About the Department
Department of Biochemistry Core Facilities
Lipidomics/Metabolomics Core Facility
This facility was a key focal point
for development of a sustainable critical mass of expertise in lipid
signaling and state of the art analytical techniques. The Laboratory is
located in newly renovated space on the 2nd floor of Sanger Hall and is
built around two tandem triple quadrupole/linear ion trap mass
spectrometers, a high-end Applied Biosystems 4000 Q TRAP and an Applied
Biosystems 3200 Q TRAP. These instruments have the necessary resolution and
sensitivity for a broad range of qualitative and quantitative lipid and
metabolite analyses required for exhaustive characterization of lipid
signaling molecules and metabolic pathways. The 4000 Q TRAP is the standard
instrument selected for its unique capabilities by the NIH-funded LIPIDMAPS
Consortium. While the 3200 Q TRAP has lower sensitivity and a narrower mass
range than the 4000 Q TRAP, it is similar in operation and has similar
capabilities, allowing its use for less demanding analyses or for training
or teaching purposes.
Cytogenetic Core Laboratory
The Cytogenetics facilities include
research and diagnostic laboratories capable of providing standard
GTG-banding analyses of chromosomes, as well as special cytogenetics
banding; prometaphase studies; numerous fluorescence in situ hybridization
(FISH) studies using a large spectrum of probes; spectral karyotyping; and
methylation testing. The research cytogenetics laboratory additionally
offers comparative genomic hybridization; paraffin-section FISH studies;
micronuclei studies; telomere length assessment studies; sperm chromosomal
complement analyses; and spectral karyotyping. It is located on the 5th
floor of Sanger Hall and is maintained by the Dept. of Pathology.
Histopathology Sared Resource
The histopathology shared resource
was initiated in September 2002 with the recruitment of an experienced
histopathology technician. The histopathology core provides essential
histological processing and analysis services; tissue processing and
paraffin-embedding; sectioning both paraffin-embedded and frozen tissue;
routine histological staining; immunohistochemical staining; Tunel Assay for
apoptosis on tissue specimens; and special work-ups of new antibodies for
immunohistochemical staining. Digital photography of microscopic slides
using the core’s digital camera system is also provided by the facility.
Access to an Arcturus II laser capture microdissection station with image
archiving is available.
Transgenic/Knockout mouse Core Laboratory
This Core offers the following
services: transgenic mouse production; knock-out mouse production, including
ES cell targeting and blastocyst injection; mouse line rederivation by
embryo transfer to eliminate pathogens; cre line X indicator line
(Gtrosa26tm1So) interbreeding, to allow characterization of cre expression
in lines of cre transgenic mice; consulting and various support services. In
addition, embryo cryopreservation is available. It is located on the top
(8th) floor of the Medical Science Building I.
Vector/Virus Shared Resource
The Vector Virus facility offers
services that include generation of replication-incompetent recombinant
adenovirus; purification of larger quantities of adenovirus for animal
studies; and testing for replication-competent adenovirus if necessary. It
is located in the Massey Cancer Center.
Nucleic Acid Synthesis and Analysis Shared Resource
This facility is located on the 5th
floor of Sanger Hall and it consists of a Sequencing Core, Nucleic Acid
Synthesis Core, Real Time PCR Core, MicroArray Core, Molecular
Interactions/Genetic Analysis Core, and a small Bioinformatics Suite. The
Sequencing Core maintains three ABI Fluorescent Sequencers, including one
3700 Prism 96 Capillary instrument. The Synthesis Core maintains two
Perceptive Biosystems DNA synthesizers. The Real Time PCR Core maintains an
ABI 7700 TaqMan™ Sequence Detector. The Bioinformatics Suite is equipped
with several Intel double boot LINUX/Windows desktop workstations containing
a variety of image analysis and quantification software. The MicroArray Core
is a large, multifunctional facility and maintains two spotted array systems
and an Affymetrix GeneChip™ System. The Affymetrix System includes a
fluidics station, a hybridization station, a scanner, and the analysis,
mining and database software required to process, analyze, and store the
data. The Bioinformatics Suite adjacent to the MicroArray Core maintains
desktop software in Window and LINUX OS for microarray analysis. The Center
for the Study of Biological Complexity (CSBC) maintains a web-available
relational database containing all the data from the MicroArray Core in the
GenexVA database installed in the Bioinformatics Computational Core
Molecular Biology Shared Resource
The Molecular Biology Core offers the following services: plasmid, phage, and insert production; subcloning; library screening; and recombinant protein production. This Core also maintains a Molecular Dynamics phosphoimager, which is available to all investigators, and a Molecular Biology Supply Center, which stocks a wide range of molecular biology and tissue culture reagents. It is located on the 5th floor of Sanger Hall.
Flow Cytometry and Imaging Shared Resources
The Flow and Imaging Cytometry Facility is located on the 2nd floor of Sanger Hall. Currently, two instruments are in use, a Coulter Elite ESP and a Coulter Elite XL-MCL (both funded by an NIH Shared Instrument Grant). The Elite ESP is a multi-laser networked system, operated only by the expert facility technician, and the XL-MCL is an automated, user-friendly system that can be operated by users of the core facility. The other focal point of the facility is the Ultima imaging cytometer, an interactive laser cytometer for anchorage?dependent cell analysis. A MoFlow cell sorter was added to this resource in 2005. Two new FACSAria Cell Sorting Systems and flow cytometry analyzers were recently purchased. A Zeiss 510 Meta confocal imaging system provides a full range of imaging services to university researchers. In addition, a Stereology and Ultrastructural Core (confocal and electron scanning microscopy and fluorescence microscopy) is located on the 11th floor of Sanger Hall.
Molecular Imaging Center
VCU has recently established a state-of-the-art Molecular Imaging Center and is developing a comprehensive research program around it. In addition to an advanced, research-grade PET scanner, the Center features a high-resolution MRI scanner, a MicroPET scanner (devoted to research), and a cyclotron to produce the radioisotopes needed for both PET scanners’ clinical and research applications. The facility is located in the basement below the hospital and is available to all researchers by appointment. Cost is at reduced rates compared to those for clinical procedures.
Hybridoma-Monoclonal Antibody Shared Resource
The Hybridoma-Monoclonal Antibody Core produces hybridoma cell lines producing monoclonal antibodies. After developing hybridoma clones, the cell lines are subcloned and grown; portions are subcloned, and cells are stored in liquid nitrogen. Additional services include antibody production, antibody purification, mycoplasma screening, and tissue culture cell production. This facility is located on the 1st floor of the Massey Cancer Center.
Functional Genomics/Proteomics Shared Resource
The Functional Genomics/Proteomics Core includes a MALDI Mass Spectrometer (Micromass); a robotic sample preparation device for MALDI, which digests samples from gels and spots the MALDI plate, using a 96-well format for high through-put; and a 2D gel apparatus with PDQUEST software for gel comparison and analysis. It is located in the Trani Center for the Life Sciences.
Mass Spectrometry Core Laboratory
The Mass Spectrometry Core has state-of-the-art instrumentation for GC/MS, LC/MS and a variety of spectrophotometric instruments along with personnel to provide expertise. This core is located on the 6th floor of Sanger Hall.
Structural Biology Shared Resources
The generation of a Structural Biology Shared Resource was initiated in the late 1980's to efficiently consolidate existing resources, and provide a basis for development of an enhanced facility to provide molecular modeling, x-ray crystallography and nuclear magnetic resonance technologies and services to the scientific community at VCU. The Structural Biology Shared Resource houses an array of resources required for the determination of molecular structure and the utilization of structural information in addressing and solving research problems.
The facility offers macromolecular X-ray Crystallography, Multidimensional Nuclear Magnetic Resonance (NMR), and Spectroscopy Molecular Modeling/Computational Chemistry. The crystallography core facility is housed in the Institute for Structural Biology and Drug Discovery (ISBDD) in the Virginia Biotechnology Park. The institute has laboratory space for crystal growth and handling, and is equipped with incubators, microscopes, glove box, wet laboratory space, and a data collection facility. Virtually all macromolecular crystallography data are collected on a Raxis II image plate detector with a Rigaku rotating anode generator equipped with Osmics mirrors and an Xstream low temperature device. A full library of software for crystallography is available on the local area network and includes CNA, CCP4, Solve, Sharp and molecular modeling software including O and Xtalview for map interpretation. The NMR facility is housed in McGuire Hall, and contains a Varian “Unity + 500” 500 MHz instrument (equipped for multidimensional experiments including a 1H, 13C, 15 N triple resonance probe and a pulsed field gradient module and high stability temperature control); a Varian “Gemini 2000” 300 MHz instrument (upgraded in Fall 2000, equipped for 1H and 13C analysis); a data processing area with a Silicon Graphics Indigo II workstation; and an area for reservations and record management. A Silicon Graphics Indigo 2 XZ workstation is available for off-instrument data processing. Molecular Modeling resources include molecular graphics, computer-assisted drug design, QSAR, and related techniques can also be used to formulate working hypotheses dealing specifically with protein chemistry, enzyme function, and drug development.
The Center of Bioelectronics, Biosensors, and Biochips (C3B)
C3B is a special, multidisciplinary center created within the VCU Department of Chemical Engineering. C3B was created in order to assist in interfacing microelectronics, materials chemistry, molecular biology, and information technology in developing technologies and high performance devices and instruments that are essential for unencumbered study of functional genomics, genetic screening, pharmacogenomics, and molecular diagnostics and monitoring. An advanced DNA microarraying facility and biochips laboratory has been established. The facility enables the production of custom and project-specific cDNA, oligo and protein microarrays and is also used in advanced microarray technology research. This facility has a 1440 sq. ft. class 1000 bioclean room, and is equipped with a Packard Instruments MultiPROBE II HT automated pipetting robot that is integrated with a DNA Engine Thermal Cycler for PCR; a Cartesian Technologies PixSys 5500SQ Pin Array and Liquid Dispensing System for DNA Microarray and Biochip fabrication; a Packard Instruments ScanArray 4000 biochip imager; and an Applied Biosystems 371 DNA Synthesis Machine.
The Division of Animal Research (DAR)
implements all animal health procedures and oversees animal care; 3 full-time and 2 part-time veterinarians and 14 veterinary technicians support the animal care and use program at VCU. DAR consults on such matters as animal selection, usage, and cost. Animal facilities are maintained in 7 buildings, with the main facility in Sanger Hall. Accommodated species include nonhuman primates, pigs, dogs, cats, rabbits, ferrets, guinea pigs, rats, hamsters, mice, and frogs. The DAR has a diagnostic laboratory in Sanger Hall that includes microscopes and other equipment for hematology, serology, and fecal parasitology. Microbiology and serum chemistry is available through the VCU hospital laboratories. Other university laboratories are used for serology, pathology, chemistry, and microbiology. DAR has a Universal 8048 (125kV, 300mAs) machine and ancillary equipment for radiology. Necropsy rooms are available for use by the veterinary staff and by investigators.
Of note are the Substance Abuse Primate Colony and the Transgenic Mouse Core. VCU maintains the only colony of primates physically dependent on opiates used to support NIDA work to evaluate the abuse potential of chemical substances. The L.T. Christian III Transgenic Mouse Core Facility provides VCU investigators an efficient and economical means for producing new lines of transgenic and knock-out mice. Services include pronuclear DNA injection for transgenic mouse production; embryonic stem cell electroporation, screening, and blastocyst injection for knock-out mouse production; mouse line rederivation by embryo transfer for elimination of pathogens; protocols (and demonstrations, if needed) for various aspects of mouse husbandry and screening, and consultation regarding vector design, animal cost calculations for grant proposals, core support letters for grant proposals, IACUC protocol preparation, and related support.
Personal computer systems operate
independently, in local networks, and tied through Ethernet to the
University mainframe systems. Microcomputer software includes standard word
processing, spreadsheet, database, reference management, scientific
graphics, PC SAS programs, and PC-based protein/DNA sequencing packages
(Microgenie Protein/DNA Sequence Data Base and Sequence Analysis Software).
University Technology Services maintain a Digital Equipment Corporation VAX
and SUN UNIX-based workstation cluster on the medical center campus
available to all investigators and provide a direct Ethernet link from the
majority of investigator and trainee desktops to the Internet. Security is
critical for research and every effort is made to ensure the security of
these machines and the data on them.
Technology Services provides support to VCU researchers for study design, site-licensed research software, collecting and managing research data, high performance computing, access to Internet2, and analysis of results. Geographic Information System data and software (and training in their use) are available as well. These resources are available to faculty, staff, and graduate students.
The School of Medicine Computer Based Instruction Laboratory (CBIL) contains 44 computers, a computer classroom, slide projectors, videodisc players, and VCRs to support the curriculum. The Lab also manages student workstations in the Foundations of Clinical Medicine small group teaching rooms in the Egyptian Building and in 14 locations throughout the Medical College of Virginia Hospitals (total of 29 additional workstations). CBIL provides many resources to assist medical students: PDA Medicine, Electronic Curriculum, Electronic Bulletin Board, Medical Resources on the Internet, FREIDA (Fellowship and Residency Electronic Interactive Database), Computerized Testing, Class Scheduler, and textbook catalog. Four full-time staff support the facility and the students and faculty who use it.
The Bioinformatics Computational Core Laboratories
The High Performance Computing Cluster contains a two tower, 64 node Beowulf Cluster with 32 Gbyte of SDRAM, 1 Terabyte of disk storage, a tape backup unit and an uninterruptible power supply; an 8-processor Sun V880 UltraSparc III with 32GB of ram and 960GB internal disk storage, and a 12-processor V1280 UltraSparc system. Over 100 genomics and proteomics software programs and databases are mounted on and maintained on the server for access across VCU. Over 150 additional processors will have been added in the past year. The HPC Cluster is networked to the University Backbone with GigaBit Ethernet and allows access to the VCU computational grid.
Lab contains state-of-the art teaching, distance learning, and video
conferencing capabilities. It has one instructor podium station and 12
student stations, projection capabilities and plasma screen displays,
distance learning and videoconferencing equipment, and other equipment
required for instruction.
The Research Core Lab contains 8 high-end Intel double boot (Windows/Linux) workstations for research applications. These workstations will be available for use by Center Fellows and Associates for short or long term applications. This Research Core also serves as a smaller scale instructional facility, with projection and teaching capabilities. These rooms are all linked to the University backbone through a dedicated Gigabit Ethernet link.
Within the School of Engineering, the Department of Computer Science houses a 32-processor distributed memory, parallel computing system (Linux OS), as well as a parallel computer with two hyper-threaded, dual-core, 64-bit, 3.4 GHz processors (effectively a four processor, shared memory system, Linux OS), having 8 Gigabytes of RAM and 500 Gigabytes each of internal and external storage.
As part of an ongoing plan to maintain its network on the leading edge, VCU has connected to the Internet2 national backbone network Abilene as a member of the Mid-Atlantic Crossroads initiative. VCU has upgraded its current Net.Work.Virginia to an OC-3 (155Mbs) connection which will serve to carry meritorious project traffic to Abilene as well as serve as the link to the commercial Internet.
Research computing support services for VCU researchers
Statistical Applications supported at VCU include: DBMS/COPY, SPSS, Insightful Miner, STATA, JMP IN, Mathematica, nQuery Advisor®, S-Plus, SAS, Sudaan, among others and are available on a variety of platforms (PC, Unix). Support and consultation for using these products for research use are available through VCU Technology Services. The DB2 Common Server, a mainframe level database engine for large scale data collection and research analysis, includes: DB2; Perl programming language, for web-based data collection and queries; SAS and SPSS used in conjunction with DB2, for analysis; PC client-based applications such as MS Access or Visual Basic for data entry; and online documentation for using DB2 at VCU.
VCU houses one of Virginia’s most outstanding academic library systems. The James Branch Cabell Library on the Academic Campus and the Tompkins-McCaw Library on the MCV Campus offer a print collection of over 1.7 million volumes and over 13,000 periodical subscriptions, along with an extensive collection of digital indexes, full-text digital periodicals, and other digital materials, to support the academic work of the VCU community. Both libraries provide leading-edge, web-based services as well as exceptional instruction and individual reference consultation to help support VCU research, teaching, and learning. With over 300 workstations within the two library facilities and powerful network-integrated systems, the VCU Libraries’ collections and resources are available from any computer on the VCU campuses, and with a VCUCard number, from any place in the world with an Internet connection. VCU Libraries is a founding member of the Association of Southeastern Research Libraries, the Scholarly Publishing and Academic Resources Coalition, and the Coalition for Network Information. It is also a resource library of the National Network of Libraries of Medicine and a member of the Virtual Library of Virginia (VIVA), and the Southeastern Library Network, among others.