Resources

The University of Vermont

Biological research at UVM occurs in 4 buildings that are all attached (Given Medical Research Building, Health Sciences Research Facility, Stafford, and Mills Buildings). This promotes ease of scientific interactions and attendance at seminars. It would be impossible to summarize all the diverse equipment and facilities available to participating faculty and trainees in the College of Medicine, in each of the individual laboratories, but key cores available to our trainees are described below.

Basic Science Facilities

All faculty have adequate space. The Vermont Lung Center (Irvin, Bates, Suratt, Wagers, Whittaker, Allen, Poynter, Weiss, Janssen-Heininger) occupies 6173 sq. feet in the Health Science Research Building. Immunobiology (and G. Davis) occupy 3700 sq. feet on the third floor of the attached Given Building.

Microscopy Imaging Center

The Microscopy Imaging Center is a College of Medicine core facility and occupies approximately 4000 square feet in the new research building (adjacent and attached to the Given Complex and the same floor as the VLC). It contains the following imaging equipment: A JEOL 1210 transmission electron microscope; a JEOL T-300 scanning electron microscope; an Olympus BX50 wide-field upright microscope for transmitted light, phase contrast, and epifluorescence microscopy; a BioRad MRC 1024ES confocal scanning laser microscope system; a Digital Instruments BioScope Nanoscope IIIa atomic force microscope; a CompuCyte Laser Scanning Cytometer; a Zeiss Axioscope 2 wide-field fluorescence microscopy system; an Arcturus PixCell II Laser Capture Microdissector system; and a Dell 400 workstation for image analysis and processing. All of these instruments are linked via ethernet connections, allowing sharing of images within the facility, as well as transmittal of the digital images off-site. Extensive image processing and analysis software packages located on the various computers housed within the Microscopy Imaging Center, including the central imaging workstation, can then be utilized for analyzing any image digitally captured. Moreover, images can be imported into desktop publishing packages and prepared for publication printing on a Fujix video printer. The facility is run by five full-time technicians and is directed by Dr. Douglas Taatjes.

Flow Cytometry Facility

The Harry Hood Bassett Flow Cytometry Facility is a College of Medicine core facility that houses a Coulter Elite flow cytometer. The unit is equipped with 3 lasers (air-cooled argon, helium-neon, and water-cooled Coherent INNOVA 90 for UV) and 8 detectors, 2 for detection of light scatter and 6 for fluorescent measurement. The instrument configurations allow for the analysis and sterile sorting of cells, multicolor analysis, and measurement of physiological responses of live cells such as calcium fluxes. Data analysis can be performed at the time of acquisition or at a later time on individual workstation. A second Coulter Excel machine is also available for multicolor analysis without the need for sorting. The facility run by a full-time technician and is directed by Dr. Ralph Budd.

DNA Sequencing Facility

This is run by the Vermont Cancer Center and is available to all investigators. Primary services offered include DNA sequencing, DNA fragment analysis and real-time quantitative PCR. The facility contains an ABI 373 XL automated sequencer with stretch plate capability, 48 lane upgrade and a recent filter wheel upgrade to enable state-of-the-art chemistry, enhanced run length and optimal signal to noise ratio for sequence runs. The facility also contains an ABI 310 Prism Genetic Analyzer. A Luminex 100 instrument has been acquired to enable high-throughput DNA hybridizations (or antigen-antibody or ligand-receptor reactions) on styrofoam beads. An ABI 7700 (TaqMan) instrument and the software have been acquired to allow real-time quantitative PCR experiments to be performed. Capacity for microarrays, including a senior faculty member and technician to direct the work, is presently being organized and should be in place by the end of 2003.

Animal Facility

A fully equipped and AAALAC-approved facility exists in the basement of the Given Research Building. A new state-of-the-art facility will be fully open by the end of 2003 in the new Health Sciences Research Facility (HSRF) which is attached to the Given building. This will be run by Charles River and contains complete Hepa-filtered in and out air supplies to individual bubble chambers that hold either 20 or 50 cages of 5 mice each. This system has been in use at Charles River for over 10 years without a single infection outbreak. The new facility will house only mice and will have capacity for about 5 times the current number of mice at UVM.

Transgenic Mouse Facility

The transgenic facility is now located at the UVM Colchester Satellite Research Facility (3 miles north of the main campus), but will be relocated in the new Health Sciences Research Facility building by the end of 2003. It is currently composed of 5 animal rooms, storage rooms, cleaning room, and a microinjecting laboratory. This laboratory is equipped with an inverted Diaphot 200 microscope, a MF-9 microforge, 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. The facility has generated 15 different transgenic mouse models for investigators in the University since it was established 3 years ago. Embryonic stem cell cultures and blastocyst implantation techniques are established now at the facility to generate knock-out mice based on support from the COBRE grant. The facility is run by two full-time technicians and is directed by Dr. Mercedes Rincon.

Inhalation Facility (Votey Facility)

The Inhalation Facility at UVM was established by SCOR funding from NHLBI approximately 20 years ago and has continued support on RO1s and PPG NIH grants from Drs. Brooke Mossman and Yvonne Janssen-Heininger. The facility utilizes 4 horizontal inhalation chambers with auxiliary support equipment for flow control and monitoring, including 4 Wright dust feed aerosol generators, 3 Timbrell dust feed aerosol generators, and a fluidized-bed aerosol generator. Airborne dust can be sampled and analyzed with Sierra and cascade impactors, Royco 225 light scattering particle detector, GCA RDM 301 mass monitor, CSI-NO2 chemi-luminescent air quality monitor, and the samples further characterized with a Sartorius 4 and 5 place electronic balance, a Cahn microbalance, a Zeiss Universal microscope with epiplan, phase contrast, brightfield and polarized-light optics, and a Zeiss Videoplan image analysis system with computer. Additional laboratory equipment includes a computerized milling machine and lathe capabilities for development of research equipment, muffle furnaces to 1400°C, autoclave, refrigerated Beckman J-21 centrifuge, 2 AT&T 6300 computers, and an AT&T 6386-20MHz workstation (in Dr. Hemenway’s office). General laboratory space is available in associated, ancillary space (2,000 ft²) as well as 150 ft² office, with 1500 ft² dedicated to the animal care and inhalation facility. This unique resource is directed by Dr. David Hemenway.

Computer

The animal physiology setups each have an associated computer (IBM Pentium II or faster). There is extensive software available for statistical analysis, data plotting or code analysis (ANADAT, SCIREQ), the latter written and developed by the Co-PI (Bates). The PI has an AppleG4 desktop and laptop computers along with printers (Hewlett Packard 2200 and Epson 1280) and a scanner (Epson 1650). Statistical consultation and analysis is also readily available through the biostatistics/biometrics department at UVM. Each computer is networked through the UVM Ethernet for data sharing, email and access to Medline, GenBank, etc. via the library facilities.

Equipment Fabrication

UVM has an extensive shop facility (IMF) which is available for the fabrication of further devices (exposure chambers, plethysmographs, etc.) on a fee-for-service basis. The College of Medicine maintains a full-service medical library and medical photo/illustration service for the making of prints, posters, slides, etc.

Clinical Science Facilities

Fletcher Allen Health Care (FAHC)

FAHC is the primary teaching institution for the Pulmonary and Critical Care Medicine fellowship training program. It is the flagship teaching hospital for the University of Vermont College of Medicine. It is a 500-bed hospital, with 46 adult ICU beds, serving the entire state of Vermont and much of upstate New York. It serves as both a primary care facility for the greater Chittenden County area (populations of approximately 200,000) and a a tertiary care referral center for its entire catchment area (in excess of 1,000,000 individuals). It is the primary site for hospitalization and ambulatory services for all the major managed care providers in the region. It is the only Level I trauma center for the entire state of Vermont. Members of the Pulmonary and Critical care Divisions at FAHC are the only providers of PCCM in the Burlington area. As such it represents a unique setting for clinical research due to single point of patient flow.

Pulmonary and Critical Care Medicine Division (PCCM)

The division is comprised of 17 faculty (14 MD, 3PhD (see Appendix 9)) and one critical care nurse practitioner. Members of the PCCM run a closed MICU service, an inpatient pulmonary service, a pulmonary consultation service, a bronchoscopy service and a pulmonary function laboratory.

Outpatient Pulmonary Clinic

The Pulmonary clinic is located on the third floor of the Medical Office Building at the Fanny Allen Campus of Fletcher Allen Health Care. The clinic is under the direction of the Pulmonary and Critical Care Medicine unit with Dr. Theodore Marcy as the Medical Director and MS. Mary Navin as the Head Nurse and administrator. The clinic has a waiting room, four exam rooms, a pulmonary function laboratory fully equipped to perform spirometry, lung volumes, diffusing capacity, complex exercise testing and inhalation challenge studies. The clinic also has its own check-in and discharge areas, medical records room, conference room and staff offices for Ms. Navin and Dr. Marcy. There are more than 1600 patient visits to the clinic annually and more than 4800 pulmonary function tests are performed. The Vermont Lung Center, which serves as the clinical research focus for the Pulmonary and Critical Care Unit, is also in the Medical Office Building, on the first and third Floors. Both Drs Kaminsky and Dixon have offices there.

Vermont Lung Center Clinical Trials Facility

The Vermont Lung Center also has a facility for clinical research within the Pulmonary and Critical Care division. It occupies approximately 1600 square feet of the first floor of the Medical Office Building at the Fanny Allen campus. This is conveniently located next to the outpatient pulmonary clinic. The center is equipped with Collins BP and GS pulmonary function testing equipment, a Medgraphics Elite plethysmograph, Medgraphics Diagnostic System (portable), Top-Gear exercise bicycle, DelVilbris Ultra Neb 99 ultrasonic nebulizer, Nellcor pulse-oximeter, one negative-pressure ventilation hood, Adams Compact II centrifuge, 1 G.E. refrigerator/freezer, 3 Dell Optipex GX110 computers, 2 IBM 300GL computers, 2 Dell Latitude Laptops, 4 HP printers, 1 HP scanner and 2 fax machines. In addition the center has 2 Olympus BFXT40 bronchoscopes with video and photographic equipment for performing bronchoscopies. Currently we are conducting 13 trials. There are three trials in progress and one pending for the ALA-ACRC. Two of these are NIH supported (TAPE, GERD). Three trials are more basic investigator driven, one funded by Merck, one by the Whittaker Foundation and one by NCRR COBRE. Industry is funding five other studies that investigate therapeutics in patients with Asthma, COPD and ILD. The center is run by 3 full-time clinical research coordinators, and directed on a day-to-day basis by Drs. David Kaminsky and Anne Dixon and who reports to Dr. Irvin for program direction.

Northern New England Critical Care Organization

To expand our capacity for research involving critically ill patients, Dr. Parsons, with Drs. Michael Young and Jason Bates at the University of Vermont, has established the Northern New England Critical Care Organization for research with investigators from two other tertiary care teaching institutions, Maine Medical Center (Drs. S. Mette, Chief of Pulmonary Medicine and Dr. R. Riker) and Dartmouth-Hitchcock Medical Center (Dr. J. Leiter, Professor of Medicine and Dr. H. Manning, Associate Professor of Medicine). These three institutions provide tertiary care for the states of Maine, New Hampshire, Vermont and part of upstate New York and account for more than 6,000 ICU admissions annually. The group has established a common data base and there are identified support personnel in each institution. The group has completed a study, Ventilation of Patients with Acute Lung Injury and ARDS: Has new evidence changed clinical practice?. A study of breath to breath measurements of pulmonary resistance in mechanically ventilated patients is underway at the three sites and a protocol is in development for a study evaluating the variability of the rapid shallow breathing index (RSBI). Dr. Kalpesh Ganatra, a fellow in Pulmonary and Critical Care Medicine and Dr. Matthew Arentz, an intern in Internal Medicine, are actively involved in the development and execution of the RSBI protocol.

General Clinical Research Center

The General Clinical Research Center at the University of Vermont has been continuously funded by the National Institutes of Health for the last 39 years. It occupies the entire seventh floor of the Baird Building in the affiliated teaching hospital, Fletcher Allen Health Care. It is configured to allow for both inpatient stays and outpatient visits and is staffed with experienced and skilled research nurses who assist in a multitude of investigative techniques. In addition, there is a research nutrition service and three core laboratories. The Biochemistry and Sample Handling Laboratory assists in the acquisition of samples, alliquoting, freezing and certain radio immuno assays. The Human Physiology Laboratory is equipped with two dual energy x-ray absorptiometers, an apparatus for testing maximal volitional exercise exertion (VO₂ Max), four delta track calorimeters, a hydrostatic weighing unit and three ultrasound machines. The Mass Spectrometry Core Facility is equipped with gas chromatography-mass spectrometers (2), isotope ratio-mass spectrometer (2) and liquid chromatography-mass spectrometers (3). There is also a systems manager who is responsible for our intranet and investigators have access to the GCRC Biostatistician.

Bioinformatics Facility Description

The overall goal of the Bioinformatics facility is to develop and maintain a comprehensive program of bioinformatics research support in the areas of biostatistics, statistical genetics and epidemiology. The staff includes seven PhD biostatisticians and epidemiologists, one PhD behavioral scientist, five MS level biostatisticians, and two support staff. Efforts are directed at research problem specification, study design, data collection and quality control, data processing, statistical modeling and analysis, and interpretation of results. A full set of standard statistical software is maintained along with other specialized packages. Fee for service consultations and longer term collaborative grant related activities are the norm.