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Urology Research Laboratory
Harrison Department of Surgical Research
Dr. Samuel K. Chacko
 
Resources
 
Basic Urology Research Laboratory
 

Laboratory:
Laboratory Facility Available for Urologic Research
The Basic Urology Research Laboratory has 6,000 sq ft renovated laboratory space, equipped with dark room, tissue culture labs, cold rooms and offices. This laboratory is located in the Glenolden Research Laboratory. The Glenolden Laboratory is located at 500 South Ridgeway Avenue in Glenolden, PA. There are five other surgical research laboratories in the Glenolden Research Laboratory.

Animals:
The Glenolden Research Laboratory has facilities for keeping large and small animals. The facility also contains surgical rooms with surgery technicians, autoclaves and other sterilization equipment and an MRI machine. This is a new state of the art facility with full veterinary support. Housing is available for large numbers of rabbits, mice, and rats and also for pigs, sheep, or dogs in limited numbers.

The University of Pennsylvania Animal Resources has sufficient housing for the proposed studies. There is a staff to ensure at the animals are taken care of properly and fed and that their cages are clean. There is also a disposal system for the carcasses. A Veterinarian is on call 24 hours a day. The room where surgery is performed is in close proximity to where the animals are housed.

Office:
Computers and printers are available in the offices and laboratories. Both Apple and IBM compatible computers with modems are available for the use of all lab personnel. E-mail is routinely sent among these various labs. Software is available for database, graphics, desktop publishing, and slide making capability.

Other:
The Urology Research Lab has a full-time Business Manager who will be available for secretarial type help. In addition, they are very competent in computer technology and will be available to help in preparing technical illustrations, etc. The Business Manager has direct access through an Internet hook up to their computer to rapidly order supplies as needed.

Equipment for physiological studies: Grass model 7D polygraph and Grass model S-88 electrical stimulator to measure contractile force of large muscle strips (3mm X 8mm); Power Lab for muscle physiology (AD Instrument), Guth Muscle Mechanic to measure force generation and simultaneous force and calcium change of relative small muscle fiber (1mm X 3mm). For mouse, rats and rabbit cystometry, cystometry equipment equiped with a computer program (Med Associates).

Equipment for histology and cell biology: Leica RM 2155 Rotary Microtome for paraffin and plastic tissue section; Fisher tissue section floatation bath and slide warmer; Leica CM 3050 Cryostat for frozen tissue section; Nikon eclipse E 800 Fluorescence Microscope and Nikon eclipse TE-2000 Inverted Fluorescence Microscope equipped with image analysis software “Image-Pro Plus”; Olympus FV1000 Confocal with Nomarski prism for 10X, 40X and 60X objectives.

Equipment for Tissue/cell culture: 6 tissue culture hoods, 6 CO2 incubators, 3 dissecting microscopes (Olympus), 3 inverted phase microscopes (Olympus) with digital camera, and refrigerated centrifuge.

 
Equipment for biochemistry and molecular biology studies:
  1. Bio-Rad equipments for protein electrophoresis and transfer: Mini Format Vertical Electrophoresis: Mini-PROTEAN 3 Electrophoresis system; Criterion Cell for Midi Format Vertical Electrophoresis; PROTEAN II for Large Format Vertical Electrophoresis; Mini Trans-Blot Cell and Criterion Blotter for Tank Transfer Systems; Semi-Dry Transfer System,
  2. Spectroscopic/imaging Instruments: Image system: GE Typhoon TRIO Variable Mode, phosphoimager/fluorimager; Bio-Rad GS -800 Calibrated Densitometer with analysis software “Quantity one”, Fluorescence/calorimetric plate reader, UV/Vis scanning Spectrophotometers, Nanodrop spectrophotometer,
  3. PCR system: Applied Biosystems 7500 Fast Real Time PCR Systems; MJ Research Peltier Thermal Cycler,
  4. Freezer and centrifuge: Sanyo Ultra-low Temperature Freezer; Forma-scientific -80?C freezer; Forma-scientific Liquid Nitrogen Freezer; Eppendorf Bench top Centrifuge,
    Sorvall RC-5B Super Speed Centrifuge; Sorvall RC70 Ultra Speed Centrifuge; Beckman Airfuge; Beckman ultra Speed Centrifuge,
  5. Protein purification: Polytron PT 1200E homogenizer; Beckman Coulter HPLC; Chromatography columns; Fraction Collector; Shimadzu Bio-mini DNA/RNA/Protein Analyzer; Ultraspe 2100 Pro Spectrophotometer, and
  6. Radiation measurement: Beckman Coulter Multipurpose Scintillation Counter; Packard Liquid Scintillation Analyzer for beta and gamma counting.
 

Dr. Chacko is a member of the Penn Diabetes and Endocrinology Research Center (DERC). The Penn DERC facilitates and supports research in diabetes and endocrinology in a variety of ways. Six biomedical research core facilities are designed to facilitate the inter-disciplinary investigations of Penn DERC scientists: Genomics and Gene Targeting Core, Mouse Phenotyping, Physiology and Metabolism Core, Islet Cell Biology Core, Radioimmunoassay / Biomarkers Core.

RESOURCES AND ENVIRONMENT PROVIDED BY THE INSTITUTION AS CORE FACILITIES AT THE UNIVERSITY OF PENNSYLVANIA FOR DR. CHACKO

MICROARRAY CORE FACILITY DESCRIPTION
Services: The Penn Microarray Facility provides instrumentation and expertise for RNA transcript profiling. DNA microarrays provide a highly parallel means of measuring the abundance of RNA for targeted genes in a biological sample. The Facility supports two microarray formats: oligonucleotide arrays synthesized by Affymetrix Inc. and arrays of probes printed in-house on glass slides. This reflects our goal of offering a range of cost and performance options suitable for a variety of experimental questions. Researchers from the University of Pennsylvania and its affiliated institutions are invited to utilize the Microarray Facility as part of their functional genomics efforts, and projects from non-affiliated institutions will be considered by special arrangement. All projects are initiated only after consultation with the facility director; this will ideally occur during the experimental design stage to ensure maximal and meaningful results.

Lab Work: Services include RNA isolation, clone set management, probe amplification and purification, microarray printing, target preparation including appropriate linear amplifications and labeling methods, array hybridization and scanning, and data formatting and analysis. Additional resources can be made available through the Facility for laser capture microdissection, cell sorting, library construction and clone set procurement.

Bioinformatics: Data analysis software associated with the Facility's instrumentation is available for client use both on and off-site. Tools for additional statistical analyses, database management, pattern recognition, and inter-project collaboration are available via the Facility's close ties to the Penn Genomics Institute.

Consultation: Appointments are available free of charge to discuss project-specific issues such as experimental design, resource identification, project status and data analysis. Please call Don Baldwin for more information, to schedule an appointment, or to arrange for a seminar or group discussion about transcript profiling and functional genomics.

Training: Individual or small group training can be arranged to learn about transcript profiling protocols, instrument operation, or bioinformatics strategies. While most Microarray Facility equipment is not available for use by persons not employed in the Facility, it is hoped that an opportunity for hands-on experience creating and using microarrays will enhance Penn students' life science education.

Equipment:
GeneChip oligonucleotide microarrays. An Affymetrix package containing two four-place fluidics stations, an Agilent Confocal laser scanner, GeneChip hybridization oven and computer workstation is used for processing GeneChip oligonucleotide arrays. These microarrays are available for gene sets from human, rat, mouse, Arabidopsis, Drosophila, yeast, E. coli and other organisms, and are available to Facility clients at substantial discounts under Affymetrix contract pricing with the University of Pennsylvania, the Cancer Center, Children's Hospital of Philadelphia and the Wistar Institute. Under the current Affymetrix Core Lab Program, Penn Microarray Facility clients receive personal copies of the software necessary to visualize GeneChips and re-quantitate results using a variety of analysis options.

Glass slide cDNA microarrays. A GeneMachines OmniGrid microarraying robot deposits oligomers or PCR amplified probes onto treated microscope slides using 48 Telechem Stealth pins, producing an array of up to 20,000 probes per slide. Hybridized arrays are scanned with a Molecular Dynamics GenePix scanner. Commercial and custom clone sets are processed and archived in 96- and 384-place microplates using a Beckman BioMek 2000 robotic workstation, an MJ Research Tetrad thermocycler and various smaller instruments for microplate spectrophotometry, centrifugation, nucleic acid purification and electrophoresis.

Biomedical core facility. The primary mission of the Biomedical Imaging Core Laboratory is to support innovative research by providing nearly unlimited access to state-of-the-art biomedical imaging equipment run by a highly experienced, professional staff. Ordinarily, this access would be available only to researchers at the highest funding levels, who had taken decades to build a professional staff. The Core releases investigators of the enormous burden of equipping, maintaining, staffing and managing a world-class imaging facility. A secondary, but very important function of the Core is to provide instruction in ultrastructural and morphological research techniques for investigators or members of their research staffs.

Services. EM services, morphometry, and some of the digital imaging operations are located nearly in the center of the Medical Center campus, in the Richards Building room 110. The Richards facility includes laboratory, darkroom and office space totaling about 1,100 square feet. Room 208, in the adjacent John Morgan Building, houses the confocal microscopes, the CCD equipped light microscope, and computers for three-dimensional image reconstruction, morphometry and other analyses of data.

This core performs a large number of in-house services dedicated to elucidating the finer points of morphology. Although the facility is a service-for-fee center, we run it as an extension of the Core users' own research laboratories. It is effectively an extension that provides expensive, specialized equipment and experienced technical staff required for performing morphological and ultrastructural analyses. We currently offer a variety of electron microscopy services, confocal laser scanning microscopy, multiphoton imaging, CCD or film based epifluorescence imaging and a complete array of computerized morphological-data analysis services. While most users desire to have the Core perform a complete analysis, many users elect other courses of assistance. More experienced users often have either just the most critical work done by the Core, or simply have the Core provide guidance and assistance as needed, while performing the work themselves. In this way we also function as a valuable training and consulting service. The Core staff is always available for consulting on the morphological aspects of a project, and is willing to custom-design services to fit any investigators needs.

SHARED RESOURCES EQUIPMENT AT PENN:
FLOW CYTOMETRY AND CELL SORTER FACILITY: Becton-Dickinson FACS IV, FACStarPlus, 2 FAC Scanners.

NUCLEIC ACID FACILITY. IN THE SCHOOL OF VETERINARY MEDICINE: Two Milligen/Biosearch Cyclone Model 8400 DNA synthesizers, Perkin Elmer
The facility also uses ABI 377 and 373A Stretch sequencers, with BigDye Taq FS Terminator or Dye Primer chemistry.

GENETICS CENTER CORE FACILITY
This facility also provides Automated Cycle Sequencing, Template Preparation & Purification, Oligonucleotide Synthesis, Gene Scan, Lage Sequencing Projects, and Sequence Analysis & Database Searches.

SERIES IV 10 LIOUID CHROMATOGRAPH WITH 2 LC 75 SPECTROPHOTOMETRIC DETECTORS. WATER WISP 710 INJECTOR

2 ISCO FOXY AUTOMATIC FRACTION COLLECTORS. Walters Delta Prep 300 with WISP Injector and Lambda Detector, and DEl HP 8457A Diode-Array Spectrophotometer.

CELL CENTER: large glassware washing, sterilization, and culture media preparation area, Beckman Ultracentrifuge, 4 table-top centrifuges, 2 Beckman microfuges, -80 freezer, 2 liquid nitrogen storage freezers, a Multican spectrophotometer and ELISA plate washer, 5 laminar flow hoods, 3 double C02 incubators, a walk-in warm room with stirrer plates for spinner culture, a roller culture incubator cabinet, a small fume hood, a Zeiss phase-immunofluorescence microscope, a Pharmacia chromatography system for purification of monoclonal antibodies, and 4 MAC computers, with access to IntelliGenetics and American Type Culture Collection data bases.

BIOSTATISTICS: 2 Compaq 3 86/20 computers with 130 MB and 60MB hard drive and an IBM-compatible 386/33 computers with 200MB hard drive, capable of running MS-DOS operating systems, statistical packages (I.e., BMDP, SAS, SPSS, Statgraphics, Egret Stat Package with Epitaxt extension, Survreg, Power, GLIM-generalized linear models), software (DBASE 111+, DBASE IV, Turbo, Pascal, Quicksilver and Paradox 3.5. Member of SMUG (Statistical Microcomputer Users Group).

MOLECULAR DIAGNOSIS: 3 low and 1 medium speed centrifuges, power supplies and electrophoretic apparatus (including pulsed field and temperature gradient) for agarose and polyacrylamide gel analysis, 2 refrigerator-freezers and a large -70 freezer, visible and ultraviolet spectrophotometer, high pressure liquid chromatographic apparatus, liquid scintillation counter, 2 IBM-compatible computers with MLINK genetic risk software; Model 4800 and Model 9600 Perkin-Elmer/Cetus Thermal Cyclers, Applied Biosystems Nucleic Acid Extractor, electrophoretic gel dryers.

PROTEIN CHEMISTRY: Biosystems 473 A gas phase microsequences with Beckman 6300 amino acid analyzer, Applied Biosystems 40 A peptide synthesizer, Applied Biosystems 270A computer-assisted 2-D gel electrophoresis system, Applied Biosystems 130 A Microbore HPLC for purification and microsequencing; plan purchase of mass spectrometer dedicated to facility (others in University).

TRANSGENIC ANIMAL: Zeiss inverted and stereo microscopes with Namarski optics; Zeiss motorized micromanipulators; World Precision iontophoresis injection devise, Eppendorf pressure injection tools, incubator, Hitachi video camera with amplifier and recorder, Narishige microforge, Sutter computerized pipette puller, Forma Scientific C02 incubator and Kinetics vibration-free table.

 

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