NSF/Science Honorable Mention Image

Others participated in the earlier development of the model, including Kendall McKenzie and Callie Holderman.

A high-resolution poster version of this image is available for download here.  Save the image by right-clicking on the link and then take it to your local copy center for printing onto glossy paper.

This model of the yeast mitoric spindle shows the spindle-pole bodies as blue spheres, the kinetochore microtubules as green cylinders, the DNA as yellow tubes, cohesin as linked red rings, and condensin linking molecules in purple.  The translucent gray shell around the spindle shows the center of the region that contains cohesin as seen in fluorescence microscopy images taken of the spindle.  The DNA and other structures are too small to be resolved in the microscope.  This is the twentieth version of the model, which has been developed over a two-year period of intense collaboration between cell biologists, computer scientists, physicists, and artists.  This was developed as part of the Computer-Integrates Systems for Microsopy and Manipulation NIH/NIBIB National Research Resource.

It is a geometric model of a hyopthetical structure that has evolved to be consistent with a number of experiments performed in the department of Biology.  Its purpose is to display, in a consistent 3D space, a model, all known aspects of the structure.  This forms a basis for discussion, which then results in new planned experiments and in changes to the model.

This image was an honorable mention in the illustration category of the NSF/Science visualization challenge 2010.

About the yeast: The yeast is Saccharomyces cerevisiae as used for baking and brewing. The strains we use are science based versions not commonly used for brewing or baking, but they are the same species.  S cerevisiae is one of the most commonly used eukaryotic model systems in biology.

Aaron Neumann and his colleagues from Cell and Developmental Biology found novel dorsal pseudopodial protrusions, the “fungipods”, formed by dendritic cells (red objects in the upper image)  after contact with yeast cells (i.e. green blobs in the upper image).

Fungipods have a convoluted cell-proximal end and a smooth distal end. They persist for hours, and exhibit noticeable growth at the contact. Aaron Neumann et al. think that fungipods may promote yeast particle phagocytosis (i.e. process of surrounding and consuming solid particles) by dendritic cells.

3D visualization of magnetic resonance spectroscopy (MRS) data. The background anatomical image is a T1 MRI image containing a bright outline that roughly corresponds to the location of a tumor. The colored spheres are a sphere-based representation of concentrations of different metabolites, which are functional markers. How it works:

• red spheres = choline
• green spheres = creatine
• blue spheres = glutamin
• yellow spheres = n-acetylaspartate
• sphere size corresponds to magnitude of the metabolite.

Segmented vesicle witih proteins

This image (and linked movie) shows a rotating 3D view of a vesicle that was semi-automatically segmented from a 3D TEM image reconstructed from a tilt series.  A handful of seed points were placed in one slice of the image and the 3D vesicle was automatically extracted.  The image also shows a very preliminary automatic segmentation of proteins extending through the vesicle wall; the extent of these proteins is currently clipped by an arbitrary global parameter setting.

The second in a series of animated videos depicting the inner workings of the human lung on a microscopic scale. “Scene 2: Clearance: A Journey” asks questions about how clearance can possibly work when the volume through which the mucus flows decreases as it moves up from the depths of the lung to the throat.

This video can also be seen on YouTube.

3D Spindle Model Close-up

This is an image of Kendall McKenzie’s 3D model of the mitotic spindle made in Maya rendered from a zoomed-in perspective.

3D Spindle Model Overview

This is an image of Kendall McKenzie’s 3D model of the mitotic spindle made in Maya rendered from an overview perspective.

This drawing shows the packing of the chromatin (orange) in the nucelus. The microtubules (green) extend out both sides of the nuclear membrane, and the chromatin is bunched/tangled up inside the nucleus. The round nucleus is about 1.5 microns in diameter.

tin is bunched/tangled up inside the nucleus.  The round nucleus is about 1.5 microns in diameter.

This drawing shows the structure of the kinetochore. A microtubule (green) with a flared end is surrounded by 8 thin rods/proteins (blue), which are then enclosed by 16 proteins (pink). This structure then connects (in a way that is not shown) to the DNA strand (yellow) while it is in a hook-like structure holding the cse4 nucleosome.

This drawing shows the spindle from end to end. It is roughly 1.5 micons in length, with the kinetochore (green) microtubules making up 350 nm on each end, and the space between them being roughly 800 nm. The interpolar microtubules are drawn in two shades different shades of purple (dark purple ones extend from the left end of the spindle and pink-purple ones extend from the right end of the spindle). The microtubules are drawn straight and rigid, with an overall spindle diameter of 250 nm. Also, the DNA strands (yellow) extend even more outwardly than the microtubules. The two outermost strands of DNA (top and bottom of the spindle) have a few loops of DNA drawn in to show that the diameter of the spindle reaches 400 nm when the loops are included. Each of the other strands has a small break in it that represents a place where extra loops of DNA are attached. They are not drawn because they would make the details of the spindle hard to see. The bottom right corner shows the layout and packing of the microtubules at the spindle pole, not in a "convergence point" formation, but in a more tightly packed formation that has a diameter of 150 nm.

This drawing shows the spindle from end to end.  It is roughly 1.5 micons in length, with the kinetochore (green) microtubules making up 350 nm on each end, and the space between them being roughly 800 nm.  The interpolar microtubules are drawn in two shades different shades of purple (dark purple ones extend from the left end of the spindle and pink-purple ones extend from the right end of the spindle).  The microtubules are drawn straight and rigid, with an overall spindle diameter of 250 nm.
Also, the DNA strands (yellow) extend even more outwardly than the microtubules.  The two outermost strands of DNA (top and bottom of the spindle) have a few loops of DNA drawn in to show that the diameter of the spindle reaches 400 nm when the loops are included.  Each of the other strands has a small break in it that represents a place where extra loops of DNA are attached.  They are not drawn because they would make the details of the spindle hard to see.
The bottom right corner shows the layout and packing of the microtubules at the spindle pole, not in a “convergence point” formation, but in a more tightly packed formation that has a diameter of 150 nm.