Biomolecule Imaging Pioneers Share Nobel Prize

Today, the Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry 2017 to Jacques Dubochet (University of Lausanne, Switzerland) and Joachim Frank (Columbia University, New York, USA), and Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK). The award is given "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution"

Cool microscope technology revolutionises biochemistry

We may soon have detailed images of life’s complex machineries in atomic resolution. The Nobel Prize in Chemistry 2017 is awarded to Jacques Dubochet, Joachim Frank and Richard Henderson for the development of cryo-electron microscopy, which both simplifies and improves the imaging of biomolecules. This method has moved biochemistry into a new era.

A picture is a key to understanding. Scientific breakthroughs often build upon the successful visualization of objects invisible to the human eye. However, biochemical maps have long been filled with blank spaces because the available technology has had difficulty generating images of much of life’s molecular machinery. Cryo-electron microscopy changes all of this. Researchers can now freeze biomolecules mid-movement and visualize processes they have never previously seen, which is decisive for both the basic understanding of life’s chemistry and for the development of pharmaceuticals.

Electron microscopes were long believed to only be suitable for imaging dead matter, because the powerful electron beam destroys biological material. But in 1990, Richard Henderson succeeded in using an electron microscope to generate a three-dimensional image of a protein at atomic resolution. This breakthrough proved the technology’s potential.

Joachim Frank made the technology generally applicable. Between 1975 and 1986 he developed an image processing method in which the electron microscope’s fuzzy two-dimensional images are analysed and merged to reveal a sharp three-dimensional structure.

Jacques Dubochet added water to electron microscopy. Liquid water evaporates in the electron microscope’s vacuum, which makes the biomolecules collapse. In the early 1980s, Dubochet succeeded in vitrifying water – he cooled water so rapidly that it solidified in its liquid form around a biological sample, allowing the biomolecules to retain their natural shape even in a vacuum.

Following these discoveries, the electron microscope’s every nut and bolt have been optimised. The desired atomic resolution was reached in 2013, and researchers can now routinely produce three-dimensional structures of biomolecules. In the past few years, scientific literature has been filled with images of everything from proteins that cause antibiotic resistance, to the surface of the Zika virus. Biochemistry is now facing an explosive development and is all set for an exciting future.

About the Nobel Laureates

Jacques Dubochet, born 1942 in Aigle, Switzerland. Ph.D. 1973, University of Geneva and University of Basel, Switzerland. Honorary Professor of Biophysics, University of Lausanne, Switzerland.
www.unil.ch/dee/en/home/menuinst/people/honorary-professors/prof-jacques-dubochet.html

Joachim Frank, born 1940 in Siegen, Germany. Ph.D. 1970, Technical University of Munich, Germany. Professor of Biochemistry and Molecular Biophysics and of Biological Sciences, Columbia University, New York, USA.
http://franklab.cpmc.columbia.edu/franklab/

Richard Henderson, born 1945 in Edinburgh, Scotland. Ph.D. 1969, Cambridge University, UK. Programme Leader, MRC Laboratory of Molecular Biology, Cambridge, UK.
www2.mrc-lmb.cam.ac.uk/groups/rh15/

What can we use from this in teaching undergraduate A&P?

• If you talk about imaging molecules in your course, this could be a way to garner student interest—considering that this is a current and ongoing effort in science. I always have a brief "shape is important in biological chemistry and here's what we can see with current tools" because they're going to see all those little odd-shaped rutabaga blobs in illustrations in their textbooks.


• If you bring up microscopy in your course, perhaps describing the types of microscopy, adding a bit of info on this could help show students that microscopy is still evolving—in exciting ways.


• Consider using the annual Nobel Prize announcements as a springboard to discuss the process of scientific discovery. 


• Consider mentioning the other major awards for scientific achievement and discuss what the judges seem to value most about scientific discoveries. The Nobel Prize is the one everyone has heard of, so it's a great place to start.


• Use the Nobel Prizes (and other awards) over time as a way to keep students aware of the history of, and progress, of human biology. One could also address the global diversity of laureates.  Or the lack of other kinds of diversity among laureates.

Want to know more?

Popular Information 

• my-ap.us/2hNGb1D 

Scientific Background

• my-ap.us/2hPtKm0

Images

Image - 3D structures (pdf 1.4 MB)

• © Johan Jarnestad/The Royal Swedish Academy of Sciences
• my-ap.us/2hNUq6o

Image - Blobology (pdf 8.5 MB)

• © Martin Högbom/The Royal Swedish Academy of Sciences
• my-ap.us/2hLMaDV

Image - Dubochet's preparation method (948 kB)

• © Johan Jarnestad/The Royal Swedish Academy of Sciences 
• hmy-ap.us/2hPtYJS

Image - Frank's image analysis (pdf 1 MB)

• © Johan Jarnestad/The Royal Swedish Academy of Sciences
• my-ap.us/2hMkU8i 

Cool Animations (literally)

Structure and gating of the nuclear pore complex

• Eibauer M, Pellanda M, Turgay Y, Dubrovsky A, Wild A, Medalia 
• my-ap.us/2hMolMe
• my-ap.us/2hKWxbd

Ion gating in the sarcoplasmic reticulum membrane

• Samsó M, Feng W, Pessah I, Allen P
• my-ap.us/2hLJCWg

Antibody structure

• Zhang L, Ren G
• my-ap.us/2hLQp2j

Native LDL particles

• Kumar V, Butcher S, Öörni K, Engelhardt P, Heikkonen J, Kaski K, Ala-Korpela M, Kovanen P
• my-ap.us/2hO4Qms

Changes in the water and ion contents of organelles during apoptosis

• Nolin F, Michel J, Wortham L, Tchelidze P, Banchet V, Lalun N, Terryn C, Ploton D
• my-ap.us/2hMTYW4

Adapted from press release at nobelprize.org
Click each image for its source/attribution

Cytotoxic T Cell Horror Flick

Liven up your A&P class with a great video showing a gruesome attack by a killer T cell on a cancer cell. It's a fantastic bit of video microscopy produced by Cambridge University.

Okay, with the oddly soothing music score instead of a more appropriate score for the graphic violence shown in this video, it's not much of a horror flick.  Especially when you consider that it's the "bad guy" cell getting whacked.  But it is graphic and dramatic and impressive.

Just the thing to liven up a discussion of adaptive immunity, which (let's face it) can often cause a catatonic state in many students.

It's a free resource available on YouTube.

Nobel Prize 2014: Super-resolved fluorescence microscopy

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2014 to

Eric Betzig

Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA,

Stefan W. Hell

Max Planck Institute for Biophysical Chemistry, Göttingen, and German Cancer Research Center, Heidelberg, Germany

and

William E. Moerner

Stanford University, Stanford, CA, USA

“for the development of
super-resolved fluorescence microscopy”

Surpassing the limitations of the light microscope

For a long time optical microscopy was held back by a presumed limitation: that it would never obtain a better resolution than half the wavelength of light. Helped by fluorescent molecules the Nobel Laureates in Chemistry 2014 ingeniously circumvented this limitation. Their ground-breaking work has brought optical microscopy into the nanodimension.

In what has become known as nanoscopy, scientists visualize the pathways of individual molecules inside living cells. They can see how molecules create synapses between nerve cells in the brain; they can track proteins involved in Parkinson’s, Alzheimer’s and Huntington’s diseases as they aggregate; they follow individual proteins in fertilized eggs as these divide into embryos.

It was all but obvious that scientists should ever be able to study living cells in the tiniest molecular detail. In 1873, the microscopist Ernst Abbe stipulated a physical limit for the maximum resolution of traditional optical microscopy: it could never become better than 0.2 micrometres. Eric Betzig, Stefan W. Hell and William E. Moerner are awarded the Nobel Prize in Chemistry 2014 for having bypassed this limit. Due to their achievements the optical microscope can now peer into the nanoworld.

Two separate principles are rewarded. 

One enables the method stimulated emission depletion (STED) microscopy, developed by Stefan Hell in 2000. Two laser beams are utilized; one stimulates fluorescent molecules to glow, another cancels out all fluorescence except for that in a nanometre-sized volume. Scanning over the sample, nanometre for nanometre, yields an image with a resolution better than Abbe’s stipulated limit.

Eric Betzig and William Moerner, working separately, laid the foundation for the second method, single-molecule microscopy. The method relies upon the possibility to turn the fluorescence of individual molecules on and off. Scientists image the same area multiple times, letting just a few interspersed molecules glow each time. Superimposing these images yields a dense super-image resolved at the nanolevel. In 2006 Eric Betzig utilized this method for the first time.

Today, nanoscopy is used world-wide and new knowledge of greatest benefit to mankind is produced on a daily basis.

This video is a brief animation of how STED works and how it improves resolution of individual particles.

This video is a longer, more detailed presentation by one of the Nobel laureates (Hell).

What can we use from this in teaching undergraduate A&P?

• Discuss how this technology has enabled us to better visualize the chemicals and structures within our cells, enabling scientists to better understand the structure and function of cell, organelles, microbiome constituents, and other structures of the human body.


• If you do a brief run-through of the theory of microscopy—perhaps in your A&P lab—you can add a mention of this technology.  


• Your textbook or other learning resource may already have an example of this type of microscopy.


• A discussion of this  Nobel Prize could evolve into a meaningful example of how science works, including how incremental improvements in classical tools for observation expand the number of questions that can be answered.


• Use the links below (and images above) to use for a handout and/or teaching slides.

Want to know more?

Resources from Nobelprize.org

• Popular Information 
• Handout: Overview information in plain English
• my-ap.us/1rh0fAJ
• Scientific Background
• Handout: More detailed information includes references to original research articles
• my-ap.us/ZdLJ69
• Advanced Information
• Handout
• my-ap.us/1rh0dsp
• Images
• Can be used in your course
• Abbe's diffraction limit
• my-ap.us/ZR0LA8
• The principle of STED microscopy
• my-ap.us/1ncRH2C
• The principle of single-molecule microscopy
• my-ap.us/1pQbAZ4
• Biographies
• Eric Betzig, 
• U.S. citizen. Born 1960 in Ann Arbor, MI, USA. Ph.D. 1988 from Cornell University, Ithaca, NY, USA. Group Leader at Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
• http://janelia.org/lab/betzig-lab
• Stefan W. Hell, German citizen. 
• Born 1962 in Arad, Romania. Ph.D. 1990 from the University of Heidelberg, Germany. Director at the Max Planck Institute for Biophysical Chemistry, Göttingen, and Division head at the German Cancer Research Center, Heidelberg, Germany.
• http://www3.mpibpc.mpg.de/groups/hell
• William E. Moerner, U.S. citizen. 
• Born 1953 in Pleasanton, CA, USA. Ph.D. 1982 from Cornell University, Ithaca, NY, USA. Harry S. Mosher Professor in Chemistry and Professor, by courtesy, of Applied Physics at Stanford University, Stanford, CA, USA.
• http://web.stanford.edu/group/moerner

Diagrram cretit: Ganbaatar

Micrograph credit: Tesselkaffee

Text adapted from press release from Nobel Media

Death spreads throughout body

C. elegans

In class discussions, we talk about what happens when the body dies.  And it's always a bit tricky when the discussion gets around to the idea that not every cell dies simultaneously.

And of course, that can lead to a discussion of how tissue death occurs, even in the case of necrosis that occurs as a result of ischemia or other damage. There are certainly many mechanisms involved—quite a few of which have yet to be clarified.

Recently, researchers have brought a step closer by mapping out some of these mechanisms.  In their report (cited below), they reveal that in the gut of the C. elegans worm, calcium ions flowing into cells cause the lysosomes to burst suddenly.  And we know what that means! Intracellular destruction leading to cell death.

What causes the calcium ions to rush into the cells? Gap-junction ion-channel proteins called innexins (analogous to connexins in humans) open up and allow calcium ions to flow into one cell then the next, producing a wave of destruction along the gut.

In interesting phenomenon is that esters of anthranilic acid (formed from the amino acid tryptophan) in the lysosomes not only produce acidosis in the cytosol, they also fluoresce brightly with a bluish glow during this process of cell death.

The video below shows an amazing anterior-to-posterior wave of fluorescent blue in C. elegans worms as this "wave of death" travels along the gut wall.

Okay, now here's the kicker.  By knocking out the innexin channels, the researchers were able to stop the wave of death!  Whoa!  A cure for . . . death?!

Not so fast.  This worked in a WORM, which is not as complex as a vertebrate like the human.  And it only worked in INJURED worms, not elderly worms dying of old age.  So it won't stave off death entirely—or unusually prolong life—but it could lead to treatments for preventing or reducing necrosis that occurs as a result of ischemia and other injuries.

This information—and that dramatic video—could be an interesting addition to your class.  It ties in why it's important to understand concepts such as:

• ions
• amino acids
• ion flow into cells
• gap-junction ion channels
• lysosomes
• cell death and organismal death
• necrosis (and factors leading to necrosis)
• use of animals in research
• the intersection of basic science research and medical applications

Want to know more?

Anthranilate Fluorescence Marks a Calcium-Propagated Necrotic Wave That Promotes Organismal Death in C. elegans. 

• Coburn C, et al.  PLoS Biology 11(7): e1001613. 2013. doi:10.1371/journal.pbio.1001613
• The original research article.  Includes FREE images and PowerPoint slides you can use in your course.
• my-ap.us/19SRjOG

Glowing, Glowing, Gone: Cell Fluorescence Casts Light on How Death Spreads Throughout Body

• By Christopher Crockett. Scientific American online 2 August 2013
• Brief, less technical, article explaining that researchers have identified a key molecular pathway for animal death that may provide clues for better managing traumatic injury and disease in humans.
• my-ap.us/13MxJjs

Brain injury in high-def with fiber tracking

U. PITTSBURGH (US) — New imaging technology will allow doctors to clearly see for the first time neural connections broken by traumatic brain injury.

Called High Definition Fiber Tracking [1], the technology shows injuries much like X-rays show a fractured bone, according to researchers from the University of Pittsburgh [2] in a report published online in the Journal of Neurosurgery [3].

In the report [4], the researchers describe the case of a 32-year-old man who wasn’t wearing a helmet when his all-terrain vehicle crashed. Initially, his CT scans showed bleeding and swelling on the right side of the brain, which controls left-sided body movement.





High definition fiber tracking reveals loss of fibers, or connections, on the injured right side (yellow) and the intact, undamaged left side (green). The patient was injured in an ATV accident and lost function in his left leg, arm, and hand. (Credit: Walt Schneider Laboratory)


High definition fiber-tracking map of a million brain fibers. (Credit: Walt Schneider Laboratory)
Straight from the Source


A week later, while the man was still in a coma, a conventional MRI scan showed brain bruising and swelling in the same area. When he awoke three weeks later, the man couldn’t move his left leg, arm and hand.

“There are about 1.7 million cases of TBI in the country each year, and all too often conventional scans show no injury or show improvement over time even though the patient continues to struggle,” says co-senior author and neurosurgeon David O. Okonkwo, associate professor in the neurological surgery department.

“Until now, we have had no objective way of identifying how the injury damaged the patient’s brain tissue, predicting how the patient would fare, or planning rehabilitation to maximize the recovery.”

HDFT might be able to provide those answers, says co-senior author Walter Schneider, professor of psychology, who led the team that developed the technology.

Data from sophisticated MRI scanners is processed through computer algorithms to reveal the wiring of the brain in vivid detail and to pinpoint breaks in the cables, called fiber tracts. Each tract contains millions of neuronal connections.

“In our experiments, HDFT has been able to identify disruptions in neural pathways with a clarity that no other method can see,” Schneider says. “With it, we can virtually dissect 40 major fiber tracts in the brain to find damaged areas and quantify the proportion of fibers lost relative to the uninjured side of the brain or to the brains of healthy individuals. Now, we can clearly see breaks and identify which parts of the brain have lost connections.”

HDFT scans of the study patient’s brain were performed four and 10 months after he was injured; he also had another scan performed with current state-of the-art diffusion tensor imaging (DTI), an imaging modality that collects data points from 51 directions, while HDFT is based on data from 257 directions. For the latter, the injury site was compared to the healthy side of his brain, as well as to HDFT brain scans from six healthy individuals.

Only the HDFT scan identified a lesion in a motor fiber pathway of the brain that correlated with the patient’s symptoms of left-sided weakness, including mostly intact fibers in the region controlling his left leg and extensive breaks in the region controlling his left hand. The patient eventually recovered movement in his left leg and arm by six months after the accident, but still could not use his wrist and fingers effectively 10 months later.

Memory loss, language problems, personality changes and other brain changes occur with TBI, which the researchers are exploring with HDFT in other research protocols.

University of Pittsburgh neurosurgeons also have used the technology to supplement conventional imaging, noted Robert Friedlander, professor and chair in the neurological surgery department, who was not involved with the study.

“I have used HDFT scans to map my approach to removing certain tumors and vascular abnormalities that lie in areas of the brain that cannot be reached without going through normal tissue,” he says.

“It shows me where significant functional pathways are relative to the lesion, so that I can make better decisions about which fiber tracts must be avoided and what might be an acceptable sacrifice to maintain the patient’s best quality of life after surgery.”

Okonkwo notes that the patient and his family were relieved to learn that there was evidence of brain damage to explain his ongoing difficulties. The team continues to evaluate and validate HDFT’s utility as a brain imaging tool, so it is not yet routinely available.

“We have been wowed by the detailed, meaningful images we can get with this technology,” Okonkwo says. “HDFT has the potential to be a game-changer in the way we handle TBI and other brain disorders.”

The study was funded by the Defense Advanced Research Projects Agency.

More news from the University of Pittsburgh: www.news.pitt.edu/ [5]

Article reprinted by CC license from Futurity.org: http://www.futurity.org
Posted By Anita Srikameswaran-Pittsburgh On March 2, 2012 @ 12:58 pm

URL to original article: http://www.futurity.org/top-stories/brain-injury-in-high-def-with-fiber-tracking/

URLs in this post:

[1] High Definition Fiber Tracking: http://schneiderlab.lrdc.pitt.edu/projects/tbi
[2] University of Pittsburgh: http://www.upmc.com/MediaRelations/NewsReleases/2012/Pages/High-Definition-Fiber-Tracking-Traumatic-Brain-Injury.aspx
[3] Journal of Neurosurgery: http://thejns.org/doi/abs/10.3171/2012.1.JNS111282?prevSearch=%255BFulltext%253A%2BOkonkwo%255D&searchHistoryKey=
[4] Read the original study: http://thejns.org/doi/abs/10.3171/2012.1.JNS111282?prevSearch=%255BFulltext%253A%2BOkonkwo%255D&searchHistoryKey=
[5] www.news.pitt.edu/: http://www.news.pitt.edu/

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Want to know more?

• Neuroscience: Making connections 
• J. Bardin Nature News & Comment 21 March 2012
• http://my-ap.us/REpcFs

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• The Human Body in Health and Disease 5th ed. p. 246-254 my-ap.us/fNN00N 

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