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Collaboration with UCSD Cancer Center
Professor James Feramisco and his associates at the UC San Diego School of Medicine's Cancer Center are collaborating with the SDSC Scientific Visualization group to create 3-D images of the interior of cells. The visualizations provide cancer researchers with valuable perspective views into the structure of cells, enabling them to perceive spatial relationships between regions that contain active proteins. The collaboration allows the SDSC Scientific Visualization group to work with researchers and develop visualization tools for their scientific application.
In a technique called immunofluorescence microscopy, purified antibodies attached to fluorescent dyes are applied to a cell or tissue section where it binds to its corresponding antigens. Illuminating the specimen with light of appropriate wavelengths causes the labeled antibodies to fluoresce. Since each dye-antibody complex binds to only a specific protein in the cell, the fluorescence acts as a structural marker for regions of interest that contain the protein. By treating a specimen with several differently colored labeled antibodies, multiple proteins can be localized within the same cell. When viewed with a high-resolution microscope, image slices can be captured representing the different cell structures. The image slices are composited and filtered, then converted into a 3-D volume that can be viewed by an interactive volume viewer, such as the Mesh Viewer or the Volume Explorer applications. The user can select different camera viewpoints and camera animation paths that are sent the VISTA Volume Renderer at SDSC to generate high-resolution rendered images and animations in the case of the Mesh Viewer. Alternatively, the user can visualize the volume in interactively in real-time at the workstation in the Moores UCSD Cancer Center Resource equipped with Volume Explorer software and a VolumePro 1000 video card.
The image slices are composited and filtered, then converted into a 3-D volume that can be viewed by an interactive volume viewer, such as the Mesh Viewer application. The user can select different camera viewpoints and camera animation paths that are sent the VISTA Volume Renderer to generate high-resolution rendered images and animations.
Adenylate Cyclase Expression in a Cardiac Myocyte
Members of Kirk Hammond's lab at UCSD/ VA Hospital have been studying the role of adenylate cyclase in cardiac function. The image shows a cardiac myocyte following infection with a replication defective adenovirus encoding adenylate cyclase, and then stained for adenylate cyclase (red), alpha-actinin (green) and DNA (blue).
The experiment was done by Mei Hua Gao and Julie Sherman of the Program of Excellence in Gene Therapy. The Program is headed by Kirk Hammond, Professor of Medicine, and also includes David Roth, Joe Witztum, Jim Feramisco, Gregg Silverman, Paul Insel, Atushi Miyanohara, Wilbur Lew, Chin Lai, Tong Tang, Jeff Drumm, Matthew Spellman, Tracy Guo, and Nancy Dalton.
The image shown is of an endomitotic megakarycyte The megakaryocyte is a bone marrow cell that is a precursor for blood platelets. It is called a megakaryocyte because it has many nuclei and is very large. The cell was stained for nuclei (blue), phosphorylated histone H3 (green) and alpha tubulin (red).
The micrographs were collected in the Moores UCSD Cancer Center Digital Imaging Shared Resource using deconvolution microscopy by Amy Geddis of the Division of Hematology/Oncology, Moores UCSD Cancer Center, with assistance from Steve McMullen. Perspective views were rendered with the Volume Explorer program.
Golgi bodies in mammalian cells. Eukaryotic cells have a myriad of internal organelles, each of which perform key functions. One such organelle is the Golgi apparatus, a region composed mainly of membranes and specific proteins. Golgi bodies are the "packaging plants" of cells, where materials manufactured by the endoplasmic reticulum are modified, stored, and shipped out to other regions of the cell or to the outside. The Golgi apparatus is extensive in cells that are specialized for secretion. For this 3-D visualization, two different protein components of the Golgi bodies (green, red) along with the genetic material of the cells (DNA, blue) were imaged using deconvolution microscopy.
Deconvolution microscopy was performed at the Digital Imaging Shared Resource of the Moores UCSD Cancer Center. The data were obtained by Drs. Maria Aparecida Pinhal and Jeff Esko, Department of Cellular and Molecular Medicine at UCSD, and Brian Smith of the Shared Resource. 3-D volume rendering was performed by Dave Nadeau and Philip Fisher-Ogden at the VisLab of the San Diego Supercomputer Center using NPACI Scalable Visualization Tools.
Members of Steve Hedrick's lab have been studying signal transduction activities initiated by mediators of innate immunity. One aspect of their work has led them to examine the actin cytoskeleton. The image shows a single fibroblast, where F-actin was stained in red, paxillin, a focal adhesion component, in green and nuclei in blue.
Members of Steve Hedrick's lab have been studying signal transduction Deconvolution microscopy was performed at the Digital Imaging Shared Resource of the Moores UCSD Cancer Center. The studies were done by Rachel Soloff, Carol Katayama, Meei Lin, Jim Feramisco, and Steve Hedrick of the Cancer Center. 3-D volume rendering was with the Volume Explorer.
Rat Ventricular Myocytes
High Resolution: 2048 x 1536 (TIFF format)
Cardiac myocytes were stained for mitochondria (red), DNA (blue), and F-actin (green) and imaged by deconvolution microscopy in the UCSD Cancer Center Digital Imaging Shared Resource. Mitochondria provide some of the energy required for cardiac cells to beat, and F-actin is critical in providing force for the contraction of heart cells.
Perspective views were rendered by Alex DeCastro at the San Diego Supercomputer Center using NPACI Scalable Visualization Tools. The work is from John W. Adams, Amy L. Pagel, Christoper K. Means, Donna Oksenberg, Robert C. Armstrong, Joan Heller Brown of the Department of Pharmacology, UCSD (Circulation Research; 2000 87: 1180 - 1187.) One of the views appeared on the cover that issue.
Phagocytotic macrophage engulfs dying cells. Phagocytosis of dying cells is an obligatory process used for sanitizing tissues and preventing inflammation. It is of special interest for the research on atherosclerosis because dead cells left in atheroma may cause thrombosis, a dreadful complication of atherosclerosis responsible for heart attack or most strokes.
The image shows a pseudopod extension from a macrophage surrounding a dying cell (stained blue) as it is engulfed. An enzyme component of the macrophage, 12/15-lipoxygenase, (stained red) concentrates in this pseudopod and colocalizes with another important protein component, polymerized actin (stained green). Actin provides the driving force behind the creation of the cellular protrusion. Yellow colored areas are indicative of maximal co-localization of the red and green staining for the two proteins.
Deconvolution microscopy was performed at the Digital Imaging Shared Resource of the Moores UCSD Cancer Center. The studies were done by Drs. Yury Miller, Jim Feramisco and Joe Witztum of the Department of Medicine, UCSD. 3-D volume rendering was with Volume Explorer by Tess Pierce.
Images show chromosomes (blue), microtubules (red) and a chromosome-associated protein (green) in a cell about to divide. Cell division is a hallmark of cancer and understanding its molecular basis is of importance to cancer research.
The data were collected in the UCSD Cancer Center Digital Imaging Shared Resource using deconvolution microscopy by Fran Putkey of the Cleveland lab of the Ludwig Institute for Cancer Research, UCSD Branch. The images were rendered at the Moores UCSD Cancer Center with a frame capture from the Volume Explorer software running on a VolumePro 1000 video card.
Altered gene expression is a hallmark of many forms of cancer. It is very important to know what these changes are, and in certain cases the altered gene expression can be detected or quantified by fluorescence deconvolution microscopy.
In the case shown, sections of tissue from a breast cancer sample were examined for altered gene expression. Images were collected in the Digital Imaging Shared Resource by Moores UCSD Cancer Center investigators Monika Szeszel and Linda Wasserman with assistance from Steve McMullen. The sample was stained for a growth factor receptor (red), a hormone receptor (green) and nuclei (blue). 3-D volume rendering was performed by Alex Decastro and Philip Fisher-Ogden at the VisLab of the San Diego Supercomputer Center using NPACI Scalable Visualization Tools.