Panoptes

The code was developed by Belinda Johnson.  A coarse-grained simulation was run, based on the SOFA platform with the addition of Brownian forces and stiffness forces, to understand what the addition of Brownian forces on the structure would do to the distribution of DNA.  The parameters of the simulation included a random force of 1228, a mass_damping of 10, a mass_radius of 0.0045, a spring constant of 628000, a hinge force of 0.548, and an object mass of 33.3 (see simulation code for the units).  We believe that this model matches the expected behavior except for: (1) the viscosity is much lower than in reality so that the simulation will run in reasonable time (we expect the behavior to be the same).  (2) The cohesin rings are too large by about a factor of two (this was a mistake in the model set up, which we think will only serve to make the rings more mobile).  (3) There is no torsional restoring force on the DNA, so there will be no impact due to twisting of the DNA strands.

The resulting movie of the simulation is available here: 0001-0167.  It shows a snapshot of the simulation every 0.1 nanoseconds up to 17.6 nanoseconds.

The simulation showed the outside of the rings pulling in and the inside of the spindle pushing out.  There was not a large net offset to the cohesin rings from their initial position (each moves, but they seem to maintain their approximate position).  The ends of the DNA are pinned in space as if to stable microtubules.  Some images of the resulting configuration are shown below.

Actin-rich fungipods attack a yeast attached to a cell membrane

Collaborator Aaron Neumann from the University of New Mexico is studying fungipods from human dendritic cells that attach to yeast.  The image above shows a combination of three different fluorophores that together show the behavior.  A green yeast is sitting on top of the cell membrane (transparent red) with three fungipods attached to it.  The fungipods are very dense in actin (blue).

1. Rotate and orientate the models but with certain points fixed. That would require the models becoming flexible.

2. Preview replicated monomers in real-time. So users don’t have to change one of the monomers, replicate more to see the structure, change the monomer again, and re-do the replication again to see how the structure looks like.

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.

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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.