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The Deep Dive: The Man Who Grew Eyes

by Moheb Costandi, Mosaic Science

The train line from mainland Kobe is a marvel of urban transportation. Opened in 1981, Japan’s first driverless, fully automated train pulls out of Sannomiya station, guided smoothly along elevated tracks that stand precariously over the bustling city streets below, across the bay to the Port Island.

The island, and much of the city, was razed to the ground in the Great Hanshin Earthquake of 1995 – which killed more than 5,000 people and destroyed more than 100,000 of Kobe’s buildings – and built anew in subsequent years. As the train proceeds, the landscape fills with skyscrapers. The Rokkō mountains come into view, looming menacingly over the city, peppered with smoke billowing from the dozens of narrow chimneys of the electronics, steel and shipbuilding factories.

Today, as well as housing the Port of Kobe, the man-made island contains hotels, medical centres, universities, a large convention centre and an Ikea store. There are also three government-funded RIKEN research institutions: the Advanced Institute of Computational Science (which is home to what was, until 2011, the world’s fastest supercomputer), the Center for Life Science Technologies, and the Centre for Developmental Biology (CDB).

At the entrance to one of the labs, a faded poster in a thin plastic frame shows the crew of the Starship Enterprise, a young Captain Kirk sitting proudly at the helm. Underneath is the famous Star Trek slogan: “To boldly go where no man has gone before.”

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These gifs depict the moment a mineral forms. Researchers at the Pacific Northwest National Laboratory trained a powerful microscope on the birth of calcium carbonate crystals, a process called nucleation.

To see the unpredictable moment when the seed of a crystal starts rapidly growing, they mixed high concentrations of sodium bicarbonate and calcium chloride in water. They then focused a transmission electron microscope that produces images in real time on the solution.

"This is the first time we have directly visualized the formation process," said materials scientist James De Yoreo. "We observed many pathways happening simultaneously. And they happened randomly. We were never able to predict what was going to come up next."

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Urban Forests Eat Ozone Pollution Economically

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by Michael Keller

It depends how high off the ground ozone floats to determine whether it is your friend or your enemy.

When it is adrift high up in the stratosphere above the weather systems, the molecule that is composed of three bonded oxygen atoms (O3) absorbs ultraviolet light. This colorless gas umbrella shields life below it from fatal doses of the radiation that would otherwise leave the planet’s surface barren. Ozone is a highly active substance, and compounds like human-made chlorofluorocarbons readily break it down. These have helped to thin large areas of the ozone layer. But in a rare bit of good environmental news, decades of efforts to let the thinning repair itself seem to be succeeding. 

Ozone also exists near the ground, the result of sunlight hitting airborne emissions from vehicles, power plants and industrial activity. This low-level ozone is the main component of smog and can harm animal and plant tissues. According to the Environmental Protection Agency, the amount of ozone near the ground, the bad stuff, decreased by 25 percent across the U.S. between 1980 and 2012. Looking at the most recent period, the improving trend decreased to a more modest 9 percent reduction in ozone concentration nationally between 2000 and 2012. Much of this reduction can be attributed to better technologies and controls that have scrubbed ozone precursors from emissions.

National averages, though, can gloss over deleterious ozone spikes in places like Houston and L.A., two of America’s most well known smoggy cities, as well as in rural locales. In fact, NASA researchers say ozone concentrations are rising globally with increasing industrial output, heavier land use and wealthier societies in countries like China, India and Brazil. Elevated ozone levels are estimated to increase global mortality by 152,000 people per year.

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Human Disease Seen In New Light With Powerful Microscope
by Michael Keller
It’s always magical to see the darkened countryside and incandescent cities silently zooming beneath the International Space Station. It really puts things in perspective to gaze at pictures like the ones above… Oh, wait. Are these actually images of jutting peninsulas and great bridges spanning bays?
No, but the technical feat that these pictures represent are just as impressive. These are close-ups of the outer covering of cells—their plasma membranes and the sugar molecules that stud the surface. 
These incredibly clear images of tiny biological structures were made by a team led by biophysicist Markus Sauer and chemist Jürgen Seibel of Germany’s University of Würzburg. To make them, the group used a method called dSTORM, or direct Stochastic Optical Reconstruction Microscopy. 
They say dSTORM is a new microscopy method that allows visualizing objects in super resolution, which reveals details 10 times better than have ever been attained before. This approach, which can resolve objects just millionths of millimeters across, will give researchers new insights into the functioning of infectious disease and cancer in human cells.[[MORE]]
To make it work, the scientists fed human cells sugars that had been engineered with fluorescent dyes that emit light in specific wavelengths. The cells metabolize the sugars and dyes, incorporating them into their structure. They also say that tumors, bacteria and viruses can exploit these sensors to invade the cell.
Their work was published in August in the journal Angewandte Chemie.
But the special dyes that they use aren’t important for the fact that they shine—many fluorescent molecules do that. Instead, they made their dyes so that they could be selectively turned off. “dSTORM microscopy uses commercial fluorescent dyes which, when exposed to light of a suitable wavelength in the presence of thiols, transition to a reduced and very stable optical ‘off’ state,” said Sauer in a statement.
Once thiols are administered, most of the dye molecules stop emitting light. The exact positions of the few that continue to shine can then be calculated. The researchers do the same process over and over again, and finally stitch together multiple images to create one very sharp one that reveals significant details about the cell.
They have now counted up the number of sugars studding the surface, finding that the average human cell is coated with 5 million of the molecules. Understanding these surface structures better is extremely important because they are some of the sensors that let the cell interact with the outside world and communicate with each other. 

[How dSTORM works in an example that imaged cellular microtubules. “Temporal separation of single emitters localized precisely by data modelling enables image reconstruction with superior resolution,” Sauer’s team wrote on their website.]

[dSTORM images of cellular nanostructures. Left: Super-resolution imaging of the cytoskeleton; microtubules (green), f-actin (magenta). Right: Super-resolution imaging of the nuclear pores in X. laevis A6 cells. Courtesy Sauer, Seibel, et al.]
Top Image: The dSTORM image shows the glycocalyx of the plasma membrane of cells with the homogeneous distribution of saccharified proteins and lipids. Visualization and quantification of the sugars on the cell surface is of particular interest in the research into infectious diseases and cancer. Courtesy Markus Sauer.

Human Disease Seen In New Light With Powerful Microscope

by Michael Keller

It’s always magical to see the darkened countryside and incandescent cities silently zooming beneath the International Space Station. It really puts things in perspective to gaze at pictures like the ones above… Oh, wait. Are these actually images of jutting peninsulas and great bridges spanning bays?

No, but the technical feat that these pictures represent are just as impressive. These are close-ups of the outer covering of cells—their plasma membranes and the sugar molecules that stud the surface. 

These incredibly clear images of tiny biological structures were made by a team led by biophysicist Markus Sauer and chemist Jürgen Seibel of Germany’s University of Würzburg. To make them, the group used a method called dSTORM, or direct Stochastic Optical Reconstruction Microscopy. 

They say dSTORM is a new microscopy method that allows visualizing objects in super resolution, which reveals details 10 times better than have ever been attained before. This approach, which can resolve objects just millionths of millimeters across, will give researchers new insights into the functioning of infectious disease and cancer in human cells.

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