Bioimaging Facility

The Bioimaging Facility makes every effort to support the greatest possible array of user requirements. One of the most basic of those is the need to be flexible with fluorescent dyes users are capable of using. To this end the facility microscopes can provide a variety of excitation and emission filters to cover a broad spectrum of fluorophores. Kimmel Cancer Center is equipped with a state-of-the-art Zeiss LSM 510 META Confocal Laser Scanning Microscope System. It is interfaced to a Zeiss Axiovert 200M inverted microscope equipped with 5 objectives ranging from 10x to 63x that can be used for both epifluorescence and brightfield microscopy. The confocal uses multiple lasers with excitation lines at 405nm, 458nm, 477nm, 488nm, 514nm, 543nm, and 633nm, allowing use of most of the common fluorochromes including DAPI, FITC, Rhodamine, Texas Red and Cy5 and the green fluorescent proteins and their variants. The system uses several PMT detectors, providing the ability to simultaneously image three (or more) fluorophores with emission between 417nm and 730nm, as well as the Zeiss META detector permitting resolution of very closely emitting dyes. The instrument is installed on a vibration isolation table and has a temperature control unit, all of which provide the means to run advanced imaging procedures on living cells including time-lapse studies, FRET, FRAP and volume rendering.

 The Facility also is equipped with a widefield epifluorescence imaging system specifically designed for high quality acquisition of living cell images. The “Live Cell System” is built around a Zeiss Axiovert 200M inverted microscope equipped with 5 objectives ranging from 10x to 100x that can be used for both epifluorescence and brightfield microscopy. The system uses a broad spectrum Xenon excitation lamp with Lambda-64 quick filter changer and built in epifluorescence reflectors produced by Chroma Technologies to provide flexible emission filtering and rapid imaging of multiply-stained samples. A Roper Scientific CoolSnap HQ CCD camera is used for image capture with Metamorph Image Acquisition and Analysis software (Universal Imaging), as well as software for deconvolution of 3 dimensional image stacks. The instrument is installed on a vibration isolation table and has a temperature control unit.

 Biostatistics

The Biostatistics Section is headed by Dr. Terry Hyslop and provides statistical assistance (with study design and data analysis) to the entire TJU community. It is also the Biostatistics Shared Resource for TJU's Kimmel Cancer Center. Members of the Section collaborate with TJU researchers on study/experimental design, grant proposal submissions, and data analyses. For advice on a study design or analysis direction under consideration, or on appropriate analytic methods, the Biostatistics Section offer courtesy consultations to Jefferson researchers. Courtesy consults are for no more than one hour and do not include data analyses. Biostatistics Section takes on more extensive consultations, typically involving data analyses, on a time-available basis. Projects are taken on a first-come first-served basis, except that priority is given to consultations for members of the Kimmel Cancer Center or the Department of Medicine (both of which provide support to the Biostatistics Section for this purpose).The Biostatistics Section commonly uses a mix of statistical packages, depending on the nature of the project and the statistical methods that are appropriate. Biostatistics section regularly uses SAS, S-Plus, Stata, as well as StatXact and LogXact (for small-sample analyses).

 Flow Cytometry

The Flow Cytometry Facility aids the Kimmel Cancer Center investigators by providing high quality, affordably priced single and multi-parameter analysis and/or purification of all types of biological particles from homogeneous or mixed cell populations, 2) training and expertise in helping investigators to choose experimental conditions and reagents to optimize their use of the facility. The most commonly used applications are for surface phenotyping and sorting, detection of intracytoplasmic cytokines at the single cell level in mixed populations, single cell real time analysis of Ca2+ mobilization kinetics, studies of apoptosis, cell cycle analysis, and sorting of viable cells in specific stages of the cell cycle. The Facility is located in a dedicated laboratory space of about 1500 sq ft on the 6th floor of the Bluemle Life Sciences Building. Its equipment includes 1 Coutler EPICS Elite flow cytometer capable of sorting, 1 Coulter XL-MCL automated analytical cytometer, 1 FACS Calibur Benchtop Analyzer, 1 FACS Vantage SE High Speed Cell Sorter, 2 Celeron 400 workstations, 1 Nikon fluorescence microscope, a 30 cu ft 4oC refrigerator, and a 10 cu ft -20oC freezer. The equipment is state-of-the-art, allowing experimental analysis and data analysis and presentation to be performed in a timely manner and with high sensitivity and accuracy. Priority for the use of this Shared Resource is given to peer-review funded Cancer Center investigators. The facility is operating at greater than maximal capacity and serves at 84.3% to assist the research of Cancer Center investigators. Significant increased usage is projected in the near future based on increased capabilities for new services, on the steady increase in the use of this resource by Cancer Center members since its establishment, and the recruitment of new investigators. 

Laboratory Animal Facility

The Laboratory Animal Facility of the Kimmel Cancer Center provides housing and quality maintenance and care for laboratory animals used by the KCC Staff. The facility also provides technical expertise in small animal surgery, administration of chemical carcinogens, and in-colony health surveillance.

 Microarray Core Facility

The Microarray Core Facility, funded in 2001 by the Kimmel Cancer Center of Thomas Jefferson University, is a State-of-the-Art facility. The functions of the facility are to support the research interests of the KCC-members and non-members in the research community. The technologies offered, mRNA and microRNA chip are powerful tools for screening and profiling any genome-wide changes in DNA, RNA and protein under normal and disease states. The proprietary technologies like high throughput gene expression profiling used in the facility are offered to the research community. The gene expression platform used is an oligo-based microarray that is designed and processed in our facility using proprietary technology.

 Nucleic Acid Facility

The Sidney Kimmel Nucleic Acid Facility (NAF) offers an array of genomic services such as DNA extraction, DNA sequencing, genetic mapping, real-time PCR, and imaging. In addition, the facility provides consulting and assisting in experimental designs to investigators.

 Pathology Core Facility

This Facility provides the KCC with five core functions:

1) Tissue procurement, banking, and distribution

2) Tissue processing and histology services; frozen and fixed tissues

3) Microdissection of tissues and laser capture of individual cells

4) Immunohistochemical staining of tissue sections

5) Quality assurance and clinical-pathologic data collection.

Note: (all protocols must have IRB approval before requesting tissues)

 Frozen and paraffin embedded tissues are available to participating scientists either from the tissue bank, or from paraffin block archives. Basic histologic services include processing, slide preparation and staining of human and animal tissues. Immunohistochemical staining is performed on paraffin sections, frozen tissue or cytologic preparations, utilizing a broad range of commercial antibodies or reagents provided by the investigator. Specimens requiring microdissection or laser capture of individual cell types are processed via microscopic evaluation by the Core surgical pathologists. All specimens are reviewed as to organ type, tumor content, and tissue viability. Where appropriate and IRB approved, clinical-pathologic data can be requested.

 Protein/Peptide Chemistry - Molecular Interaction

The Protein/Peptide Chemistry/Molecular Interaction Facility unites in one resource under the direction of Dr. Alex Shaw, PhD, three important facilities: the Protein Chemistry Laboratory; the Peptide Chemistry Laboratory and the Molecular Interaction Laboratory.

The Protein Chemistry Laboratory of the Kimmel Cancer Institute is a central core facility which offers assistance and support in the purification and characterization of proteins and peptides and the high sensitivity sequence analysis and mass spectral analysis of protein and peptide samples to investigators of the Kimmel Cancer Institute and the Kimmel Cancer Center.

The Peptide Chemistry Laboratory of the Kimmel Cancer Institute is a central core facility which offers assistance and support in the design, synthesis, purification, and characterization of peptides to investigators of the Kimmel Cancer Institute and the Kimmel Cancer Center.

The main purpose of the Molecular Interaction Laboratory is to provide investigators of the Kimmel Cancer Institute with a comprehensive technique to analyze reversible binding interactions between biomolecules involved in the complex biochemical processes associated with various biological functions.

 Proteomics Core Facility

Thomas Jefferson’s Proteomics Core Facility is a state-of-the-art laboratory designed to aid researchers in the separation, quantitation, identification, and characterization of expressed proteins in any given biological sample. Using the techniques available in this laboratory, a researcher will be able to ascertain what proteins are being expressed in any particular sample type under any given conditions, to what extent each of these proteins is being expressed, and finally, to determine the presence of any post-translational modifications in proteins of interest. The laboratory is equipped with the following instrumentation to allow such analyses.

 Shared Computer Facility

The Shared Computer Facility is an essential and important computer resource both for basic science and clinical research at the Kimmel Cancer Center, providing shared computer hardware and software infrastructure, software development, and consultative services for computer-related concerns.  

In support of basic science at KCC, this is the primary Facility for scientist support with DNA/Amino Acid Sequence Analysis, and is a computational resource for the Structural Biology group which includes molecular modeling and x-ray crystallography. The Shared Computer Facility also support clinical research, providing computer resources for the Clinical Trial Support Services, the Jefferson Cancer Network, various program projects, and individual clinical researchers. Applications have been developed to provide controlled and secure access to clinical data, laboratory data, and protocol information for research and the management of clinical trials. 

 For both KCC basic scientists and clinicians, the Shared Computer Facility provide the basic computing infrastructure, including network-accessible mass (disk) storage, Internet/World Wide Web access, and hardware and software expertise. The SCF staff works closely with the University's information systems department, supplementing the generic network support provided by TJU with more comprehensive services attuned to the specific needs of cancer research. Additionally, SCF staff are available to KCC members for consultation on computer specifications and purchases, hardware and software installation and configuration, application use, and trouble-shooting computer use problems.

 Transgenic/Knockout Mouse Facility

The Kimmel Cancer Center Transgenic/Knockout Mouse Facility laboratory is located on the 6th floor of the Bluemle Life Sciences Building (BLSB) with separate areas for microinjection and cryopreservation located within the building's 11th floor Laboratory Animal Facility.

 X-Ray Crystallography Facility

This facility serves the needs of KCC research groups in crystallization, data collection, structure solution, refinement, structural interpretation and mutagenesis of macromolecules. The facility has a HydraPlusOne crystallization robot for HT crystal screening and maintains two diffractometers: a Rigaku RU200 rotating anode X-ray generator ported to R-AXIS IIc and R-AXIS IV++ detectors, each with MSC Blue Confocal optics, and cryosystems, and Enhance Ultra sealed tube X-ray generator with Osmic Confocal Max-Flux optis, Xcalibur kappa 4-circle diffractometer, Cryojet XL and a 165 mm Onyx CCD detector.  The facility has the computational capabilities and the software for data collection, data reduction, structure determination and refinement.