Shared Resources
Flow Cytometry
The Cancer Center Flow Cytometry Shared Resource has been integrated in the Institutional Flow Cytometry Core Facility and has been in existence for 23 years. It is located in room 5.044V at the University of Texas Health Science Center at San Antonio (UTHSCSA) and occupies 800 sq. ft. It is administered through the Office of the Vice President for Research in coordination with the Executive Director of the Cancer Center. It serves > 35 Cancer Center members in several campuses including the UTHSCSA the Greehey Children’s Cancer Research Institute (GCCRI) and the Institute for Drug Discovery (IDD). Access to the flow lab is available to all investigators in the Cancer Center with priority given to NIH-funded -investigators and Cancer Center members. The Flow Cytometry Shared Resource is based on 3 advanced Becton Dickinson (BD) Flow Cytometers: 1) FACSAria cell sorter/ analyzer, equipped with 3-lasers allowing simultaneous sorting and analysis by up to 13 colors, and simultaneous sorting of 4 different cell populations at a speed of up to 20,000 events/sec. 2) FACStar Plus cell sorter/analyzer, equipped with two lasers, and upgraded through an NIH SIG grant to a TurboSort with sorting of 5,000 events/sec and 4-color analysis, and 3) FACSCalibur analyzer, equipped with 2-lasers. Shared resource personnel include the Director with over 30 years of experience in flow cytometry and two experienced operators (20 and 4 years). All personnel are Becton-Dickinson certified operators. Services include multicolor sorting and analyses, phenotyping and cloning of subpopulations of lymphocytes, tumor cells, stem cells and cells expressing fluorescent transgene proteins; cell sorting according to cell cycle position; measurements and kinetics of nitric oxide, oxygen peroxide and free radicals, reduced glutathione, pH, Ca++ fluxes and fluxes of different vial dyes; quantitation of multiple cytokines using fluorescent microspheres (CBA/BD); study of mitochondrial damage; determination of multiple activated caspases; consulting services; and assistance in grant writing and publication services. The shared resource supports 26 NIH-funded, P30 members holding 20 NIH grants of over $6 million/year in direct costs. Thirty-nine peer reviewed papers were published by P30 members in 2007-2008 (over 150 publications in the past 5 years) with pertinent use of flow cytometry, attesting to the productivity of the cancer investigators and the integral role flow cytometry plays in their ongoing research projects.
The mission of the Flow Cytometry Shared Resource is to enhance basic, preclinical and clinical cancer research. It is the goal of the shared resource to assist individual faculty members in their research endeavors, promoting interdisciplinary and inter-institutional research activities, and the education of graduate students, fellows and clinicians in the Cancer Center and its affiliated institutions. The shared resource is committed to providing professional, efficient, and reasonably priced Flow Cytometry Services.
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Genomics
The Genomics Shared Resource provides state-of-the-art services to the members of the Cancer Center by providing access to two complementary platforms, the Illumina platform, used for primarily for high-throughput genotyping of single nucleotide polymorphisms, and the Agilent Technologies platform, used primarily for array comparative genomic hybridization and expression microarray analysis. In addition to these genomic services, the shared resource offers Cancer Center members assistance in automated nucleic acid isolation, real-time quantitative PCR, and sample banking. The banking of samples range from isolating DNA, processing blood specimens, establishing lymphoblastoid cell lines and long term storage of samples. The shared resource has been reorganized with a single overall coordinator and two co-directors, one per platform. All three have extensive experience in genomics and provide Cancer Center members with consulting services to assist in experimental design. This shared resource combines two previous funded cancer center shared resources, the Cytogenetic and Genetics Shared Resource and the Microarray Shared Resource.
A genomic approach to cancer research is key to the discovery of new biomarkers that can be applied to the diagnosis and staging of cancer. The Genomics Shared Resource provides two high throughput platforms to aid the researcher in genomic analyses.
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Macromolecular Interactions
The Macromolecular Interactions Shared Resource provides Cancer Center researchers with state-of-the art capabilities for the characterization of protein-protein, protein-lipid, protein-nucleic acid and protein-small molecule interactions. The facility provides resources for the complete characterization of macromolecular interactions in solution. This includes a description of the kinetics, thermodynamics and assembly state of the interaction. The strengths of surface plasmon resonance (SPR) include the determination of binding kinetics and equilibria, the determination of active protein concentrations, assay development and drug screening, and binding site and epitope mapping. The strengths of analytical ultracentrifugation (AUC) include the ability to characterize distributions of molecular weight and degree of globularity for macromolecular mixtures simultaneously, and to determine the partial concentration of individual solutes, aiding in the study of conformational changes and sample composition, solution molecular mass, stoichiometry of assembled complexes, and providing rigorous thermodynamics for self-associating systems. Static and dynamic light scattering (LS) are useful tools in the study of the size and size distribution of cells, viruses, micelles, and macromolecules such as proteins, macromolecular assemblies, polysaccharides, and nucleic acids. LS is also useful for the kinetic study of macromolecular assembly and disassembly in real time. By having all of these biophysical tools available in a single shared resource facility, we are able to offer our Cancer Center researchers an extraordinarily high level of rigor and sophistication for the study of the macromolecular complexes and drug targets that have become such an important part of modern cancer research.
The Macromolecular Interactions Shared Resource provides state-of-the-art resources to members of the Cancer Center enabling the solution state analysis of biological macromolecules that play critical roles in cancer from the basic science level through drug discovery and development.
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Macromolecular Structure
The Macromolecular Structure Shared Resource (MSSR) is comprised of the X-ray crystallography (X-ray) and the Nuclear Magnetic Resonance (NMR) laboratories. X-ray crystallography and NMR are highly complementary methods for elucidating three-dimensional structures and for studying macromolecular interactions. Together, they provide Cancer Center members with comprehensive methodologies to understand how cancer-related biological macromolecules function in normal and diseased states at the molecular level. Cancer Center investigators will be advised and assisted in utilizing these sophisticated technologies to determine structures of cancer-related biological macromolecules and to investigate their interactions with other macromolecules and with potential therapeutic agents by the Directors of the X-ray and NMR laboratories, P. John Hart, PhD and Andrew P. Hinck, PhD, respectively. The X-ray component of the MSSR includes an Art Robbins crystallization robot and two state-of-the-art Rigaku-MSSR X-ray data collection systems. The instrumentation provides full capabilities for conducting all modern X-ray diffraction experiments and is suitable for obtaining high quality three-dimensional structures of proteins, nucleic acids and their complexes. The NMR component of the MSSR includes state-of-the-art Bruker spectrometers equipped with high sensitivity cryoprobes operating at 500, 600, and 700 MHz. The instrumentation provides full capabilities for conducting modern NMR experiments with 15N, 13C, and 2H labeled macromolecules and is suitable for obtaining three-dimensional solution structures and investigating interactions with other macromolecules and potential therapeutic agents. The MSSR is made accessible to the broader Cancer Center Membership by PhD-trained technical managers, Alex Taylor, PhD, and Udayar Ilangovan, PhD, for the X-ray and NMR laboratories, respectively, who provide guidance at each step in the process, from sample preparation to interpretation and presentation of results. The MSSR provides a comprehensive array of methodologies with which to visualize and functionally characterize cancer-related biological macromolecules.
The key to determining the function of a molecule and how it is altered by mutation is facilitated by elucidating the higher level structure. The Macromolecular Structure Shared Resource provides NMR and X-ray crystallography capabilities to cancer center members. This information obtained by this shared resource provides essential information not only for basic research, but also for translational applications.
NMR
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X-Ray
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Mass Spectrometry
The Mass Spectrometry Shared Resource offers a wide range of analytical capabilities to support the needs of Cancer Center investigators and other researchers at UTHSCSA and in the nearby community. Mass spectrometry instrumentation is as follows: Thermo Fisher LTQ ion trap mass spectrometer used in conjunction with an Eksigent NanoLC 2D HPLC system to perform nanospray HPLC-ESI-MSn analyses; Thermo Fisher Quantum-AM triple quadrupole mass spectrometer used with a Michrom BioResources Paradigm MS4 micro HPLC system; Thermo Fisher LCQ ion trap mass spectrometer used in conjunction with a Michrom BioResources Paradigm MS4 micro HPLC system; Applied Biosystems Voyager DE-STR matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF/MS); Thermo Fisher DSQ quadrupole mass spectrometer which is able to perform GC/MS and direct probe analyses using electron impact and chemical ionization with positive and negative ion detection. A Thermo Fisher LTQ-Orbitrap Velos-H/ETD mass spectrometer and Eksigent NanoLC Ultra-2D HPLC system will be installed in Fall 2009. In addition to the mass spectrometers, devices that greatly facilitate protein characterization are available in the facility, including an imager, densitometer, gel spotcutter and PDQuest gel analysis software (all from Bio-Rad) and SameSpots gel analysis software from Nonlinear Dynamics. The major protein analysis services provided include molecular mass determination, protein identification from solution or polyacrylamide gel, sequence characterization, elucidation of sites of post-translational modification, and gel electrophoresis. Detection limits in the sub-picomole range are routinely obtained, making it possible to characterize proteins and peptides isolated from biological samples. Quantitative analysis of lipids and intermediary metabolites by GC/MS is also performed on a regular basis.
Mass spectrometry is essential for a wide variety of investigations that are part of the Cancer Center programs.
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Optical Imaging
The Optical Imaging Shared Resource provides ongoing service to the Cancer Center and its members by providing access to state-of-the-art optical imaging equipment, including multiparameter digital imaging workstations, confocal microscopes, and multiphoton microscopes. Highly experienced personnel in the shared resource are available to consult with users of the facility regarding the appropriate instrumentation or imaging technique for their specific needs. Advice on experimental design is offered, including recommendations on specimen preparation and probe selection. Users are initially introduced to the equipment and assisted in feasibility studies. Once feasibility is demonstrated, users are trained by the staff to be primary operators of the instrumentation. Once trained, users have access to the facility on an as-needed basis following reservation of instrument time. Alternatively, assistance with image acquisition, analysis, and processing are also offered as a service of the shared resource.
High-end instrumentation for acquisition and analysis of optical data is expensive and requires continued maintenance and improvements. The necessary commitment to this technology is often difficult to maintain within individual laboratories, especially when optical imaging is not a major focus for the laboratory. Therefore, the Optical Imaging Shared Resource fills a critical need of Cancer Center investigators by offering access to state-of-the-art technology for imaging of living cells, tissues, and animals; consultation, education and assistance regarding the theory and application of optical imaging techniques; and technical advice on specimen preparation techniques and probe selection.
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Pathology
Pathology Documents
The purposes of the Pathology Shared Resource are to provide high quality, economical, and timely pathology-related services to P30 investigators and to provide them with a source of human tissues and fluids for investigation. The specific procedures/services provided by the Pathology Shared Resource include histochemical services such as routine histology/histochemistry (e.g., preparing paraffin blocks and H&E slides), special histochemistry, and immunohistochemistry. In addition the shared resource offers apoptosis (TUNEL) assays and DNA in situ hybridization. Specialized services that have been developed include laser capture microdissection, tissue arrays and photomicroscopy and image analysis. The shared resource has banked tumor samples that are available to investigators without identifiers. In addition to these services, the Pathology Shared Resource provides consultation and collaboration with experienced technologists and pathologists.
The mission of the Pathology Shared Resource is to provide technical and professional expertise in the handling of human and animal tissues. By interacting with the shared resource facility, P30 members are educated in how histologic approaches in experimental design can enhance their research. The P30 tissue/tumor bank makes appropriate tissue/tumor bank specimens available to P30 members to generate and test hypotheses in vivo in humans.
Contacts:
Pathology Shared Resource Director
I-Tien Yeh, M.D.
Phone: (210) 567-6722
Email: YehI@uthscsa.edu
Laboratory
Phone: (210) 567-5066
Biostatistics and Informatics
The Biostatistics and Informatics Shared Resource (BISR) provides biostatistics and informatics resources to the Cancer Therapy and Research Center (P30) at the University of Texas Health Science Center at San Antonio (UTHSCSA). This centralized shared resource provides flexible, cost-efficient services to basic, translational, clinical and population-based researchers by providing biostatistical consultation in study design, statistical analysis and interpretation of research findings as well as support for data collection and information management. The BISR maintains the cancer center informatics infrastructure and assists individual investigators or groups with the database design, data security, and research computing needs. The BISR supports the data management personnel of the Office of Research Administration (ORA). Informatics solutions have streamlined many regulatory operations such as quality assurance review, automated reporting of adverse events, and accrual monitoring. BISR biostatisticians are active members of the Protocol Review Committee and the Data Safety Monitoring Committee.
The specific functions of this shared resource include: protocol development support, quality assurance, statistical analysis, computer-based data management support, and support for the educational mission of cancer center researchers.
The BISR facilitates the development of new research investigations by providing biostatistics consultation in study design and protocol development and determination of computing resources needs. Services are provided in a manner responsive to the needs of individual researchers while optimizing the common use of our shared resources across the entire cancer center.
In the current grant period, we successfully recruited a diverse team of core biostatisticians who are integrally involved in all of the research programs of the P30, we developed and implemented a state-of-the-art information management system to support cancer research, and we have begun to develop strong bioinformatics support capabilities which will be strengthened by the integration of caBIG tools into our research informatics infrastructure.
