Departmental Cores

Atomic Force Microscopy Core
Cardiovascular Research Center
1428 Madison Avenue
Atran Building, 3rd floor, Room 3-23
New York, NY 10029

Kevin Costa, PhD, Director
Tel: 212-241-2362 (x4AFMC)
Fax: 212-241-4080
kevin.costa@mssm.edu

The Atomic Force Microscopy (AFM) Core is a shared facility within the Cardiovascular Research Center that allows users to perform cutting-edge nanotechnology studies with an atomic force microscope that is integrated with state-of-the-art, real-time confocal fluorescence imaging. Established with funding from the National Institutes of Health (NIH) and the American Recovery and Reinvestment Act (ARRA), the instrumentation is designed to serve the needs of investigators from multiple disciplines. Current users of the facility include ISMMS research groups from Cardiology, Radiology, Systems Biology, Structural Biology, and Orthopaedics.

The Core emphasizes sub-optical resolution imaging and a greater understanding of how physical forces impact biological function of tissues, cells, and molecules. For these purposes, the facility has expertise in bioengineering, physics, and computational modeling in addition to cell biology, with a particular focus on cardiovascular systems. We can provide technical assistance with short-term projects or train users for larger-scale AFM research efforts. For more information, refer to the AFM Core facility site.

Bioinformatics Laboratory
Department of Medicine
Annenberg Building, 2^nd floor, Room A2-80H
One Gustave L. Levy Place
New York, NY 10029

Weijia Zhang, PhD, Director
Tel: 212-241-2883 (x42883)
weijia.zhang@mssm.edu

The Bioinformatics Laboratory provides resources and support to the research community of the Department of Medicine and affiliated researchers. Our mission is to promote multidisciplinary collaborations between medical research, biostatistics, and computer science. We strive to develop a bioinformatics infrastructure that integrates the analysis of diverse data from genome and proteome level analysis to clinical investigations. To facilitate effective use of existing and emerging computational technologies by researchers, we provide bioinformatics support, including training and consultation. For more information, refer to the Bioinformatics Laboratory site.

Cancer Registry
5 E 102nd St., 8th Floor, Room 856
New York, NY 10029 

Mary Johnson, CTR, Supervisor
Tel: 212-241-5201
mary.johnson@mountsinai.org

The Cancer Registry is a group of qualified health professionals who assist doctors by developing and maintaining a computerized database relevant to the diagnosis, treatment, and lifetime follow-up of cancer patients cared for by the Mount Sinai Health System. The registry carefully reviews medical records, written correspondence, and telephone contact with the managing physicians and patients. The Cancer Committee of the Medical Board provides important guidance and direction in the areas of policy, procedure, and clinical data quality.

The information collected by the Registry provides a foundation for clinical oncological investigations and medical education. The comprehensive database, with a starting date of January 1989, is also used by basic researchers interested in studies such as the cell biology, genetics, and epidemiology of specific types of cancers. 

Investigators wishing to utilize the Cancer Registry will be asked to fill in a form specifying the nature and purpose of their study. The Registry's staff will then search the computerized database and prepare a written report containing the requested information. 

Cytopathology Core
Annenberg Building, 15th Floor, Rooms 15-64 and 15-65
One Gustave L. Levy Place
New York, NY 10029

David Burstein, MD, Director
Tel: 212-241-0364 or 212-241-7378 or (x40364 or x47378)
david.burstein@mountsinai.org

The primary activity of the Cytopathology Core is diagnosing cancer, precancerous lesions, and infectious diseases. It allows clinical and basic researchers to perform diagnostic evaluation of various organ and tissue samples as well as cells from body fluids like CSF, urine, and effusions.

Viable tumor cells identified in effusions may be adaptable to cell culture growth in vitro; body cavity fluids of appropriate, consenting patients are therefore made available to investigators wishing to obtain cultures for further study of tumor cells and substances they shed into the fluid.

Cytological evaluation of fine-needle biopsies frequently precedes surgical excision of tumors. Upon request, the Core will convey these diagnoses to investigators interested in particular cancer types, thereby permitting them to arrange for obtaining tumor tissue during subsequent surgical procedures.

The Core is equipped with microscopes and laboratory tools needed for cytopathological examination of cells and organisms in specimens from various body sites, and with a combined diagnostic and investigative immunoperoxidase facility for detecting the presence of specific proteins in cytology specimens.

The Core's expertise in the investigative application of tests for specific antibodies, oncogene products, growth factors, and nuclear proteins is also available to the research community. The staff can perform these tests for medical school investigators or provide advice on procedures they may wish to carry out in their own lab.

Genomics Core Facility
Departments of Genetics and Genomic Sciences
1425 Madison Avenue
New York, NY 10029

Office Location
14th Floor - 14-20E

Main Laboratory
13th Floor, Room 13-02

Sequencing Instrument Room
14th Floor, Room 14-59

Robert Sebra, PhD
Director, Technology Development
robert.sebra@mssm.edu

The Genomics Core Facility is a Clinical Laboratory Improvements Amendments (CLIA)-certified laboratory. As a technology hub, we enable ISMMS investigators to carry out cutting-edge basic and translational genomics research. In addition, we leverage emerging next-generation sequencing and other genomic technologies for clinical diagnosis and resulting applications. We help investigators and clinicians analyze research and clinical samples, identify genetic variants contributing to disease risk, and explain pathogenic mechanisms in human disease. For more information, refer to the Genomics Core Facility site.

Life Sciences Technology Laboratory
Annenberg Building, 18th Floor, Room 18-221
One Gustave L. Levy Place
New York, NY 10029 

Jin Chen, MD, PhD, Research Specialist
Tel: 212-241-3763
jin.chen@mssm.edu

The recent technologies in the fields of genetics, genomics, and proteomics are not always within the reach of our investigators and clinicians. The goal of the Life Sciences Technology Lab is to integrate the latest genetics, genomics, and proteomics technologies, and to provide high-quality genomics and proteomics services and technical support to researchers at the ISMMS Department of Medicine and affiliated research scientists. By promoting collaboration between basic and translational research, we are aiming to bridge the gap between lab bench and patient care. For more information, refer to the Life Sciences Technology Laboratory site.

Molecular Modeling Core
Icahn School of Medicine at Mount Sinai, 16th Floor, Room 75A
1425 Madison Avenue
New York, NY 10029

Mihaly Mezei, PhD, Director
Tel: 212-659-5474 (x85475)
mihaly.mezei@mountsinai.org

The Molecular Modeling Core specializes in supporting research on macromolecular structures in silico studies of proteins and nucleic acids. Such studies can include:

Visualization

• Ab initio structure prediction of small molecules (either using quantum mechanics or molecular mechanics)
• Homology modeling of proteins
• Virtual screening (docking)
• Computer simulations (molecular dynamics or Monte Carlo)

The Core offers help in:

• Installing and using visualization software (e.g., Pymol or VMD)
• Structure prediction and manipulation software (e.g., Marvin, Avogadro)
• Using software installed on our supercomputer, Minerva (e.g., Gaussian, Charmm, Amber, NAMD, and MMC; as well as several docking programs, such as Autodock-4, Autodock-Vina, eHiTS, PLANTS, and DOCK)

Students interested in molecular modeling tools can take the course “BSR2104 Intro to Computer Modeling & Macromolecules.” For assistance in using the Core, as well as tutorials and consultations, refer to the Mezei Laboratory site.  

Tumor CytoGenomics Core
Icahn School of Medicine at Mount Sinai
1425 Madison Avenue
Box 1622, Icahn L9-02 
New York, NY, 10029

Vesna Najfeld, PhD, Director
Tel: 212-241-8801
Fax: 212-426-2427
vesna.najfeld@mssm.edu

The Tumor CytoGenomics Core provides consultation expertise in cancer cytogenetic techniques and is available to perform cytogenetic analysis for clinical and basic science researchers whose research requires these techniques. One of the major special services provided is identification of chromosome abnormalities in hematological disorders using the chromosome, FISH (fluorescence in situ hybridization), and array CGH+SNP studies.

The laboratory is equipped with three Zeiss Microscopes and CCD cameras for an automatic karyotyping system (Leica, Applied Imaging). The system is attached to the GSL (genetic slide loader/metaphase finder), which detects the location of metaphase spreads on glass slides and permits rapid determination of the karyotype of a particular cell. The attached printer immediately produces black and white photographs of a karyotype.

The Core also has a second group of three imaging systems (Leica/Applied Imaging) capable of imaging fluorescence hybridization signals. The system is attached to the Zeiss microscope equipped with a CCD camera, fluorescent device, and filter sets. The system is driven by a computer containing multiple software for digitizing multicolor images. The printer is capable of producing both black and white and color photographs. The Leica system also has a capability of imaging metaphase spreads, and both the karyotypes and fluorescence hybridization signals can be viewed simultaneously.

In addition, the Core has Agilent platform for array CGH+SNP using Baylor Cancer 400 x 400 array for detection of loss, gain, and CN-LOH. 

Cytogenetic analysis of cells from tumors and other tissues is usually performed for investigators wishing to obtain information on whether the conditions in vivo favor the proliferation of cell populations with a particular chromosome rearrangement, or whether chromosome changes have taken place during growth in vitro. In long term cultures of human derived cell lines, karyotyping is used to determine if interspecies contamination has occurred.

Chromosome studies of tumor cell populations prior to culturing are being carried out with the goals of:

• Detecting neoplastic cells
• Establishing the clonal origin of tumors
• Evaluating neoplastic progression or regression
• Providing diagnostic and/or prognostic results

FISH studies are carried out to determine the:

• Numerical chromosomal abnormalities in dividing and non-dividing cells
• Origin of marker chromosomes
• Fusion of genes without chromosomal translocations
• Detection of chimerism in bone marrow transplantation
• Presence of minimal residual disease

For researchers interested in gene mapping, the FISH technique is offered for localization of gene(s) on human chromosomes as determining exact breakpoints in chromosomal rearrangements.

Agilent array CGH+SNP Baylor cancer platform is offered to researchers interested to know the loss, gain, or CN-LOH in malignant cells. The array offers 355,515 DNA segments and 596,646 SNP with probe spacing 2.4 kb. Detection of mosaicism is 15-20%.

The Tumor CytoGenomics Laboratory offers clinical cytogenetic, FISH and array CGH+SNPs for:

• Numerical and structural chromosomal abnormalities
• Disease-specific gene rearrangements
• Disease-specific locus deletion
• Amplification of loci
• CN-LOH          
• Monitoring engraftment, chimerisam, and minimal residual disease after hematopoietic stem cell transplantation

The research aspect of the laboratory includes delineation of genetic events involved in multistep pathogenesis of myeloid disorders. For more information, refer to the Tumor CytoGenomics site.