CISMM

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.

This drawing shows the form DNA takes when it is between the microtubule (green) end and a gap from which a loop extends. The microtubule is attached to the DNA by the kinetochore structure (pink), which is 80 nm long. The kinetochore attaches to the DNA (yellow) at a hook-like space near the cse4 nucleosome (shown at the end). There are 55 histones (orange) on each of the "top" and "bottom" of the structure. Roughly 75% of the length of the DNA strand is tangled in "loop" structures, and the other 25% is between loops in a straighter line. Condensin (blue) binds to the DNA at the bottoms of the loops. Condensin (purple) wraps around and encloses the DNA within the loops and where there is a space on the far right. The small green asterisks show where the GFPs are placed on cohesin and condensin in the lab.

This drawing shows the form DNA takes when it is between the microtubule (green) end and a gap from which a loop extends.  The microtubule is attached to the DNA by the kinetochore structure (pink), which is 80 nm long.  The kinetochore attaches to the DNA (yellow) at a hook-like space near the cse4 nucleosome (shown at the end).
There are 55 histones (orange) on each of the “top” and “bottom” of the structure.  Roughly 75% of the length of the DNA strand is tangled in “loop” structures, and the other 25% is between loops in a straighter line.
Condensin (blue) binds to the DNA at the bottoms of the loops.  Condensin (purple) wraps around and encloses the DNA within the loops and where there is a space on the far right.  The small green asterisks show where the GFPs are placed on cohesin and condensin in the lab.

This drawing shows a cross section of the mitotic spindle, with a diameter of 250 nm. The 16 kinetochore microtubules are green, the 8 interpolar microtubules are orange, and the strands of DNA are represented by purple squiggly lines.

This drawing shows a cross section of the mitotic spindle, with a diameter of 250 nm.  The 16 kinetochore microtubules are green, the 8 interpolar microtubules are orange, and the strands of DNA are represented by purple squiggly lines.

Simulated image generation in FluoroSim is fast enough to enable interaction with specimen models while watching real-time updates of the expected fluorescence image. This video shows some of FluoroSim’s main capabilities.

Cilia-driven mucus flow visualization by David Borland

David Borland developed a flow visualization technique and used the output of Brian Eastwood’s ImageTracker program to construct this visualization of cilia-driven mucus flow on a human lung cell culture video from David Hill.  He overlaid the flow on the cell background determined by ImageTracker.

Flow speed is encoded both by color (blue lowest, through gray to red).  Flow direction is along the lines and in the direction pointed to by the arrows.

virtual-lung-final-video32

The first in a series of animated videos depicting the inner workings of the human lung on a microscopic scale. “Scene 1: Into the Mucus River” explains how air gets into healthy lungs, how the body defends itself against harmful airborne pathogens, and how mucus and cilia interact with the air particles.

This video can also be seen on YouTube.

Slice through epithelial cell culture.

The image to the right shows one frame from a stack of images taken of a human lung epithelial cell culture.  The well-separated spots were thought to be cross sections through cilia sticking out the tops of cells.  There are some bright spots on the labeled cells and others (near the left of the image) that were thought to be above cells.

ImageSurfer 3D view of epithelial cells

The ImageSurfer image shown below to the right revealed that they were in fact isolated blobs of dye that were outside of the cells.

In this movie, we show a fibrin network stretched using an AFM tip and then tracked using CISMM’s video spot tracker.  The distribution of fiber strains within the network is then analyzed.  The goal is to understand the influence of single fiber mechanics on the properties of entire networks.

Download the original movie here.

iMiJ.pdb: Native Chicken Fibrinogen rendered using broad illumination on the BASS (NIH 1S10RR023069-01)

CISMM is one of the primary users of the Biomedical Analysis and Simulation Supercomputer (BASS) system that was commissioned yesterday.  One of the first uses of the machine was to construct a high-resolution rendering of fibrinogen (blood clotting molecule of interest to our thrombisis collaborators Susan Lord, John Weidel, Martin Guthold, and Alisa Wolberg).  This is a prototype for the PDB rendering project in collaboration with David Banks at with the Klaus Schulten NCRR on Macromolecular Modeling and Bioinformatics.