay Gonyea, MS-Administrative Director
Scott Hipko, BS-Senior Research Technologist

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Proteomics Facility

Director: Dr. Ying Wai Lam

The Proteomics Facility of the Vermont Genetics Network (VGN) is an interdisciplinary core facility in collaboration with the Department of Biology, Department of Chemistry, and the College of Medicine at the University of Vermont. The facility provides a central resource of proteomics measurements to identify, characterize and quantify the proteins present in different biological and biomedical samples by using the state-of-the-art mass spectrometry.

  •     Protein identification by peptide mass fingerprint using MALDI-TOF-MS (limit: single protein)
  •     Protein in-solution digestion and identification by LC-MS/MS
  •     Protein in-gel digestion and identification by LC-MS/MS
  •     Identification of proteins in a mixture by LC-MS/MS (limit: < 200 proteins in a mixture)
  •     Identification of protein posttranslational modifications: phosphorylation, methylation . . .
  •     Determination of protein complexes from client-supplied protein mixtures
  •     Identification and quantification of specific peptides from proteins using selected ion monitoring
  •     Assistance with system biology methods

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Protein Core Facility

Assistant Director: Steven Flemer

Seeded with the equipment from two NIH Shared Instrumentation awards, the Protein Core was established by Dr. Robert Hondal in 2004. Over the years it has provided researchers with hundreds of peptides and access to our MALDI mass spectrometer.

Current services include:

  •     Custom made peptides
  •     A limited mass spectrometry service

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Bioinformatics Core

Director: James Vincent

The VGN Bioinformatics Core provides bioinformatics support for researchers throughout Vermont. We meet with researchers to discuss the scope of projects, develop plans to meet research needs and then carry out the bioinformatics work. The bulk of our current efforts are focused on projects utilizing massively parallel sequencing.

Bioinformatics services provided:

  •     Microarray

        -Expression: GeneChip
        -Microbial diversity: PhyloChip

  •     Proteomics

        -Quantitative proteomics

  •     Massively Parallel Sequencing (MPS)
  •     Metagenomics

        -Taxonomic profiling:
            -16S amplicon
            -whole metagenome
        -Functional profiling (beta):
           -Whole metagenome

  •     Transcriptomics

           -Reference-based expression profiling
           -De novo transcript assembly
            Reference-based annotation

  •     Assembly & Annotation

        -Microbial single-genome assembly
        -Draft genome annotation

Ancillary services provided:

  •     Storage

        -Data management plans
        -Large-scale sharing
        -Project data management

  •     Computing

        -Local Galaxy instance
        -NSF XSEDE
        -On-demand cloud clusters

  •     Training

        -Galaxy workshops
        -Outreach modules
        -Bioinformatics courses

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COM Biostatistics Unit

Director: Taka Ashikaga

A biostatistics research and service unit providing capabilities in Biostatistics, Statistical Genetics, Epidemiology, Randomized Clinical Trials, Experimental Design, Data Management and Processing, and Survey Research.

  •     statistical analyses
  •     image processing and analysis
  •     data translation from one application format to another (e.g. spreadsheet to SPSS, SAS, etc.)
  •     curve fitting and nonlinear estimation for compartmental models
  •     sophisticated plots or charts
  •     database/application development

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Flow Cytometry Center

Director: Jonathan Boyson

The Harry Hood Bassett Flow Cytometry Center (FCC) is a College of Medicine Core Facility designed as a multi-user resource for the high speed analysis and sorting of cells. The FCC contains two state-of-the-art flow cytometers, the BD LSRII analytical cytometer and the BD FACS Aria high-speed cell sorter. Each instrument is equipped with 3 solid state lasers that allow multicolor analysis. This equipment was purchased through a National Institute of Health Shared Instrumentation Grant. Investigators who bring samples to the FCC for sorting or analysis pay a fee, which is used to partially offset operating expenses. The FCC provides professional consultation and assistance with equipment use, experimental design, and interpretation.

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Animal Resources Center

The University supports an AAALAC-accredited animal research laboratory facility utilized for teaching and research activities.

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Center for X-ray Crystallography (CXX)

The Center for X-Ray Crystallography is the hub for high-resolution structural biology at the University of Vermont. X-ray crystallography allows biological and biomedical researchers to visualize proteins, RNA, DNA and their complexes at atomic resolution. The molecular details of specimens as small as DNA binding domains and as large as the ribosome have been elucidated via this powerful method. The CXX provides resources for all stages of macromolecular structure determination:

  •     screening of samples for 'crystallizability' via dynamic light scattering
  •     automated high-throughput (robotic) screening for crystallization conditions
  •     crystal incubation at various temperatures from 4C to 30C
  •     preparation of heavy-atom and anomalous derivatives (including high-pressure noble gas infusion)
  •     collection and reduction of x-ray diffraction data (cryogenic or room temperature)
  •     solution and analysis of structures with state-of-the-art clustered computing hardware

Unlike the crystallographic laboratories at most other universities, the CXX is run as a facility available to researchers across the UVM campus who wish to add high-resolution macromolecular structural characterization to their research program. The CXX is located in rooms E312-E316 of the Given Building. For further information, contact:

  •     Mark Rould (CXX Director) 6-9532,
  •     Sylvie Doublie (CXX Supervisor) 6-9531,
  •     Stephen Everse (CXX Supervisor) 6-8271,
  •     Kelvin Chu (CXX Supervisor) 6-0064,

The CXX operates within guidelines set by the UVM Radiation Safety Office and the UVM Environmental Safety Office.

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Cryoelectron Microscopy Facility

Director: Michael Radermacher

Research focuses on the three-dimensional structure determination of macromolecular assemblies using electron microscopy combined with image processing.

Transgenic Mouse Facility

Director: Mercedes Rincon

Dr. Mercedes Rincon, a member of the Immunobiology faculty, directs this facility. This facility is located within the Animal Facility in the Health Sciences Research Facility. It contains five bubble chambers for newly derived transgenic founders, storage rooms, and clean room housing the microinjecting laboratory. This laboratory is equipped with an inverted Diaphot 200 microscope, a MF-9 microfuge, a Sutter horizontal pipette puller, a PLI188 Nikon picoinjector, M0188 hydraulic manipulator, a gooseneck light guide-coupled SMZ-U stereoscope, CO2 incubator, refrigerator, CCD B&W camera, Panasonic Monitor and VCR. The transgenic facility itself has been created as a strict barrier facility to maintain a pathogen-free environment. It is funded partially by a Howard Hughes Medical Institute grant to UVM. Dr. Rincón has generated over 30 different transgenic mouse models for her own research and other investigators in the University since she established this facility four years ago. Embryonic stem cell cultures and blastocyst implantation techniques are established now at the facility by Dr. Rincón and John Dodge, the facility research coordinator, to generate knock-out mice.

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Dana Medical Library

The Charles A. Dana Medical Library serves the information needs of the Academic Health Center at the University of Vermont. The Academic Health Center is comprised of the faculty, staff and students at UVM's College of Medicine and the College of Nursing and Health Sciences, as well as the physicians and other health care providers at Fletcher Allen Health Care. The Library also meets the health sciences information needs of the University of Vermonts undergraduate and graduate programs and is open to the citizens of the state of Vermont with health sciences information questions.

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