While working on generating protofibrils in Chimera, I thought it’d be great if the software can do:
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.
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.
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 cerevisiaeas 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.
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 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
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.
