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Hopkins Core Facilities

Microarray Facility: The JHMI Microarray Core Facility is located on the 3rd floor of the BRB adjacent to the JHICC space. The JHU Microarray Core Facility houses two Affymetrix GeneChip Hybridization 640 ovens, one 320 oven, two GeneChip Fluidics 450 Stations, and one high resolution Affymetrix GeneChip Scanner 3,000 with autoloader. Affymetrix data resides in two Dell computers, 900MHz Pentium III, with 500 MB RAM and 35 GB hard disk space NT Workstations, backed up in two external hard drives while transitioning to an Oracle LIMS server. The facility holds a Core Lab program package contract with Affymetrix, with outstanding service on arrays, software, and training, and with technical, sales, and marketing support. In addition, the Core Facility houses an Axon GenePix4000B cDNA array dual channel scanner and all the necessary equipment for the hybridization, staining and scanning, and data analysis procedures involved in the microarray environment under both of two platforms: GeneChip oligonucleotide arrays from Affymetrix, and custom-made spotted cDNA arrays. The Core Facility offers service partitioned into a hybridization unit, and an analysis and database unit. The current inventory of software to be supported by the analysis unit includes: GenePix (Axon), Imagene (BioDiscovery), Spot (Speed), Cluster/Treeview (Eisen), SAM (Stanford group), GeneSight (BioDiscovery), GeneSpring (Silicon Genetics), Spotfire Decision Site (Spotfire), Microarray Suite (Affymetrix), Data Mining Tool (Affymetrix), dChip (Li and Wong), and Bioconductor. Currently the Core services are running 2 Sun Fire servers, each with more than 2 CPUs and at least 4 GB of memory, and the Core also has several workstations (5 PCs with Windows XP/2000 Professional, 1 Mac with OS X and other platforms) that are used by its clients to run the software packages mentioned above, or for tutorial and other activities with Core staff. The Core Facility is directed by Dr. Jef Boeke, and employs two research assistants, a hybridization core manager, a biostatistician for data analysis, a bioinformatician, a network/database administrator and a part-time computer programmer (75% appointment). Shortly, the Microarray Core Facility will maintain its own network. Detailed information about the Core can be found at its website: http://www.microarray.jhmi.edu.

Microscopy Facility: The School of Medicine Microscope Facility occupies over 3,000 sq. ft. of recently renovated space in the Basic Science complex of the Medical School. The Director (Dr. Scott Kuo) and three technical experts provide direct laboratory assistance for fluorescence and confocal imaging; consult with investigators on specimen preparation and labeling strategies; train students on all aspects of image acquisition and processing; and maintain and supervise equipment. The Core Facility contains state-of-the-art instruments for light microscopy, including: (1) Three confocal microscope systems, including two Perkin-Elmer UltraView spinning disk confocal microscopes and an Applied Precision "DeltaVision" deconvolution imaging system. These systems allow state-of-the-art colocalization of molecular species at the light microscope level. (2) A Philips CM120 transmission electron microscope and a Leo field emission scanning EM. The highly skilled staff of the facility provides services for immuno-electron microscopy (the next step beyond confocal microscopy for subcellular localization), and cryo-thin sectioning for immuno-localization, plus services for conventional EM preparations. The Leo field emission SEM allows protein level resolution of surfaces of plasma membranes and organelles, tissues and embryos, and specimen substrates.

Machine Shop: There are several machine shops within the School of Medicine campus. The one which we have been using and developed a collaborative relationship is the Neuroscience machine shop which is located in PCTB928. The shop covers about 400 sq. ft. of floor space and is fully equipped and staffed by an expert machinist, Mr. Terry Shelley. He is outstanding and capable of custom-design and fabrication of sophisticated and high-precision instruments, large and small, used in physiology, molecular biology, biochemistry and behavioral research. This is a full-service machine shop that can design, fabricate and perform maintenance on scientific equipment. The shop supports the research activities of all faculty and staff on an hourly-charge basis.

Neuroscience NINDS Cores: Hopkins has an NINDS Core Center specifically designed to support 85 NINDS – funded basic and clinical research grants at the School of Medicine. The Core Center consists of three Core facilities: (1) Multiphoton Imaging/Electrophysiology Core to provide instrumentation for analyzing protein localization, protein dynamics, and protein-protein interactions with high resolution; (2) Embryonic Stem Cell Engineering Core to accelerate research programs that depend on the development of genetically altered mouse models (knock-outs, knock-ins, and inducible knock-outs) that require ES cell manipulation; and (3) Monoclonal Antibody Core to generate mouse and rat monoclonal antibodies against proteins studied by NINDS investigators at the JHU School of Medicine. The funding for these three Core facilities began on 09/01/2005 and they are fully functional. The facility is located in the Department of Neuroscience in an adjacent building and directed by Dr. Alex Kolodkin, Professor and HHMI investigator. This facility is available for certain validation and assay development activities.

Medicinal Chemistry Core: Johns Hopkins Department of Pharmacology has a strong history of drug development with special strength in neuropharmacology. It has a large group of faculty members specialized in a number of areas including cancer, infectious diseases, neuropharmacology, medicinal chemistry, novel assay technologies and proteomics. The Department of Pharmacology, chaired by Dr. Philip Cole, M.D. & Ph.D., is highly interactive and has played a critical role in a number of university-wide initiatives including joint initiatives with the Department of Oncology involving anti-cancer agents, and with the Department of Medicine involving anti-infective drugs. The collective expertise in pharmacology, medicinal chemistry and clinical trials is a strong asset to the Hopkins community.


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