Training Research Cores

Director: Phillip G. Allen (Charles River Campus)

Rotating in the MNI core will expose students to a variety of imaging technologies including: Zernike Phase contrast, DIC phase contrast and various near and far field fluorescence technologies. In addition detector/camera characterization, sample preparation and some aspects of image processing/quantitation could be explored. They will be exposed to instrument setup for various types of imaging experiments (microscopes and cameras; Phase and DIC; fluor -quant and corrections; Photobleach & Corr; Cells on scopes; Ratiometric imaging; Ca2+ imaging lab; TIRF imaging and Confocal imaging) as well as individual researchers who use the imaging core. Other hands on experience will include cleaning, maintaining and aligning instruments, designing software “macros” for specialized acquisition strategies and image processing. Students will interact with both the core director and other users of the core to be exposed to the use of microscopic imaging in modern research.

Director: Elise Morgan

Students will be exposed to micro-computed tomography (μCT), which is a three-dimensional, X-ray-based imaging modality that can image tissues, organs and whole organisms as well as nonorganic structures with a resolution as high as 6-10 μm. μCT systems provide rapid, quantitative, high-resolution and three-dimensional assessment of both microstructure and density.  μCT is nondestructive and can scan ex-vivo samples as large as 75 cm3 in approximately several hours. There are two μCT scanners in the Orthopedic and Developmental Biomechanics Laboratory:  a Scanco μCT40 system and a Scanco μCT80 system.  These two systems are calibrated on a weekly basis. The systems have the manufacturer-supplied software that provides routines for identifying sub-regions for analyses, image segmentation, and image analysis.  The image analyses can be performed on three-dimensional regions of interest to quantify porosity and other features of the microstructure. Two-dimensional analyses can also be performed to quantify bone area, bone area fraction, cross-section area, and moment of inertia. Images can be rendered and exported in a variety of file formats. Numerical results can be exported in tabular form. A stand-alone, identical workstation is available for image analysis, for a total of 10 TB of data storage. In addition to Scanco and Zeiss software, the facility maintains a license for Amira (FEI Visualization Sciences) for additional image processing. The facility is at the forefront of technical capabilities for imaging bone, cartilage, other soft tissues, and vessels.

Directors: Michael T. Kirber and Orian Shirihai

In this Cellular Imaging rotation students will be given exposure to numerous digital imaging microscopy systems for studying cells and tissues. The systems that are available training include: IonOptix calcium imaging system, Olympus DSU spinning disk confocal microscope, Two-photon confocal, Nikon deconvolution wide-field Epifluorescence system, Zeiss LSM 710-Live Duo scan, and the Olympus stereo fluorescence imaging microscope. The basic design and function of the microscopes will be reviewed as well as the limitations and advantages of different confocal modes. Students will learn what instruments are designed for different cell and tissue set-ups, including time-lapse high-speed imaging of intracellular calcium in living cells using Fura 2, time lapse of fast events such as protein translocation or electrophysiological events in fixed or living samples, imaging at subcellular resolution using UV excitable dyes for co-localization studies in fixed or live samples, as well as the use of confocal for specimen imaging. Students will have the opportunity to learn from researchers currently using the core as well as have training from core directors.

Director: Vickery Trinkaus-Randall

Students will have the opportunity to learn about confocal microscopy services for cell imaging and analysis and be involved in project/experiment planning. In this rotation students will be exposed to light microscopic imaging technologies including: Phase contrast, DIC phase contrast and fluorescence technologies. Students will be trained on the Zeiss LSM confocal microscopes by the core director and her assistant, and shadow the entire process that includes working with the researchers to help them plan experiments. Both short and long term live imaging will be performed using DIC and fluorescent technologies. Students will be exposed to Ca2+ imaging using a flow through system and micromanipulator, software set-up and analysis, including physiology and time series programs, and tileware. The basic design and function of the microscopes will be reviewed as well as the limitations and advantages of different confocal modes. The students will be exposed to and learn care of the instruments. Students will interact with both the core director and other users of the core to be exposed to the use of microscopic imaging in modern research.

Director: Jennifer Snyder-Cappione

This rotation will focus on flow cytometry for analysis and sorting of cells, as well as the opportunity to participate in consultation sessions for project/experiment planning. Students will have the option to use and be trained on different FACScan analyzers, including one FACSCalibur analyzer, one LSRII analyzer, one FACSARIA and one MoFlo cell sorter. Students will review basic principles of how cells in a laminar flow medium interact with laser light, including measurement of forward and side scatter properties and fluorescence, as well as understand how these specific properties offer a source of information about the state of cellular DNA synthesis and cell cycle, surface markers, signal transduction and apoptosis. Students will learn about sorting strategies and fluorescence compensation in the FACS analyzer, multiparameter data analysis and computational methods of gating and handling large numbers of events/rare events, and advanced techniques such as staining of intracellular antigens for signaling and sorting of different types of stem cells.

Director: TBD

Students will acquire an understanding of an overview of the High Throughput Screening process. They will be exposed to projects run by researchers and the core director that demonstrate that High Throughput Screening can be used for both pathway- and target-validation, and for early stage drug discovery. They will have the opportunity to discuss and partake in small molecule High Throughput Screening, and will learn about different classes of small molecule libraries. Students will also learn about advantages and limitations of two prevailing screening methods: target- based and phenotype-based. They will have an opportunity to see and use the microplate reader and the HCA reader. They will acquire knowledge about target-based and phenotype-based screens, as well as understand the implications of the data produced in an HTS screen, and how this data can be stored, mined, and analyzed.

Director: Xuemei Zhong

Students will acquire knowledge about the variety of IHC services for human and animal tissues to biomedical researchers. Students will become familiar with the principles underlying IHC, the scope of the instruments available for use in the IHC core and how the equipment can be used to probe biological systems. Students will have the opportunity to explore the following applications: applications include: distribution and localization of biomarkers, differential expression of proteins in different parts of a tissue, diagnosis of abnormal cells, analysis of antibody deposition on inflamed tissue, cell proliferation, activation, apoptosis in a tissue using specific markers, visualize different cell types in blood smear and study cultured cells using cytospin or cover slips.   Students will also be trained in microscope and image processing software.

Director: Kenneth Albrecht

Students will review and apply the general principles guiding the generation of transgenic and knockout models. They will have the opportunity to understand the application of different models in various research inquiries. Through interaction with core directors and researchers, they will understand how the use of these technologies has allowed the exploration of the role of a variety of genes during development, as well as the importance of genes for certain physiological and biochemical processes and for the development of disease.

Director: Yuriy Alekseyev

Students will have the opportunity to learn and utilize the Microarray Resource Core that offers the full line of microarray products available from Affymetrix, including expression profiling, miRNA, exon, genotyping, resequencing, and tiling arrays, as well as experimental design and data analysis. Students will review the different aspects of microarray technology including underlying principles, fabrication of such arrays and the collection/processing/analysis of samples. Students will also learn about the available technologies and the adavantages and disadvantages of each. Students will have the opportunity to work with researchers and core directors to understand the major applications of genomic technologies and how they are revolutionizing science and medicine.

Director: Erdjan Salih

Students will review principles underlying mass spectrometry and its application in the field of proteomics and protein chemistry research. They will learn about design and interpretation of proteomics experiments. The design of various instrumentation will be discussed as well as different techniques including: interpretation of mass spectra, tandem mass spectra (MS/MS), protein identification via a database search using both peptide mass fingerprint (PMF) and MS/MS data, assignment of PTMs, use of isotope tags, sample purification, fractionation and separation strategies, design of a differential proteomics experiment and meta-analyses of protein data. Students will have the opportunity to work with researchers and core directors to see examples of ongoing clinically relevant biological projects.

Director: Lynn Lingyi Deng

The core provides teaching and support to trainees and investigators through cutting-edge analytical instruments to facilitate research and education. Instrumentation includes: RT-PCR System StepOne Plus (X2) or 7900 HT Fast Real-Time PCR System; Gel Imaging or Luminescent Image Analyzer; PhosphoImager FluoS; Oxygen Analyzer; Liquid Scintillation Counter (LSC); Nanodrop Spectrophotometer; HEMAVET 950 FS Auto Blood Analyzer; Free Flow Electrophoresis; Tecan Microplate Reader and 2-D PAGE Apparatus & Imager.

Note: As the program develops, other research cores will be considered and added/deleted to/from the program, pending approval of Graduate Medical Sciences (GMS) and the program executive committee.