VBRN Proteomics Facility is supported by INBRE funding (P20GM103449) and is located in the Firestone Medical Research Building at the University of Vermont. It occupies 1,514 sq ft of lab, data processing unit, office, and consultation space. The Proteomics Facility enables investigators to use an array of state-of-the-art mass spectrometry-based techniques for proteomics experiments, ranging from routine protein identification, post-translational modification characterization and finding protein interacting partners, to large-scale quantitative proteomics analyses using stable isotopes (dimethyl labeling, SILAC, TMT). Since its inception in 2006, the facility has analyzed over 20,000 samples and supported more than 200 publications (https://vbrn.org/proteomics-publications/). The facility personnel train investigators in experimental design and proteomics methods, while assisting with data interpretation, manuscript preparation, and grant submission. Our user base includes investigators from UVM and from institutions in 15 states.

A summary of the facility’s impact on the development of the network can be found at https://vbrn.org/proteomics-impact/.

Core Facility website: https://vbrn.org/proteomics/

The goal of the Data Science Core is to provide support for the design and analysis of molecular biological experiments. To accomplish this goal we meet with investigators to identify consensus needs and then develop pipelines consisting of support services that efficiently satisfy these needs.

The MIC Live Imaging and Physiology Core is a division of the Microscopy and Imaging Center of the UVM Larner College of Medicine. The Live Imaging and Physiology Core provides a wide range of imaging techniques mainly for live-cell, live-tissue and in-vivo preparations. We maintain a Noran/Prairie Technologies OZ LSCM (laser scanning confocal microscope), a DeltaVision RT restoration microscopy system, a Zeiss LSM 7 MP dedicated multiphoton LSCM, a Nikon TIRF (total-internal reflection fluorescence) system, a Nikon/Yokogawa CSU-W1 spinning disk microscopy system, a Nikon SMZ-1500 fluorescence stereoscope, and an Iconeus functional ultrasound system. Patch-clamp electronics are available for use on most microscope systems, and each system has an integrated perfusion setup. The core can also fabricate small apparatus for experiments with our Formlabs 3D printer.

The Functional Magnetic Resonance Brain Imaging Program (FMR-BIP) is located within the Clinical Neuroscience Research Unit (CNRU) of the Department of Psychiatry. Its primary goal is to perform functional brain imaging studies collaboratively with the Department of Radiology utilizing the new 3 Tesla Phillips Achieva scanner and the CNRU experimental image capture and analysis system. In addition, the FMR-BIP works collaboratively with other laboratories within the Psychiatry Department to serve mutual research interests. The FMR-BIP collaborates across the Neuroscience Consortium with investigators in the Departments of Neurology, Anatomy, Psychology, as well as GCRC investigators to further develop brain imaging expertise at UVM. This is a collaborative effort between the departments of Psychiatry and Radiology. The functional imaging experimental and analysis expertise reside in CNRU-Psychiatry. Technical personnel necessary to operate the imaging program including MR physicist, fMRI radiologist, and technicians are employed by the Department of Radiology in the College of Medicine.

This facility is centrally located on the third floor of the Health Science Research Facility and includes infrastructure that provides comprehensive support for the design, execution, and analysis of experiments involving Next Generation Sequencing through access and use of the Illumina HiSeq 1500 sequencer. All next generation sequencing projects are reviewed using an integrated approach to experimental design, workflow, and sample collection in collaboration with the UVM bioinformatics core facilities to ensure high quality results. The facility is directed by Julie Dragon and Scott Tighe, and performs a wide range of analysis including target preparation for RNAseq, Exome Seq, ChIP seq, Methyl Seq, whole genome sequencing, and small RNA sequencing.The core is heavily involved in all aspects of Nanopore sequencing

The Harry Hood Bassett FCCS Facility is located Given Medical Research Building Room C316-UVM. The facility provides state-of-the-art flow cytometers to the UVM community as well as others Colleges nearby. Additionally, FCCS Facility personnel provide scientific and technical consultation to faculty and staff in the design of flow cytometric experiments, and assistance in data analysis and interpretation.

Dry Lab Personnel: Julie Dragon, Korin Eckstrom, Ramiro Barrantes, John Hanley (bioinformatics)

Wet Lab Personnel: Scott Tighe, Kris Finstad, Cassandra Orr

Services: Experimental Design, Metagenomics, Comparative Expression Analyses, Variant Analyses, and Systems Biology

IMF Labs specializes in the design and development of prototypes to advance research. Experienced design engineers are on staff to complete product development in Solidworks and testing in Labview. A comprehensive machine shop exists to turn a variety of materials into functional prototypes.

At the light and electron microscopic levels, it provides state of the art, quality assured, morphologically oriented services. The MIC is operated on a fee for service basis and provides professional consultation and assistance with equipment use, experimental design and interpretation.
The MIC occupies approximately 2000 square feet in the Health Science Research Facility at the University of Vermont and contains the following imaging equipment:

1.JEOL 1400 transmission electron microscope with AMT 11 megapixel digital camera.

2.JEOL JSM 6060 scanning electron microscope with attached Oxford INCA energy dispersive spectroscopy detector for element analysis.

3.Nikon Air HD confocal scanning laser microscope.

4. Nikon C2 confocal scanning laser microscope.

5. Andor Spinning Disk confocal microscope

6. Zeiss LSM 7 Multiphoton confocal microscope

7.Nikon STORM super-resolution light microscope.

8.Olympus BX50 research microscope for transmitted light, phase contrast, and epi-fluorescence microscopy.

8. Asylum Research MFP-3D BIO atomic force microscope.

9. Asylum Research Cypher Environmental atomic force microscope

10. Arcturus XT-Ti Laser Capture Microdissector system.

11.Olympus IX70 inverted microscope with associated Applied BioPhysics Electri Cell-Substrate Impedance Sensing (ECIS Ztheta) system.

12. Leica VERSA 8 whole slide imager

11 Dedicated Dell workstations containing Molecular Devices MetaMorph image analysis software for complex quantitative image analysis, Indica Labs HALO software, Improvision Volocity, MBR StereoInvestigator

PLEASE SEE OUR WEB SITE FOR DETAILED INSTRUMENT DESCRIPTION AND RECENT PUBLICATIONS.

For over forty years, the Instrumentation & Model Facility (IMF) has been the University of Vermont's centralized source for custom instrumentation design, fabrication, and 3D modeling. We provide creative, high quality, cost effective, and timely services and products for researchers, students, educators, other universities, state government, healthcare institutions, and innovative companies enhancing Vermont’s economic future. IMF engineers employ technical expertise in mechanical, materials, electrical, optical, and programming disciplines to solve application problems for customers. We have a complete machine shop with CADD/CAM and can work with a variety of materials, Objet Polyjet 3D printing, and a electronics/computer development laboratory. This service is available at reasonable rates with estimates provided if requested.

The Clinical Research Center provides UVM and UVM Medical Center Researchers with the necessary infrastructure for the conduct of efficient and productive high quality clinical research. The CRC provides a conducive environment for studies of normal and abnormal body function and for investigations of the cause, progression, prevention, control, and cure of human disease. Use of the Center for interdisciplinary, collaborative research and training in medical research is encouraged. The CRC is available to investigators from all medical specialties and from the basic sciences. Extramurally funded research (grant, foundation and industry sponsored) as well as investigator-initiated studies are all welcome.

The Clinical Research Center is physically located on the 2nd floor of the Shepardson Building at the University of Vermont Medical Center in Burlington, VT. We support primarily Outpatient studies, although, depending on the specifics, we can handle intensive, Inpatient studies as well. The Clinical Research Center has the capacity to support, as inpatient subjects, up to twelve individuals per day for overnight stays. Services available to our investigators include Research Administration, Research Nursing, Research Nutrition Services, Research Laboratories (Biochemistry, Physiology, Imaging Core) and Informatics. Referrals to Biostatistics and Research Pharmacy services are available.

The Office of Animal Care Management oversees the operation of research animal facilities at the University of Vermont. The University's research animal facilities currently house approximately 8,000 animals of which over 98% are mice and rats. The majority of the research rodents are high-health status animals maintained under barrier conditions. Animal models facilitate discovery in the areas of infectious disease, endocrinology and metabolic disease, cancer and chemotherapy, immunology and respiratory disease, among others. The University of Vermont's Animal Care program is fully accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC, International).

The VCC Biostatistics Shared Resource provides consultative and collaborative support to VCC investigators in the general areas of study design, data collection and quality control, data processing, data management, statistical methods development, statistical analysis and interpretation, and manuscript preparation.

Facilities are available on a fee-for-service basis for robotic set-up of crystallization trials (for protein and/or DNA/RNA samples) and for collection of x-ray diffraction data from macromolecular crystals. (Note: This facility is not equipped to collect diffraction data from crystals of 'small molecules' ~<1000 Daltons MW.)

This facility, sponsored by the NIH/NIGMS COBRE program, provides consulting expertise, training and many sophisticated pieces of equipment for performing molecular biology, proteomics, cell culture, histology and microscopy. The following major pieces of equipment are available in the core: Zeiss Palm Microlaser, Biotek Synergy H4 Plate Reader, Ciphergen SELDI-TOF, Countess Cell Counter, Microbrightfield Neuroleucida Morphometrics system, Odyssey Infrared Imager, BioRad Calligrapher microarray printer, Qiacube robots, BioRad Experion and much more. Use of the equipment is currently free for all users.

The Laboratory for Clinical Biochemistry Research (LCBR) is housed in the Colchester Research Facility (CRF) of the College of Medicine, three miles from the main campus. The LCBR is under the coordination of Dr. Russell P. Tracy, and includes the independent research activities of Drs. Tracy, Cushman, Huber, Jenny, and Doyle and approximately 25 technicians, students and Fellows. The LCBR is staffed by an administrative assistant (Ms. Pam Burton) and an overall laboratory coordinator (Ms. Elaine Cornell); it encompasses 6,668 sq ft broken out as laboratory space (2847 sq ft), office and ancillary space such as cold rooms (2071 sq ft), and freezer storage space (1200 sq ft). The laboratory houses equipment and personnel engaged in clinical and pre-clinical cardiovascular research, in three general areas: 1) large scale epidemiological studies, 2) clinical trials, and 3) animal models. In the first two areas we engage in assay development and large scale assay work in many areas, with emphasis on coagulation, inflammation and fibrinolysis. Measurements are made in blood, urine and DNA samples. Assays are done for phenotypes as well as genotypes using equipment such as automated microtiter plate readers, Dade Behring BNII nephelometer, automated coagulation instruments (Stago STA-R), Roche Integra 400 and Roche Elecsys 2010, Bio-Rad BioPlex Protein Array System for bead-based Luminex technology, MesoScale Discovery Multi-array analyzer, Beckman Coulter LH 500, Tosoh Hematology analyzer, PCR thermocyclers, ABI Prism 7900 for automated, taqman-based SNP analysis. In the third area, we focus on mouse models of atherosclerosis and the roles of inflammation and immunity in development of early lesions (fatty streaks), using different strains of mice, and various transgenic and knock-out animals.
The LCBR provides an excellent facility for assay performance, whether the assays be clot based, chromogenic, immunometric or nucleic acid-based. All assays are performed under strict quality assurance standards, and a complete procedure manual is available. Over the last 18 years, we have measured samples from over 70,000 people, and our Sample Repository currently houses ~140 freezers with a total inventory of over 3 million aliquots of serum, plasma, urine, cryopreserved white cells and isolated DNA. In these samples are pre-prepared sample sets for establishing normal ranges, examining biovariability, and developing DNA-based assays (with anonymized samples).

Teaching and research facilities of the Materials Science program are primarily located in Cook Physical Sciences Building (Physics, Chemistry) and Votey Hall (Electrical and Mechanical Engineering). Votey and Cook are adjacent to one another and are located on the central campus of UVM.

Many of the faculty in the Materials Science Program have developed individual laboratories to conduct their chosen research topics. In those laboratories the capabilities to perform a variety of experimental investigations including thin film growth, polymer studies, nondestructive studies, micromechanical measurements, and chemical synthesis have been developed. The Materials Science Program shares the Chemistry Department Facilities and Microscopy Imaging Center. Individual departments also maintain user laboratories which include the sophisticated characterization facilities listed below.

Light Scattering
Small-Angle Neutron Scattering
X-ray Diffraction and Scattering
Material Processing
Micromechanical Force Measurements
Microscopy
Spectroscopy
Noninvasive Ultrasonic Imaging
Rheology
Thermal Analysis