Grant Language: Boilerplates
VCU Flow Cytometry Core Laboratory:
"The VCU Flow Cytometry Core Laboratory was established in 1976, and has been constantly modernized since that time. It currently occupies over 1500 sq ft in the Kontos Medical Science Building and the Molecular Medicine Research Building, and provides a comprehensive instrumentation suite and technical services in support of both cell sorting and analysis on a fee-for-service basis. The core currently features six primary instruments. Cell sorting is conducted using two multi-laser BD Aria II sorters. One of the Aria units is enclosed in a Baker BioProtect Hood, enabling the sorting of human and biohazardous tissues. In addition, the core supports three analyzers, a BD Canto II, a Coulter FC500, and a Coulter XL-MCL. Capabilities include up to 9 color simultaneous detection (including UV and violet laser capability) and up to 4 simultaneous sorts per Aria II. In addition to flow instrumentation, the core also maintains a Biacore T100 surface plasmon resonance (SPR) instrument for determination of protein interaction constants. The director, Daniel H. Conrad, has over 25 years of experience in flow cytometry. The laboratory manager and head technician, Julie Farnsworth, is highly trained in flow cytometry has been with the core for more than 9 years. The resource provides a wide range of services, including instrument training, routine fluorescence analysis, and development of innovative custom analysis and sorting protocols. Walk-up instrument time is also available to trained users. This core maintains a stable base of instrumentation, expertise, and trained personnel and currently provides services and training for multiple users in over 60 research groups from 21 departments at VCU. The Flow Cytometry Core laboratory is supported, in part, by funding from the NIH-NCI Cancer Center Support Grant (P30 CA016059)"
VCU Transgenic Mouse Core:
“The VCU Transgenic Mouse Core laboratory, established in 2000, provides a comprehensive suite of services for the creation of genetically modified mice. The facility, located on the 8th floor of the Molecular Medicine Reseach Building occupies ~1000 sq ft of space, including a 600 sq ft laboratory, a 150 sq ft tissue culture room, and a 250 sq ft animal holding room. The facility is well-equipped (primary instrumentation includes a Olympus IX-71 inverted injection scope with DP-72 digital camera and stage cooling, Narishige micromanipulators, and a Celtram air microinjector), and offers the production of both transgenic and knock-out or knock-in mice. All stages of transgenic mouse production are offered, including consulting, creation of targeting vectors, ES cell electroporation, screening of ES cell clones, blastocyst injection, and breeding of chimeras. In addition, the core laboratory also has extensive expertise in the mouse line re-derivation by embryo transfer, embryo and sperm cryopreservation, tail DNA preparation and genotyping. The core also maintains an IVIS spectrum imager for live animal imaging. The core is directed by Dr. Jolene Windle, who has been actively involved in developing genetically engineered mouse models since 1986. She is supported by Resource Manager Greg Campbell, who has worked with transgenic animals since 1996, Laboratory Specialist Jillian Stifflinger, and Research Associate Dr. Mark Subler. The Transgenic Mouse core laboratory is supported, in part, by funding from the NIH-NCI Cancer Center Support Grant (P30 CA016059)”
VCU Structural Biology Core Laboratory:
“The VCU Structural Biology Core Laboratories, established in 1999, facilitates access to a comprehensive suite of instrumentation and computational resources in support of macromolecular structure determination. There are three main components to the core --X-ray crystallography, Nuclear Magnetic Resonance (NMR), and Molecular Modeling. The overall administrative director of the core is Dr. Jan Chlebowski, who oversees managing directors for each subcore. The subcores are as follows: 1) X-ray crystallography (managers Martin Safo, Ph.D., Tony Wright, Ph.D., and Faik Musayev, Ph.D.) resources include a Rigaku Raxis-IV++ imaging plate system, MicroMax-007 rotating anode, a Blue Max-flux confocal optical system, an x-stream cryogenic system, and a RAXIS-IV++q stage; 2) NMR (manager Neel Scarsdale, Ph.D.) operates a Bruker Avance III 700 MHz instrument (new in 2009) suitable for 1D, 2D, 3D or 4D homo- or hetero-nuclear experiments. The instrument features three RF channels with pulse field gradients, permitting the acquisition of data for triple or pseudo-quadruple resonance experiments; 3) Molecular Modeling (manager Glen Kellog, Ph.D.) is supported by a suite of 8-core ApplePro and HP linux 4 Core graphics workstations, supplemented with a Linux-cluster back-end with over 2000 compute cores provided by the VCU Center for High Performance Computing. Software supported by the Molecular Modeling includes the commercial Tripos Sybl suite, and a number of other packages, including CCP4, GOLD, Dock, AutoDock, HINT, NAMD, Hex, etc.). In addition to instrumentation, the core provides training and consultation, both through formal classes, and one-on-one with individual investigators. The Structural Biology Core laboratory is supported, in part, by funding from the NIH-NCI Cancer Center Support Grant (P30 CA016059)”
VCU Biological Macromolecule Core Laboratory:
“The VCU Macromolecule Core Laboratory (Director, Shirley Taylor, Ph.D.), newly established in 2010 by the consolidation of the former Molecular Biology and Virus Vector core laboratories, provides a range of services to the VCU research community on a fee-for-service basis. The focus of the core is the production of biological macromolecules for multiple endpoints. In addition to routine molecular biology support services such as DNA preparations, insert purification, and DNA transformation, value-added services include the production of research grade vector virus particles (adenovirus, adeno-associated virus, retrovirus, and lentivirus), production of targeting vectors for the production of knock-in/knock-out mice (in conjunction with the transgenic mouse core) and somatic cell lines, and other specialized or challenging custom DNA projects. With the addition in 2010 of a new Co-Director (Darrell Peterson, Ph.D., a protein biochemist), the core is now able to offer an extensive range of protein expression and purification services. Recombinant proteins are available from bacterial, yeast, insect, and mammalian origin. The core laboratory is housed in two locations. There is a 900 sq ft general molecular biology lab on the 6th floor of Sanger Hall with a 100 sq ft tissue culture area and a 150 sq ft office. In addition, viral vectors are produced in an access-limited 900 sq ft facility equipped with a Forma double-unit CO2 incubator, a Nikon tissue culture microscope, and a Beckman ultracentrifuge. Bacterial protein production is carried out in a facility at the Virginia Biotech Research Park using a BioFlo4500 biofermentor, supported by additional equipment available in Dr. Peterson's adjacent protein purification laboratory. The Macromolecule core laboratory is supported, in part, by funding from the NIH-NCI Cancer Center Support Grant (P30 CA016059).”
VCU Nucleic Acids Research Facility Core Laboratory
“The Nucleic Acids Research Facility (Director Gregory Buck, Ph.D.), located in approximately 2000 sq ft on the 5th floor of Sanger Hall, was established 1986, and provides five primary service lines on a fee-for-service basis to VCU researchers. These are: 1) A DNA sequencing core that provides both NextGen and traditional Sanger-based approaches to DNA sequencing and related genomics applications including transcriptomics, ChIP-seq, and methylation analysis. NextGen sequencing instrumentation includes a pair of Roche 454 GS-FLX (running Titanium chemistry), an Illumina GAIIx, and new in spring 2011, an Illumina HiSeq2000, cBot workstation, and Covaris nebulizer. Sanger sequencing is supported with an ABI 3730XL and an ABI 3130 sequencers; 2) A DNA microarray core that provides transcriptomics and genotyping / SNP analysis, supported by a suite of instrumentation (fluidics workstation, hybe station, and scanner) supporting Affymetrix DNA arrays, as well as an Illumina Beadstation 500x; 3) A Real-Time PCR core supported by an ABI 7900/HT suitable for Taqman and other popular PCR based assays; 4) A gene synthesis core now specializing in cost-efficient synthesis in FRET probes for Taqman PCR. Service arrangements also exist with commercial providers for overnight delivery of standard oligonucleotide probes. To support the various business lines, the NARF now employs 7 FTE positions, including new positions created in 2011 of an instrument tech and a bioinformatican devoted to support of NextGen sequencing methods. The Nucleic Acids Research Facility is supported, in part, by funding from the NIH-NCI Cancer Center Support Grant (P30 CA016059)”
VCU Center for High Performance Computing:
“The VCU Center for High Performance Computing (CHiPC; Director Gregory Buck, Ph.D.) is located in approximately 2000 sq ft of total space, predominantly on the third floor of Harris Hall on the Monroe Park Campus. The mission of the CHiPC is to provide high performance computing services for the VCU research community. To accomplish this goal, the CHiPC maintains four major supercomputing clusters, each specialized for different computing environments. They may be summarized as follows (descriptions current as of May 2011): 1) teal.vcu.edu is the primary cluster intended for large scale parallel computing, and is especially well suited for applications such molecular dynamics simulations. Teal consists of ~2480 64 bit AMD compute cores, each with 2-4 GB RAM/core, 8 TB of /home space, and tmp space of 180 GB per node. High speed network infrastructure is provided by a 20 Gb/second infiniband architecture; 2) bach.vcu.edu is the cluster designated for serial and small parallel applications. Bach consists of a total of ~764 AMD 64 bit cores, each with a minimum of 2 GB/core RAM, 1 TB total RAM, 2 TB of /home space, and /tmp space of 50-164GB per node. Networking infrastructure is gigabit ethernet; 3) godel.vcu.edu is a cluster optimized for bioinformatics applications, with ~244 Opteron 64 bit cores, each with 2 GB RAM/core, 6 TB of /home space, tmp space of 180 GB/node, and a mixture of gigabit and 10 Gb ethernet networking; 4) watson.vcu.edu is a small cluster dedicated to specialized bioinformatics applications, with Sun V1280 12 Sparc IV+ cores, 96 GB of RAM and 2 TB of storage. Network is provided by gigabit ethernet. The clusters are collectively served by ~200TB of networked storage. To support this infrastructure, the CHiPC employees 6 FTE positions, (J. Mike Davis, Technical Director; John Noble & Carlisle Childress, Systems Analysts; John Layne, Applications Analyst; Neel Scarsdale, Ph.D., Assistant professor and Applications specialist, and Nihar Sheth, Bioinformatics Applications Specialist). In addition to maintaining the hardware, the CHiPC works collaboratively with the user base to maintain and optimize a large number of applications and development tools (NAMD, Gaussian, Gromacs, Charm, C/C++, Fortran compilers, etc.)”
VCU Tissue and Data Analysis and Acquisition Core Laboratory
“The VCU Tissue and Data Analysis and Acquisition Core (TDAAC; Directors Catherine Dumur, Ph.D., and David Williams, M.D.), established in 2002 and located in the 6,400 sq ft VCU Molecular Diagnostics Facility, has as its goal the acquisition of human specimens and associated clinical and pathological findings to support translational research. This is done both through the aegis of the VCU-IRB approved “Tissue Acquisition System to Support Cancer Research” (TASSCR) protocol, which supplies specimens to a biorepository supporting cancer research through acquisition of residual tumor and normal tissue samples along with informed consent from patients with cancer. In addition, TDAAC collects tissue, hematopoietic and serum samples which support specific investigator initiated IRB approved research projects. The specimen acquisition process ensures that the primary purpose of the specimen for patient care is maintained and the quality of the specimen is optimal for biomedical research. These services are achieved through leveraging a network of interdepartmental and informatics relationships within the VCU Health Systems. TDAAC staff in collaboration with Department of Pathology based Molecular Morphology Genomics Laboratory and Laser Capture Microdissection Laboratory provide samples of extracted, quality controlled RNA and DNA from human tissues, frozen sections, and cryopreserved samples of viable hematopoietic neoplasias. Because TDAAC is an outgrowth of a multicenter grant that focused on gene expression microarray studies on multiple cancer phenotypes, some samples have associated gene expression data as a part of their annotation. The VCU Molecular Diagnostics Laboratory is a state-of-the art CLIA-certified laboratory and performs clinical as well as research molecular testing with state-of-the-art equipment, including one bioanalyzer (Agilent 2100), two robotic systems for automated nucleic acid extraction (Roche MagNA Pure LC System), automated DNA sequencers (ABI 310, and 3100), several real-time PCR instrumentation systems (including ABI 7700 and 7500, as well as a Roche LightCycler™ System), a Thermo Spectrophotometer; a Leica CM1850 Cryostat, four Thermo Scientific Revco PLUS Ultra-Low Temperature Freezers, three Thermo Scientific Locator 4 PLUS Cryobiological Storage Vessels, a NanoDrop ND 1000 Spectrophotometer, an Applied Biosystems MagMAX Express nucleic acid extractor, and a complete Affymetrix GeneChip® workstation for DNA microarray technology. All temperature-sensitive equipment is constantly monitored by an electronic system (CheckPoint: 24/7 monitoring system) and all ultra-low freezers have a built-in LN2 backup system that automatically releases LN2 into the freezer in case of temperature failure. The VCU TDAAC is supported, in part, by funding from the NIH-NCI Cancer Center Support Grant (P30 CA016059)”
VCU Mid-Atlantic Twin Registry:
“The Mid-Atlantic Twin Registry (MATR; Scientific Director Judy Silberg; http://www.matr.vcu.edu/) is located at the Virginia Institute for Psychiatric and Behavioral Genetics (VIPBG), under the Office of the VP Research at Virginia Commonwealth University (VCU). The MATR is a population-based registry of twin pairs ascertained from birth records and school system records of Virginia, North Carolina, and South Carolina. The registry’s mission is to identify, trace and recruit population based samples of twins and their families to participate in research undertaken by scientists at VCU and other institutions. The registry conducts and/or facilitates such research through collection of preliminary data and referral of eligible subjects to investigators while protecting the rights and privacy of study participants. The subjects have primarily been drawn from the more than 170,000 identical and fraternal twin pairs born in the three states between 1913 and 2009. Many of the twins and their family members have participated in numerous research projects. To fulfill its goal to be a model for the protection of the privacy of research participants, the MATR has established a privacy policy and strict Standard Operating Procedures (SOPs) to protect the confidentiality of participant data. These SOPs address such issues as respect to participants, protection of privacy, confidentiality of data transmission etc. Employees sign an understanding that breach of these procedures is grounds for dismissal. The MATR twin pairs join the registry with an interest in promoting genetic and health research and are therefore willing to provide appropriate samples as requested by studies. The MATR can promote research in various ways, including arranging DNA collection (blood, bucal swab, or saliva), mailed or web surveys, telephone recruitment, or advertisments in the MATR newsletter distributed annually to all registrants. MATR also coordinates with researchers to ensure proof of human subjects protection review and other subject protections prior to initiation of any study.
VCU Microscopy Core Laboratory
“The VCU Microscopy Core Laboratory (Director Scott Henderson, Ph.D.), housed within the Department of Anatomy and Neurobiology, is located in an approximately 2500 sq ft facility spread over several rooms on the 9th floor of Sanger Hall, is a fee-for-service core which provides the instrumentation and expertise to facilitate a comprehensive spectrum of imaging methods and techniques. Instrumentation and services include: 1) Electron microscopy (TEM, SEM) is supported with a Jeol JEM-1230 TEM equipped with a Gatan UltraScan 4000SP 4K x 4K CCD camera, and a Zeiss EVO 50 XVP SEM equipped with digital image acquisition, SE, VPSE & BSD detectors, extended variable pressure (up to 750 Pa), Deben coolstage and a water vapor introduction kit; 2) Confocal laser scanning microscopy, supported by two systems: A Leica TCS-SP2 AOBS (inverted) with a spectrophotometer scan head, a high resolution Märzhäuser MCX-2 motorized XY stage and three confocal detectors (PMTs) (plus a transmitted light detector). The system has five lasers: blue diode (405 nm), Argon (458, 476, 488, 514 nm), green HeNe (543 nm), orange HeNe (594 nm) and red HeNe (633 nm). The spectrophotometer scan head allows the user to “tune” the detectors to any emission wavelength. The second is a Zeiss LSM 510 META (inverted) with 2 standard confocal PMTs, a transmitted light detector and the META detector (for spectral imaging). The system has four lasers: blue diode (405 nm), Argon (458, 476, 488, 514 nm), green HeNe (543 nm) and red HeNe (633 nm). This later system is suitable for multi-photon laser scanning microscopy; 3) The facility boasts five wide-field fluorescence instruments. The primary instruments are: Olympus BX51 fluorescence microscope equipped with UV, FITC, TRITC, and FITC+Texas Red filtersets, a Prior Proscan XY motorized stage, a Heidenhain microcator, an Olympus OLY-750 color CCD camera, and an Optronics Magnafire camera; the second primary fluorescence instruments second is a Nikon ECLIPSE E800M fluorescence microscope equipped with UV, FITC, TRITC, GFP and FITC+TRITC filtersets, and a Diagnostic Instruments Spot RT CCD camera; a third instrument is a Zeiss Discovery V20 Stereo zoom microscope with transmitted, reflection and fluorescence illumination, 0.63x, 1.25x and 1.5x lenses, filter sets for GFP, CFP, YFP and DsRed and a Axiocam MRc CCD camera; 4) Total internal reflection (TIRF) microscopy is supported by an Olympus TIRF microscope system (IX 81 inverted stand) equipped with a 100x/1.45 NA Plan Apochromat TIRF objective, DIC and phase optics, filter sets for detection of blue, green and red fluorescence, an Exfo X-cite illumination system and a Hamamatsu Orca ER CCD camera. The system has Argon (458, 476, 488, 514 nm) and 561 nm diode lasers, each with independent beam steering optics for two-channel TIRF and an LSM Technologies AOTF to regulate beam intensity; 5) The facility is equipped with a Veeco BioScope II Atomic Force/Scanning Probe. The AFM/SPM resides on a Zeiss AxioObserver Z1 inverted microscope stand equipped with fluorescence optics, an Exfo X-cite fluorescence illumination system and an AxioCam MRm CCD camera for the concurrent imaging of fluorescent signals. A heater/perfusion chamber is available to permit live-cell imaging. The entire system is housed within a TMC Acoustic Vibration Isolation System. This equipment suite (supported by sputter coaters, ultramicrotomes, critical point dryers, etc.) allows the core to offer many types of imaging methods and sample preparation services including: Sample preparation; Live-cell imaging; Immuno-localization (fluorescence, EM); Fluorescence in situ hybridization (FISH); Fluorescence recovery after photobleaching (FRAP); Fluorescence resonance energy transfer (FRET). The core also provides image analysis and histological techniques. Training is available for all of the imaging modalities and methods offered. The VCU microscopy core laboratory is supported, in part, by the NIH-NINDS centre core grant 5P30NS047463-02.”
VCU Nanomaterials Characterization Core Laboratory:
“The VCU Nanomaterials Characterization Core Laboratory (Director Everett Carpenter, Ph.D.), founded in 2010, is VCUs newest core laboratory. The nanomaterials core provides a comprehensive instrumentation suite for VCU researchers interested in nanomaterials, or surface characterization. The facility features a ThermoFisher ESCAlab 250 X-ray photoelectron spectrometer. The ESCALab is multitechnique platform for studying the surface of materials. The instrument is equipped with a 95 mm field emission gun for Auger spectroscopy and SEM imaging with a 90nm spatial resolution and a UV photoelectron lamp. The sample stage is an automated 5-axis stage for angle resolved XPS with heating and cooling from 77K to 600K. The system also has a High Pressure Gas Cell for introduction of reactive gases for absorption studies. The center also has two scanning electron microscopes and a transmission electron microscope: a Hitachi SU-70 FE-SEM, a Jeol JSM-5610 LV ZEISS libra 120 TEM. The Hitachi SEM is a field emission unit which allows for a 1nm spatial resolution. The unit also is equipped with a STEM options, a Nabity Lithography System and Genesis EDAX system with low element windows for detection of Be to Pu. The Jeol system is also equipped with an Oxford EDS system and is equipped for High Vacuum SEM as well as Low Pressure SEM functions. The Libra is Zeiss workhorse microscope which features point to point resolution of 0.34 nm. Included in the scope is a in-column Omega filter which allows for energy electron lose spectroscopy (EELS) with an energy resolution of <1.5 eV. The microscopy features a GATAN bottom mount camera for acquisition of digital images. The center also houses a VEECO ICON atomic force microscope. The ICON features VEECO's latest technology providing AFM with less than a 35 pm signal to noise operating in tapping mode. The instrument is capable of operating in multiple modes including lateral force (LFM), magnetic force (MFM), surface potential, scanning capacitance (SCM), Tunneling (TUNA or STM), and conductive (CAFM). The instrument is equipped with a variable temperature stage and a wet cell sample holder. Acquisition of instrumentation in the Nanomaterials Characterization Core laboratory was funded, in part, by grants from the National Science Foundation.”
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