A model of the yeast mitotic spindle in metaphase was constructed based on a looping model of DNA distribution, where the loops are tied together at their base by condensin and they are linked by slip-rings of cohesin.    This model was created in collaboration between Kerry Bloom and his group and CISMM personnel.  The geometry of the model at its initial state is shown below.

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.

The image below is a proposed structure for the mitotic spindle of yeast during metaphase that was produced in a collaboration between Russell M. Taylor II, Andrew Stephens, Kerry Bloom, Leandra Vicci, Jolien Verdaasdonk, Steven Nedrud, Matt Larson, and Michael Falvo.

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

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.

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

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 the packing of the chromatin (orange) in the nucelus.  The microtubules (green) extend out both sides of the nuclear membrane, and the chroma

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

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