Research Core Facilities

To register for advice or use of one of the core facilities, please fill out a Request Form. (Separate application required for each Core.)

I. Research Imaging Core

II. Microscopy Core

III. Flow Cytometry Core

IV. Micro-array Core

V. Biobehavioral Core

VI. Biostatistics Core


I. RESEARCH IMAGING CORE:

The design and construction of the core facilities are underway and will be functional by the end of 2009. Some individual components are currently in use.

Core Manager:
Wafa Tawackoli, PhD
tawackoliw@cshs.org
310-423-8070

A. Molecular and Micro-Imaging

Dan Gazit, PhD - Core Director; Wafa Tawackoli, PhD - Associate Director; Yifang (Jimmy) Zhou, PhD - Associate Director

With the ever-increasing complexity of science and engineering, collaborative, multidisciplinary teams are required to address complex research problems. At the Molecular & Micro Imaging Core, we have designed and built a state-of-the-art facility to support the research interests of a wide range of investigators from multiple disciplines. The growing number of rodent experiments, coupled with advances in micro-imaging systems such as a Tri-modality system (microPET, microSPECT, and microCT), optical (bioluminescence/fluorescence) systems and microMR, has necessitated the creation of a technical center for pre-clinical imaging. The pre-clinical imaging systems are used by primary medical research and drug development teams in both academia and biotech industries to study disease processes, and to track interactions of cells at the molecular level. Key application areas include cardiology, neurology, oncology, and stem cell research. As a core facility, our main goal is providing state-of-the-art imaging capability. Requirements to satisfy both research and regulatory oversight have been critically examined. Support is provided for investigator training, study scheduling, data acquisition, archiving, image display, and analysis. We have created a facility that maximizes our resource utilization while providing optimal investigator support, as well as the means to continually improve the quality and diversity of the science by integrating physical and biological sciences.

Equipment:

1. Optical imaging systems

  • Bioluminescence (Bioluminescence, Fluorescence): Xenogen/Caliper (Spectrum)
  • Fluorescence: CRi (Maestro)
  • Confocal Microscope: Optiscan (Five1)

2. Nuclear imaging systems

  • MRI/MRS: Bruker BioSpin (94/20 USR)
  • Tri-Modalitiy (PET, SPECT, CT): Gamma Medica-Ideas (Triumph)

3. X-Ray based imaging systems

  • Micro-CT: Scanco (VivaCT 40)
  • Fluoroscan C-arm Imaging: Hologic (InSight II mini C-arm)

B. Large Animal and Human Imaging

Dan Berman, MD - Core Director

The imaging research laboratory (IRC) occupies over 10,000 square feet in the Davis Research Building and is comprised of two parts: one is devoted to molecular and micro-imaging (see above) and the other to large animal and human subject imaging research.

The large animal and human subject imaging research capabilities will provide comprehensive, advanced imaging for research in all organ systems. This component of the IRC has three large imaging rooms, housing the latest instrumentation in advanced imaging in magnetic resonance imaging (MRI), computed tomography (CT), and positron emission tomography (PET/CT).

Equipment:

  • MRI: Magnatom Verio 3T (Siemens Medical Systems)
  • CT: Definition AS Dual Source CT (Siemens Medical Systems)
  • PET/CT: Biograph 64 PET/CT (Siemens Medical Systems)


II. MICROSCOPY CORE

Kolja Wawrowsky, PhD - Core Director

Core Manager:
Kolja Wawrowsky, PhD
wawrowskyk@cshs.org
310-423-4429

The confocal core facility supports research through high resolution imaging of cells and tissues. The core provides two confocal microscopes and one 2-photon system.

The Leica TCS WL is the first of its kind in the United States. It uses a white light laser for imaging. Researchers can image any sample without being limited to a small number of dyes as is the case with conventional confocal instruments. This makes it the most flexible imaging system available today. The instrument can image live cells and tissues with the help of a temperature, humidity, and CO2 controlled environmental chamber. It acquires images with a resolution of up to 8000 x 8000 pixels and speed of 300 images per second.

A 2-photon microscope allows the imaging of cells in live animals. This is an important capability for the detailed study of neuronal processes, the function and physiology of the immune system and the discovery of new treatments for diseases. 2-photon systems have higher penetration depth in tissues at a similar resolution of a confocal system.

In summary the core offers the state of the art in biomedical microscopy.

Equipment:

  • Leica TCS/SP5 WL confocal
  • Leica TCS/SP confocal
  • Leica TCS/SP 5 2-photon

III. FLOW CYTOMETRY CORE

David Underhill, PhD - Core Director

Core Manager:
Patricia Lin
linp@cshs.org
310-423-7715

Flow cytometry uses fluorescent probes targeted to specific cell-associated molecules to characterize the diversity in makeup and function of complex populations of cells. As individual cells flow through a detection chamber, lasers excite the fluorophors, and an array of detectors analyzes them. At up to tens of thousands of cells analyzed per second, flow cytometers can rapidly acquire enormous amounts of data about populations of cells. In this way, even very small populations of cells within large mixtures can be identified and analyzed. For example one can rapidly analyze CD4/CD8 expression in populations of lymphocytes, or identify small populations of stem cells in blood.

A fluorescence activated cell sorter can individually select cells with a defined phenotype and sort them into collection tubes for isolation of select populations of cells. Flow cytometry is widely used by immunologists, hematologists, and other investigators who work with complex mixtures of cells.

The flow cytometry facility located on the 4th floor of the Davis building is available to all members of the Cedars-Sinai research community. The flow cytometry facility at Cedars is staffed by a full time technician who is available to assist in running samples and for training in the use of the analyzers. Users are charged for the time spent working on the machines.

Equipment:

  • Analyzers: 8 color Dako CyAn (excitation at 488, 405, 610 nm); 3 color BD Biosciences Facscan (excitation at 488 nm)
  • 10 color Becton Dickinson LSRII, equipped with four lasers. The system has the ability to detect 2 colors and forward and side scatter off the blue laser (488 nm), 3 colors off the yellow-green laser (561 nm), 2 colors off the violet laser (405 nm) , and 3 colors off the red laser (640nm). The yellow-green laser optimally excites PE and PE tandem dyes and therefore will provide greater signal sensitivity. It will also be able to detect DsRed and all its variants as well as all the fruit named fluorescent reporter proteins such as mCherry and mStrawberry
  • Sorter: 8 color Dako MoFlo (excitation at 488, 380, and 610 nm)

IV. MICRO-ARRAY CORE

Charles Wang, MD, PhD - Core Director

Core Manager:
Charles Wang, MD, PhD
wangcx@cshs.org
310-423-7361

Gene expression is the transcription of genetic information from genomic DNA to messenger RNA (mRNA). By assessing the level of mRNA expression of hundreds to thousands of genes simultaneously, micro-array technology allows high-throughput molecular profiling of tissues or cells. Although there are some variations in the details of array construction, all depend upon parallel hybridization of unknown molecules (samples) to localized, surface-bound known molecular probes.

While a variety of technologies are available, the CSMC Micro-array Core uses the Affymetrix GeneChip system, which offers the highest density and allows global whole genome gene expression profiling. In addition, the Core offers GE SuperArray pathway based oligo arrays, which allow researchers to characterize gene expression associated with a specific biological pathway in a more focused and cost-effective manner. The Oligo GEArrays contain 96 to 440 oligonucleotide probes, representing genes associated with a specific biological pathway. A current list of pathway specific arrays is available by contacting the Core. The Micro-array Core also provides comprehensive bioinformatics support on micro-array data mining, visualization and pathway analysis.

Equipment:

  • ABI 7700 Sequence Detection System (quantitative gene expression by qRT-PCR)
  • Agilent Bioanalyzer 2100 (for RNA/DNA quality determination)
  • GE Supperray-pathway based micro-array system
  • The Buffalo Terastation (1Tb HD) for data back up
  • Affymetrix GeneChip® Analysis Systems
  • Fluidic station 450
  • GeneChip® hybridization oven 640
  • Affy GeneChip scanner 3000 G7 scanner
  • PC workstation
  • GeneChip® Operating Software (GCOS)

Computer programs:

  • Affymetrix GCOS
  • Stratagene’s PathwayArchitect 1.01
  • Stratagene’s ArrayAssist 4.0
  • Partek Genomics Suite
  • Mathworks’ Matlab 7.0.1 R14
  • JMP 5.1



V. BIOBEHAVIORAL CORE

Robert Pechnick, PhD - Core Director; Catherine Farrokhi, PhD - Associate Director

Core Manager:
Catherine Farrokhi, PhD
farrokhic@cshs.org
310-423-3689

The Preclinical Biobehavioral Core provides two primary functions: 1) behavioral phenotyping; and 2) standardized neurobehavioral assessments in rodents. Behavioral phenotyping generates a comprehensive description of the phenotype produced by the genetic manipulation and can be used to identify neurobehavioral deficits in transgenic and knockout animals. Neurobehavioral assessment plays a key role in the development and utilization of translational animal models for studying behavioral, neuropsychiatric and endocrine disorders, such as mental retardation, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Cushing’s disease, schizophrenia, anxiety disorders, depression, and drug abuse. The core also can be used to assess the neurobehavioral consequences of drug and other types of therapies (e.g., gene, immune, vaccine and stem cell therapies). Information on the behavioral effects of the treatment can be used to satisfy requirements for moving from preclinical testing to the filing of an investigational new drug (IND) application.

Testing in the Core ranges from the assessment of general health and neurological function (reflexes, sensory and motor function) to evaluating complex behaviors such as memory and learning in both mice and rats. Testing of individual behavioral domains and well as batteries of tests can be carried out. Custom tests can be developed upon request. Assistance is available for the submission of IACUC protocols using the Core, and data summaries can be provided at the end of testing. Testing can be conducted by the Core staff or research staff from the PI’s laboratory can be trained to carry out the experiments using the Core equipment.

Equipment:

  • Computer-linked activity chambers
  • Telemetry system
  • Cylinder test; Pole test
  • Wire hang
  • Grip strength
  • Rotarod and Rotometer
  • Elevated plus maze
  • Porsolt test
  • Tail suspension test
  • Passive and active avoidance systems
  • Conditioned place preference
  • Conditioned fear responding
  • Prepulse inhibition
  • Acoustic startle response
  • Object recognition
  • T mazes; Y mazes; Barnes mazes
  • Video recording and video tracking software.

The Barnes Mazeis used to measure hippocampal function in preclinical models of Alzheimer’s disease. The maze consists of a flat circular surface with 20 equally spaced holes. Only one hole is open and allows the animal to escape the illuminated surface area. With repeated trials, animals with an intact memory system show a significant reduction in the number of errors and time it takes to locate the open hole. If the open hole is moved to another location in the maze, normal animals rapidly disengage from the previously learned information and relearn the new location. A deficit in learning and/or memory produce impaired performance in this test.

The Novel Object Recognition Testis used to measure learning and memory by assessing the ability of rodents to identify a previously introduced novel object. The test consists of two phases: in phase one, 2 identical objects are placed in an open field and the animal freely explores both objects; in phase 2, one of the objects is replaced with a new novel object. Normal animals tend to spend more time exploring the novel object compared to the familiar one, whereas animal with deficits in memory and learning do not recognize the new object as being novel. Impairment is detected by measuring the amount of time an animal spends with the familiar object in comparison to the novel one.


VI. BIOSTATISTICS CORE

André Rogatko, PhD - Core Director

Faculty and staff at the Samuel Oschin Comprehensive Center Biostatistics Core provide expertise and consultation on a variety of research projects including clinical, laboratory, pre-clinical, and pilot studies. The Core serves as a focal point from which investigators may draw statistical expertise for planning, management, and analysis of their studies.

The support and collaboration that is offered includes, but is not limited to:

  1. a full range of data analytic services including data review, statistical analysis, and interpretation and presentation of results
  2. statistical expertise in sample size and power determinations for grants, protocols, and IRB submissions
  3. collaboration with investigators on design of experiments and studies including research protocol development
  4. assistance with writing the statistical methods section of grants, protocols, and manuscripts

To request consultation with the Biostatistics Core staff, please click on this link to go to the Service Request form: http://www.cedars-sinai.edu/cancercenter/biostatrequest.asp.