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Wednesday, April 05, 2017

Think of CEM this way: It is comparable to standing on the moon and watching a tennis match on Earth.





Cryoelectron microscopy

Cryoelectron microscopy is a method for imaging frozen-hydrated specimens at cryogenic temperatures by electron microscopy. Specimens remain in their native state without the need for dyes or fixatives, allowing the study of fine cellular structures, viruses and protein complexes at molecular resolution.


From the Van Andel Institute:

Why we're betting on cryo-electron microscopy - VAI


We just invested in a new Cryo-Electron Microscope (Cryo-EM) Core facility, including installation of one of the world’s most powerful microscopes and recruitment of several outstanding scientists. Here’s why.

The imaging resolution available with the FEI Titan Krios from Thermo Fisher Scientific, the largest of our microscopes, is akin to watching a bouncing tennis ball on Earth from the surface of the moon. The possibilities with that kind of visual power are immeasurable. We believe cryo-EM has the potential to usher in a wave of discovery that parallels a handful of crucial developments in the history of science.

Consider the X-ray. Invented in 1985 by German physicist Wilhelm Röntgen, the first X-ray machine was bulky, expensive and technically difficult to build. However, early adopters of these machines, delivered groundbreaking and prolific contributions to our understanding of the human body.
Suddenly, scientists could see kidney stones passing into the ureter, phalanges of hand deformities, food moving through the digestive system, and a penny lodged in a child’s throat.

Similarly, the first compound microscopes led to discovery of several fundamental tenets of biology. Dutch scientists discovered cells by observing the honeycomb structure of a sliver of cork. They offered visual confirmation of bacteria, which were teeming in a droplet of lake water. They revealed the stunning complexity of tiny insects like fleas, lice and gnats.

Analogous breakthroughs in imaging abound. The first telescopes offered irrefutable visuals of the sun as center of our solar system. Electron microscopes allowed for the first images of DNA and viruses.

Now, the latest generation of cryo-electron microscopes are revealing the atomic and molecular interactions at the foundation of life. Scientists can see, for the first time, the exact size, shape, and function of profoundly complex proteins and enzymes.

We can watch as chemicals inside a nucleus assemble and begin the process of DNA replication. We can visualize the atom-by-atom structure of α-synuclein proteins, which are thought to impair the brains of people with Parkinson’s disease. We can image cell-signaling pathways thought to encourage tumor growth. The list goes on.

We believe these discoveries are only the beginning. And we believe cryo-EM represents a critical component of our unwavering commitment to improving the health and enhancing the lives of current and future generations.


There is at least one reason for Berkeley to exist...


Cryo-Electron Microscopy Achieves Unprecedented Resolution Using ...

newscenter.lbl.gov/.../cryo-electron-microscopy-achieves-unprecedented-resolution-u...


Cryo-electron microscopy (cryo-EM)—which enables the visualization of viruses, proteins, and other biological structures at the molecular level—is a critical tool used to advance biochemical knowledge. Now Lawrence Berkeley National Laboratory (Berkeley Lab) researchers have extended cryo-EM’s impact further by developing a new computational algorithm that was instrumental in constructing a 3-D atomic-scale model of bacteriophage P22 for the first time.

Complete capsid of bacteriophage P22 generated with validated atomic models that were derived from a high-resolution cryo-electron microscopy density map. (C. Hryc and the Chiu Lab, Baylor College of Medicine)

Over 20,000 two-dimensional cryo-EM images of bacteriophage P22 (also known as the P22 virus that infects the common bacterium Salmonella) from Baylor College of Medicine were used to make the model. The results were published by researchers from Baylor College of Medicine, Massachusetts Institute of Technology, Purdue University and Berkeley Lab in the Proceedings of the National Academies of Sciences earlier in March.

“This is a great example of how to exploit electron microscopy technology and combine it with new computational methods to determine a bacteriophage’s structure,” said Paul Adams, Berkeley Lab’s Molecular Biophysics & Integrated Bioimaging division director and a co-author of the paper. “We developed the algorithms—the computational code—to optimize the atomic model so that it best fit the experimental data.”

Pavel Afonine, a Berkeley Lab computational research scientist and paper co-author, took the lead in developing the algorithm using Phenix, a software suite used traditionally in X-ray crystallography for determining macromolecular structures.

The successful rendering of bacteriophage P22’s 3-D atomic-scale model allows researchers to peek inside the virus’ protein coats at resolution. It is the culmination of several years of work that previously had enabled Baylor College researchers to trace out most of the protein’s backbone, but not the fine details, according to Corey Hryc, co-first author and a graduate student of Baylor biochemistry professor Wah Chiu.

“Thanks to this exquisite structural detail, we have determined the protein chemistry of the P22 virus,” Chiu said. “I think it is important that we provide detailed annotations with the structure so other researchers can use it for their future experiments,” he added. Chiu’s lab has been using cryo-EM and computer reconstruction techniques to build 3-D molecular structures for almost 30 years.
And the findings could have valuable biological implications as well.

Thanks to the 3-D atomic-scale model, it’s now “possible to see the interactions between the pieces making up the P22 virus, which are critical to making it stable,” Adams said. This helps researchers figure out how to make chemicals that can bind to certain proteins. Adams underscores that the ability to understand the configuration of atoms in molecular space can be used to generate new insights into drug design and development.

The National Institutes of Health funded this work.

Golly, NIH, I hope you still have enough money left over to buy each AmeriKKKan a gross of rubbers.


TheChurchMilitant: Sometimes anti-social, but always anti-fascist since 2005.

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