Tag Archives: electron microscope

A two-color electron microscopy image of endosomal uptake of peptide proteins, a first of its kind. Credit: Cell Chemical Biology

Presenting the electron kaleidoscope: the first ever colour electron microscope

A two-color electron microscopy image of endosomal uptake of peptide proteins, a first of its kind. Credit: Cell Chemical Biology

A two-color electron microscopy image of endosomal uptake of peptide proteins, a first of its kind. Credit: Cell Chemical Biology

Electron microscopy is arguably one of the most successful inventions of the past century. As the name implies, this instrument fires beams of electrons onto a sample to create a magnified image of it, typically up to two million times. Since it was invented in the 1930s, this tools has proven invaluable for research whether it’s looking at how viruses’ infect cells or how neuron synapses fire, but there’s one major drawback: the images it produces are in grayscale. Now, using a novel technique researchers at the University of California San Diego School of Medicine and Howard Hughes Medical Institute demonstrate a new electron microscopy that can image samples in multiple colours.

A touch of colour in an otherwise bleak nano world

You, me, and just about anything with eyes sees things because light particles known as photons bounce off objects and hit the retina. But some things — most of them — are smaller than an individual photon. Once you dive well into the nano world, photons become clumsy and useless for imaging purposes. So, naturally, scientists resorted to image tiny objects with the smallest particle they could easily use: the electron. Think of imaging objects like carving furniture. Naturally, you want your cutting tool to be smaller than the bulk material you want to sculpt.

The working principle of an electron microscope is fairly simple. Firstly, a beam of electrons is fired onto a sample that is prepared beforehand, typically by treating it with lead because it loves electrons so much. Everything takes place inside a vacuum chamber because electrons don’t travel optimally through the air. Instead of an optical lens you’d use in a microscope, an electron microscope (EM) employs coil-shaped electromagnets through which the electron beam travels. Just like a glass lens bends or refracts light to magnify objects sitting behind it, the EM’s coils bend the electron beams in much the same way.

The resulting EM image reveals shapes, textures or contours with incredible resolution — but no colour. This can be a problem when there are multiple features belonging to individual objects. A trained eye can get away with it, of course, and colours can be added later by hand, sort of like photoshop. But scientists’ lives could be made a whole lot easier if there was a way to produce coloured EM images from the beginning.

A snowflake as seen by an EM.

A snowflake as seen by an EM.

That’s where Mark H. Ellisman, PhD, professor in the Department of Neurosciences and director of the National Center for Microscopy and Imaging Research, and his team came in. Among the co-authors of the new paper was also Roger Tsien, PhD, professor of pharmacology, chemistry and biochemistry. Tsien won the Nobel Prize in chemistry in 2008 and, sadly, passed away this year on August 24. Now, Tsien’s legacy lives on not only through the green fluorescent proteins he conceived but also through the first ever multicolor EM.

This new technique starts off like any usual EM imaging. The sample, say a cell or protein, is treated with lead then loaded with electrons to create a grayscale image — this is the base layer. Next, the specimen is treated again, this time with rare earth minerals called lanthanides. This class of metals are very picky and only stick to certain molecule types, meaning these are the only things the microscope can see. It’s then only a matter of processing the resulting image, assigning it a colour like green, then stacking the image over the grayscale based layer. You can add multiple stacks this way and come up with variously coloured images.

“The ability to discern multiple specific molecules simultaneously adds a new dimension. It reveals details, actions and processes that aren’t necessarily visible—or even suspected—in a more monochromatic view,” Ellisman said.

“A transmission electron microscope can distinguish each of these metals by electron energy-loss to give elemental maps of each that can be overlaid in color on the familiar monochrome electron micrograph,” said first author and project scientist Stephen R. Adams.  “Each color highlights a different component of the cellular ultrastructure.”

Right now, the researchers were only able to stack two or three colours atop the base layer, as reported in the journal Cell Chemical Biology. The challenge lies in treating samples with earth metals in sequence without contaminating them. Nevertheless, today was a very good for science!

“This new method gives a more complete and easily detectable readout of the cellular components as colors,” said Adams. “In theory, we should be able to add many more colors if we can develop more ways of precipitating additional lanthanides. The method is quite simple to do, uses easily made chemicals and requires detectors that are already present on many transmission electron microscopes so it is potentially readily transferable to other laboratories. Further research is needed to improve the chemistry and sensitivity of the method, but this work will hopefully inspire other groups to devise similar methods in this field.”

This vinyl playing under an electron microscope is mesmerizing

Vinyl just sounds better, doesn’t it? It’s as if all the scratches and tiny imperfections in the recording work to make the sound perfect.

But how exactly does it work? How do you get sound from a piece of grooved plastic? Well, let’s start with this image tweeted by Vinyl Loop.

That huge spike you see in the picture is the player’s needle, magnified 1000 times. The groves are analog representations of sound vibrations, etched into the record. As the table turns, the needle follows the grove and moves on two axis — up and down, left and right.

The needle’s arm is attatched either to a piezoelectrical crystal or a series of small magnets placed near a coil. The arm moves the two magnets relative to the coil, generating small electrical currents which are picked up, amplified, and turned into sound — Andrei covered this in more detail here. The scratch sounds you sometimes hear on a vynil are either particles of dust cought in the grove — that needle up there is only about 1-2 mm thick — or actual scratches on the grove.

And now, through the wonder of modern technology, you can see how vynil stores sound in this video Applied Science put together of a record under the electron microscope. It’s a really nice video, but skip to ~4:25 if you’re only interested in seeing the groovy action. Enjoy!

 

Sturdy virus might help us treat infectious diseases

Scientists are studying a virus that survives in extremely hot environments, in the hope that it will give us better ways of fighting infectious diseases. SIRV2 might be the key to defeating future epidemics.

Edward H. Egelman with the massive Titan Krios microscope that’s buried in tons of concrete under Fontaine Research Park. Image via University of Virginia.

Extremophiles have fascinated biologists for many years. There are organisms that can survive in extremely acidic or basic environments, organisms that don’t require oxygen for growth, and of course, organisms that survive in extreme temperatures. The nonenveloped, rod-shaped virus SIRV2 (Sulfolobus islandicus) can survive very high temperatures, and the biotechnology industry has been studying it for quite a while. One application is the creation of artificial derivatives from proteins, named affitins, and now, another point of interest is discovering a way to prevent infectious agents from overcoming the body’s protective systems.

“What’s fascinating and bizarre is with the power to see how proteins and DNA may be put collectively in a way that’s utterly safe beneath the harshest circumstances conceivable,” said Edward H. Egelman, PhD, of the UVA Department of Biochemistry and Molecular Genetics. “We’ve discovered what appears to be a main mechanism of resistance – to heat, to desiccation, to ultraviolet radiation. And understanding that, then, we’ll go in many different directions, along with creating strategies to package deal deal DNA for gene treatment.”

SIRV2 lives in acidic scorching springs, where temperatures often range past 175 Fahrenheit (80 Celsius), and understanding how it survives in such an extreme environment can help us better understand how infectious agents can resist our bodies’ protective systems – and how we can stop that from happening.

“Some of these spores are liable for very, very horrific sicknesses which is perhaps arduous to cope with, like anthrax. So we current on this paper that this virus really options in a similar technique to a variety of the proteins present in bacterial spores,” he said. Spores are moreover formed by C. difficile, which now accounts for about 30,000 deaths per yr inside the U.S. and has been categorized by the Centers for Disease Control and Prevention as having a menace diploma of “urgent.” “Understanding how these bacterial spores work supplies us in all probability new skills to destroy them,” Egelman said. “Having this main scientific evaluation leads in a lot of, many directions, most of which might be unimaginable to predict, with regards to what the implications are going to be.”

It appears that for SIRV2, the key to survival lies in its DNA.

“This is, I really feel, going to highlight as quickly as as soon as extra the contributions she made, because of many people have felt that this A-form of DNA is just found inside the laboratory beneath very non-biological circumstances, when DNA is dehydrated or dry,” Egelman said. “Instead, it appears to be a standard mechanism in biology for shielding DNA.”

Researchers were able to study the virus using UVA’s new Titan Krios underground electron microscope. The Titan Krios is the most powerful and flexible high resolution electron microscope for 2D and 3D characterization of biological samples.

Journal Reference: Frank DiMaio, Xiong Yu2, Elena Rensen, Mart Krupovic, David Prangishvili, Edward H. Egelman. A virus that infects a hyperthermophile encapsidates A-form DNA. DOI: 10.1126/science.aaa4181

The team's small prototype neutron microscope is shown set up for initial testing at MIT's Nuclear Reactor Laboratory. The microscope mirrors are inside the small metal box at top right.

MIT readies neutron microscope – new kind of imaging

A cylindrical mirror of the type the MIT and NASA researchers have developed for a novel type of neutron microscope is shown on a test stage in the lab, with light reflected through it to test the precision polishing of its shape.  (c) NASA

A cylindrical mirror of the type the MIT and NASA researchers have developed for a novel type of neutron microscope is shown on a test stage in the lab, with light reflected through it to test the precision polishing of its shape. (c) NASA

A joint project between scientists at NASA and MIT is focusing on creating a new kind of microscope that uses neutrons instead of beams of light or electrons to create high-resolution images. Since the subatomic particles are electrically neutral, such a microscope would allow scientists to peer through places otherwise inaccessible today, like inside metals even if these are in motion.  Also, neutron instruments are also uniquely sensitive to magnetic properties and to lighter elements that are important in biological materials.

The concept of a neutron microscope isn’t entirely new, however other neutron instruments developed so far can be considered primitive to say the least.  These are crude imaging systems that simply let light through a tiny opening, resulting in low-resolution images.

The team of researchers at MIT want to build something that rivals in quality current atomic force microscopes or electron microscopes. With this in mind, MIT postdoc Dazhi Liu, research scientist Boris Khaykovich, professor David Moncton, and four others are currently exploring an innovative idea that’s been on the table for more than 60 years.

“For neutrons, there have been no high-quality focusing devices,” Moncton says. “Essentially all of the neutron instruments developed over a half-century are effectively pinhole cameras.” But with this new advance, he says, “We are turning the field of neutron imaging from the era of pinhole cameras to an era of genuine optics.”

“The new mirror device acts like the image-forming lens of an optical microscope,” Liu adds.

The team's small prototype neutron microscope is shown set up for initial testing at MIT's Nuclear Reactor Laboratory. The microscope mirrors are inside the small metal box at top right.

The team’s small prototype neutron microscope is shown set up for initial testing at MIT’s Nuclear Reactor Laboratory. The microscope mirrors are inside the small metal box at top right.

The main challenge in developing a neutron optical device is that the particles minimally interact with matter, which makes it practically impossible to focus a beam of neutrons in the same way you would light or electrons. A basic means of manipulating neutron beams was expressed in the mid 1950s, even though the original idea was used for X-rays, involving concentric mirrors. Neutron beams interact weakly, much like X-rays, and can be focused by a similar optical system.

A neutron microscope

The instrument currently in development by the researchers uses several reflective cylinders nested one inside the other, so as to increase the surface area available for reflection. The resulting device could improve the performance of existing neutron imaging systems by a factor of about 50, the researchers say — allowing for much sharper images, much smaller instruments, or both.

So far, the team have digitized their concept, and have even created a small-version of the instrument as a proof of concept and demonstrated its performance using a neutron beam facility at MIT’s Nuclear Reactor Laboratory. Such a new instrument could be used to observe and characterize many kinds of materials and biological samples; other nonimaging methods that exploit the scattering of neutrons might benefit as well. Because the neutron beams are relatively low-energy, they are “a much more sensitive scattering probe,” Moncton says, for phenomena such as “how atoms or magnetic moments move in a material.”

 

Roger Pynn, a materials scientist at the University of California at Santa Barbara who was not involved in this research, says, “I expect it to lead to a number of breakthroughs in neutron imaging. … It offers the potential for some really new applications of neutron scattering — something that we haven’t seen for quite a while.”

The concept was outlined in a paper published in the journal Nature Communications.

Graphene, probably the most fascinating material discovered thus far, is capable of self-repair, as carbon atoms naturally attach themselves to free spots in the lattice, new study finds.

Graphene sheets can repair themselves naturally

Graphene is one of the most phenomenal materials discovered in science. It’s so thin, it can be molded into sheets just 1 atom thick, yet despite this, it’s so strong that you can actually pick it up. It has the highest current density (a million times that of copper) at room temperature, the highest intrinsic mobility (100 times more than in silicon), and conducts electricity in the limit of no electrons. Also, graphene now holds the record for conducting heat — it’s better than any other known material. But wait, there’s more – graphene is the most impermeable material ever discovered – so neatly packed together, that not even helium atoms can squeeze through.

Graphene, probably the most fascinating material discovered thus far, is capable of self-repair, as carbon atoms naturally attach themselves to free spots in the lattice, new study finds.

Graphene, probably the most fascinating material discovered thus far, is capable of self-repair, as carbon atoms naturally attach themselves to free spots in the lattice, new study finds.

Are you impressed yet? Well, add self-repair to the list. Yes, a team of researchers at University of Manchester, UK, including Konstantin Novoselov the co-discoverer of graphene and Nobel Prize laureate, have found that this amazing material can actually perfectly fill gaps within its sheets simply by bombarding it with pure carbon. I think I’m in love!

The researchers initially set out to study the effects of adding metal contacts to strips of graphene, the only way to exploit its phenomenal electronic properties. This typically leads to forming holes in the graphene sheet, a curious fact which scientists set out to study more in depth. After firing electron beams through graphene sheets and studying the damage with an electron microscope, the researchers were surprised to find that the carbon atoms in the metal molecules snapped to the graphene sheet.

When damaged sheets were bombarded with pure carbon atoms, not only did the carbon wash away any metal molecules from the surface of the graphene, but they also perfectly aligned in the gaps, forming an uninterrupted lattice of hexagons – the shape of graphene.

“If you can drill a hole and control that ‘carbon reservoir’, and let them in in small amounts, you could think about tailoring edges of graphene or repairing holes that have been created inadvertently,” Dr Ramasse said.

“We know how to connect small strips of graphene, to drill it, to tailor it, to sculpt it, and it now seems we might be able to grow it back in a reasonably controlled way.”

The findings were reported in the journal Mesoscale and Nanoscale Physics.

Oval shaped gold particles are 5nm diameter with lines, layers of atoms, across them.

Electron microscope based on revolutionary technique set to provide highest resolution images ever

Since they were first introduced more than 70 years ago, electron microscopes have aided researchers from a diverse array of fields of science reach some of the world’s greatest scientific breakthroughs – most often they’ve been considered indispensable. They’ve well reached their limits, however, and University of Sheffield researchers sought to find an alternate route for sub-atomic imaging.

Oval shaped gold particles are 5nm diameter with lines, layers of atoms, across them.

Oval shaped gold particles are 5nm diameter with lines, layers of atoms, across them. (c) University of Sheffield

After three years of hard work, the scientists reached a breakthrough, after they developed a new method, called electron ptychography, which they claim will lead to highest resolution images in the world. The findings were published in the journal Nature Communications.

The scientists scrapped the electrostatic and electromagnetic lenses used by the conventional electron microscope, and instead chose to reconstruct scattered electron-waves after passing through the sample using computers. The new technique allowed for a five-fold increase in resolution over the electron lens. The researchers are confident enough to claim their breakthrough will transform sub-atomic scale transmission imaging.

Project leader Professor John Rodenburg, of the University of Sheffield´s Department of Electronic and Electrical Engineering, explains how the electron ptychography microscope works.

“We measure diffraction patterns rather than images. What we record is equivalent to the strength of the electron, X-ray or light waves which have been scattered by the object – this is called their intensity. However, to make an image, we need to know when the peaks and troughs of the waves arrive at the detector – this is called their phase.

“The key breakthrough has been to develop a way to calculate the phase of the waves from their intensity alone. Once we have this, we can work out backwards what the waves were scattered from: that is, we can form an aberration-free image of the object, which is much better than can be achieved with a normal lens.

“A typical electron or X-ray microscope image is about one hundred times more blurred than the theoretical limit defined by the wavelength. In this project, the eventual aim is to get the best-ever pictures of individual atoms in any structure seen within a three-dimensional object.”

Besides the obvious high resolution capabilities, when coupled with visible light the new microscope allows scientists to image living cells very clearly without the need to stain them, a process which usually kills the cells. Also, the living organisms can be imaged directly through their culture containers, like petri dishes or flasks, and thus offer the opportunity to study them as they develop without disturbing.

source – Sheffield University