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Facilities & Resources

Our Department consists of research laboratories, preparatory and service labs, a seminar/classroom, a library, and Departmental offices.  All of our laboratories are properly equipped to utilize biophysical, cellular, molecular, and/or structural approaches to biological problems.  Major items of equipment available in our Department include: all the equipment listed below in addition to preparative ultra-centrifuges (Beckman), BioCAD Sprint (PE Biosystems) chromatography systems, and various beta & gamma counters. 

Core Instrumentation

The Given Analytical Facility was originally started by the Department of Biochemistry with the purchase of a Beckman Model E ultracentrifuge, a Beckman liquid scintillation counter and a Perkin Elmer 60MHz NMR with a NIH Shared Instrument grant in 1969.  The Facility has grown over the years to include the specialized instruments described below.  The Facility has been supported during its 37 years of operation by the Department of Biochemistry and the College of Medicine.  A recharge mechanism is used to capture some of the costs involved in running the facility.

XL-I Analytical Ultracentrifuge (Beckman)

XL-I Analytical Ultracentrifuge (Beckman). This instrument was purchased in 1996 on a NIH Shared Equipment grant.  It can be used to determine the following information about solutes (typically DNA and/or proteins in our hands): 1) solution molecular weight measure of the degree of homogeneity with respect to mass; 2) the overall hydrodynamic shape of a solute in solution; 3) the stoichiometry and equilibrium constants for interacting solutes; and 4) whether aggregates exist, and if so whether the aggregation is a reversible or an irreversible process. 

RSM 1000: Rapid Scanning Monochromator for Absorbance, Fluorescence and Circular Dichroisms (OLIS) purchased in 1998 on a NIH Shared Equipment grant.  The Olis RSM 1000 is a dual beam (or single beam) based absorbance or fluorescence spectrometer with routine data collection rates from 1 to 1,000 scans per second.  The RSM utilizes photomultiplier tubes (PMTs) because PMTs are the most sensitive and fastest detectors available and large dynamic wavelength ranges.  The RSM is designed for maximum flexibility and modularity; the

SM 1000: Rapid Scanning Monochromator for Absorbance, Fluorescence and Circular Dichroisms (OLIS)

hardware and software can be optimized for each experiment.  Additionally a CD module was purchased to obtain CD spectra.

PTI QuantumMaster Spectrofluorometer is an easy-to-use, benchtop, open architecture spectrofluorometer with extremely high sensitivity.  Excitation and emission wavelength are selected by means of auto-calibrated, computer-controlled, scanning QuadraScopic monochromators with continuously variable slits.

PE Biosystems Voyager DE Pro was purchased in 2001 with a NIH Shared Instrumentation grant.  The Delayed Extraction (DE) technology significantly improves mass resolution by increasing the signal-to-noise ratio by decreasing the background. Therefore, analysis of proteins and protein mixtures from various sources can be performed with great accuracy. Additionally the high sensitivity allows for analysis of samples in the femtomole range for proteins and picomole range for oligonucleotides, thereby preserving precious sample. Our use of the Protein Prospector (UCSF) software is able to narrow the parameters and significantly reduce the number of masses necessary to make a valid assignment.  The

PE Biosystems Voyager DE Pro

software also allows identification of proteins by searching a virtual digestion database.

FluoroMax-2 Spectrofluorometer (ISA, Inc.) The FluoroMax-2 has been an invaluable resource in determining physical and chemical characteristics of proteins and their interactions in complexes.  The system is equipped with a 150W Xenon lamp for excitation, a modified Czerny-Turner spectrometer with 1200 grooves/mm, adjustable entrance and exit slits, and a R928 detector that allows detection from 290-850nm.  The FluoroMax-2 can also be used to study the association and dissociation of complexes using polarization and/or anisotropy measurements.  Polarized light is scattered by objects in solution based on their rotational velocity, which is dependent on size.  As molecules in solution associate their size increases, slowing their rotational velocity and increasing the amount of light scattered.  These measurements can be used to calculate association/dissociation constants in the determination of molecular interactions.

Total Internal Reflection Fluorescence Spectroscopy (TIRFS) TIRFS measures surface dependent binding events.  Unlike traditional, discontinuous, non-equilibrium ELISA-type binding assays which cannot accurately model dynamic binding mechanisms, TIRFS permits continuous investigation of surface binding phenomena.  TIRFS is based upon fluorescence excitation by means of an exponentially decaying surface energy wave (evanescent wave).  The penetration depth of the evanescent wave allows excitation only of molecules at or near the surface.  Further, since the fluorescence signal is collected through the quartz element which forms the base of the interaction vessel, rather than through the sample solution, highly opaque solutions can be used in TIRFS studies.

Institutional Resources

Cell Imaging Facility
The UVM College of Medicine operates a Cell Imaging Facility to provide researchers and students throughout the University with state-of-the-art imaging capabilities.  Major items of equipment include: Confocal imaging systems, Atomic force microscope, a Olympus BX50 light microscope for fluorescence <i>In Situ</i> hybridization, both scanning and transmission electron microscopes, Optimax image analyzer, as well as the photographic quality color laser printers. 

Center for X-ray Crystallography (CXX)

Center for X-ray Crystallography

In 1998 the CXX was established as a campus facility to expand structural biology at the University of Vermont.  Its creation and operation is supported by a Howard Hughes Medical Institutes Award to the College of Medicine.  The center is jointly run by four new crystallographers [ K. Chu (Physics), S. Doublié (MMG), S.J. Everse (Biochemistry) and M.A. Rould (MPB) ] and includes a Rigaku RU200 generator, two MAR345 image plate detectors, two mirror systems for focusing the x-rays, and two cryostreams for reducing radiation damage. 

In addition, the CXX has obtained all the equipment necessary to purify and crystallize proteins, including a Gilson 925 high-throughput crystallization robot, DynaPro DLS, and a Pharmacia Akta purification system.  Incubators for growing crystals and dissection microscopes for observing/mounting crystals are also available in the facility.  Liquid nitrogen dewars are available for storing crystals awaiting a trip to the synchrotron and a Xenon-Cryositter is now available for making Xeon derivatives.

With the establishment of the CXX, the College of Medicine has made a strong commitment to structural biology.  In that regard, the College received a second award from the Howard Hughes Medical Institute which brought two Cryo-electron microscopists Michael Radermacher and Teresa Ruiz (Physiology) and two electron microscopes to UVM to augment this initiative.

Dana Medical Library
In 2005, the Dana Library moved into the Medical Education Center providing over 1,200,000 volumes, a complete collection of scientific and medical journals (paper as well as electronic), as well as over 30 workstations for computer-aided literature searches and classrooms for teaching.  The Library connects the University of Vermont and Fletcher Allen Health Care campuses and is flooded with natural light from skylights, furnished with tables and study carrels designed and built by Vermont craftsmen.

Flow Cytometry Center
A NIH Shared Instrumentation Grant has facilitated the purchase of two state-of-the-art flow cytometers for the high speed analysis and sorting of cells and the College supports specialist to assist in their use.  This facility is heavily used by several of the members of our Department.

Life Science Computer Center
The primary mission of the LSCC is to expose our students (both undergraduate and graduate) to structures and the insights they can provide about function.  The room (Given E311) is designed as a classroom with a state-of-the-art projection system.  Individual workareas are equipped with seven G4 PowerMacs to provide students with the opportunity to view or even solve structures.  Publication quality figures are frequently designed at the LSCC and can be printed on the center's printers.

Mass Spectrometry
With current focus on proteomics, mass spectrometry has become the technique of choice. The facility, being built out of Dr. Matthew's laboratory, includes 6 mass specs with new machines arriving each year.

Automated solid-phase peptide synthesizer from Protein Technologies

Microarray Facility
The Microarray Facility (HSRF 305) is the result of a productive collaboration between the Vermont Genetics Network, the Vermont Cancer Center, and the College of Medicine.  The goal of the facility is to provide large scale gene profiling of organisms ranging from prokaryotes to eukaryotes.

Protein Core
The Protein Core was established in 2004 and is managed by Robert Hondal, Ph.D. (Biochemistry).  The facility, housed in the Given Basic Science Building, includes an automated solid-phase peptide synthesizer from Protein Technologies and preparative and analytical HPLC systems obtained with a NIH Shared Instrumentation grant.  A technical support person is supported by the College of Medicine.