Winning the fight against influenza

Annual influenza epidemics and episodic pandemics continue to cause widespread illness and mortality. The World Health Organization estimates that annual influenza epidemics cause around 3–5 million cases of severe illness and up to 650,000 deaths worldwide. Seasonal influenza vaccination still remains the best strategy to prevent infection, but the vaccines that are available now offer a very limited breadth of protection. Human broadly neutralizing antibodies (bnAbs) that bind to the hemagglutinin (HA) stem region provide hope for a universal vaccine (Figure 1a)1,2. Binding of these bnAbs prevents the pH-induced conformational changes that are required for viral fusion in the endosomal compartments of target cells in the respiratory tract and, hence, viral entry in our cells.

>Read more on the SSRL at SLAC website

Image: Complex of Influenza virus HA with (a) Fab CR6261, (b) llama single domain antibody SD36, and (c) JNJ4796.

How stained glass can help in the battle against superbugs

Ancient skills meet cutting edge technology in the battle against antibiotic resistance

Bacteria can form colonies (known as biofilms) on the surface of objects. This is a particular problem when it occurs on medical devices implanted into the body, such as catheters, prosthetic cardiac valves and intrauterine devices, as biofilms can display resistance to both antibiotics and the body’s immune response. Any incision into the body risks a surgical infection, and if a biofilm takes hold it can be difficult to eradicate. With the rise in antibiotic resistance, scientists are seeking new ways to prevent infections, and there is increasing interest in impregnate medical devices with antimicrobial substances. In work recently published in ACS Biomaterials Science & Engineering, researchers from Aston University in Birmingham, led by Dr Richard Martin, explored the antimicrobial potential of phosphate glasses doped with cobalt, and found them to be effective against Escherichia coli, Staphylococcus aureus and Candida albicans when placed in direct contact, suggesting that cobalt-doped bioactive glasses could be developed with antimicrobial properties. The technique they discovered is similar to those used to make stained glass in medieval times.

>Read more on the Diamond Light Source website
Image: Images of the copper (left) and cobalt (right) doped bioactive glasses.
Credit: Dr Richard Martin

Scientists design organic cathode for high performance batteries

The new, sulfur-based material is more energy-dense, cost-effective, and environmentally friendly than traditional cathodes in lithium batteries.

Researchers at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have designed a new, organic cathode material for lithium batteries. With sulfur at its core, the material is more energy-dense, cost-effective, and environmentally friendly than traditional cathode materials in lithium batteries. The research was published in Advanced Energy Materials on April 10, 2019.

Optimizing cathode materials

From smartphones to electric vehicles, the technologies that have become central to everyday life run on lithium batteries. And as the demand for these products continues to rise, scientists are investigating how to optimize cathode materials to improve the overall performance of lithium battery systems.
“Commercialized lithium-ion batteries are used in small electronic devices; however, to accommodate long driving ranges for electric vehicles, their energy density needs to be higher,” said Zulipiya Shadike, a research associate in Brookhaven’s Chemistry Division and the lead author of the research. “We are trying to develop new battery systems with a high energy density and stable performance.”

>Read more on the NSLS-II website

Image: Lead author Zulipiya Shadike (right) is pictured at NSLS-II’s XPD beamline with lead beamline scientist and co-author Sanjit Ghose (left).

The most complete study of battery failure sees the light

An international team of researchers just published in Advanced Energy Materials the widest study on what happens during battery failure, focusing on the different parts of a battery at the same time. The role of the ESRF was crucial for its success.

We have all experienced it: you have charged your mobile phone and after a short period using it, the battery goes down unusually quickly. Consumer electronics seem to lose power at uneven rates and this is due to the heterogeneity in batteries. When the phone is charging, the top layer charges first and the bottom layer charges later. The mobile phone may indicate it’s complete when the top surface level is finished charging, but the bottom will be undercharged. If you use the bottom layer as your fingerprint, the top layer will be overcharged and will have safety problems.
The truth is, batteries are composed of many different parts that behave differently. Solid polymer helps hold particles together, carbon additives provide electrical connection, and then there are the active battery particles storing and releasing the energy.
An international team of scientists from ESRF, SLAC, Virginia Tech and Purdue University wanted to understand and quantitatively define what leads to the failure of lithium-ion batteries. Until then, studies had either zoomed in on individual areas or particles in the cathode during failure or zoomed out to look at cell level behavior without offering sufficient microscopic details. Now this study provides the first global view with unprecedented amount of microscopic structural details to complement the existing studies in the battery literature.

>Read more on the ESRF website

3D X-ray view of an amber fossil

Research team unravels secrets of 50-million-year-old parasite larvae

With the intense X-ray light from DESY’s particle accelerator PETRA III, researchers have investigated an unusual find: a 50-million-year-old insect larva from the era of the Palaeogene. The results offer a unique insight into the development of the extinct insect, as the team reports in the journal Arthropod Systematics & Phylogeny.
When the biologist Hans Pohl from the Friedrich Schiller University in Jena tracked down an insect fossil trapped in amber on eBay, the joy of discovery was great: it was a special specimen, a 50-million-year-old larva of an extinct twisted-wing insect from the order of Strepsiptera. But in order to be able to investigate it in detail, he needed the help of materials researchers from the Helmholtz Centre in Geesthacht, which operates a beamline at DESY’s X-ray source PETRA III.
Strepsiptera are parasites that infest other insects, such as bees and wasps, but also silverfish. “In most of the approximately 600 known species, the females remain in their host throughout their lives,” says Pohl. “Only the males leave it for the wedding flight, but then live only a few hours.” But there are exceptions: In species that infest silverfish, the wingless females also leave their host.

>Read more on the PETRA III at DESY website

Image: The fossil in amber. Its age lies between 42 to 54 million years. This fossil was scientifically examined at the Institute for Zoology and Evolutionary Research at the University of Jena.
Credit: FSU, Hans Pohl 

A novel synchrotron technique for studying diffusion in solids

Bragg coherent diffraction imaging (BCDI) offers insights for nanoparticle synthesis

Understanding and controlling how the diffusion process works at the atomic scale is an important question in the synthesis of materialsFor nanoparticles, the stability, size, structure, composition, and atomic ordering are all dependent on position inside the particle, and diffusion both affects all of these properties and is affected by them. A more thorough understanding of the mechanisms and effects of diffusion in nanocrystals will help to develop controlled synthesis methods to obtain the particular properties; however, conventional methods for studying diffusion in solids all have limitations.
Given the need for imaging techniques that are sensitive to slower dynamics and allow the diffusion behaviour in individual nanocrystals to be investigated at the atomic scale and in three dimensions (3D), a team of researchers used the strain sensitivity of Bragg coherent diffraction imaging (BCDI) to study the diffusion of iron into individual gold nanocrystals in situ at elevated temperatures. Their work was recently published in the New Journal of Physics.

Image, third of three figures: Reconstructed amplitude and phase images near the centre of the nanocrystals before and after iron deposition (1 pixel = 16.28 nm). The direction of the Q-vector, which is along the (11-1) direction, is shown by the arrow in the control phase images. See all here.

Analyzing the structural disorder of nanocrystals

Research applies unprecedented technique in Brazil for the investigation of crystalline nanoparticles

The development of faster and more efficient electronic devices, better catalysts for the chemical industry, alternative energy sources, and so many other technologies depends increasingly on the in-depth understanding of the behavior of materials at the nanometer scale.
The properties of particles on this scale may be completely different from the properties of the same material in its macroscopic version. In addition, nanoparticles of different sizes and shapes can have completely different characteristics, even though they are formed by the same material.
The possibility of regulating the optical and electrical properties of nanoparticles by controlling their composition, shapes and sizes opens the door to an immense variety of applications. In this context, nanocrystals – nanometric particles that have a crystalline structure – have attracted great interest.
A crystal is a type of solid whose atoms or molecules are arranged in a well-defined three-dimensional pattern that repeats itself in space on a regular basis. The optical and electrical properties of crystalline materials depend not only on the atoms or molecules that constitute them but also on the way they are distributed. Therefore, defects or impurities present during crystal formation cause a disorder in the crystal structure. The consequent modification in the electronic structure of the crystal can lead to changes in its properties.

>Read more on the Brazilian Light Source Laboratory website
Image: PDF analysis obtained from electron diffraction data for nanocrystals before (ZrNC-Benz) and after ligand exchange (ZrNC-OLA).
Credit: Reprinted with permission from J. Phys. Chem. Lett. 2019, 10, 7, 1471-1476. Copyright 2019 American Chemical Society.

In a first, researchers identify reddish coloring in an ancient fossil mouse

X-rays reveal an extinct mouse was dressed in brown to reddish fur on its back and sides and had a tiny white tummy.

Researchers have for the first time detected chemical traces of red pigment in an ancient fossil – an exceptionally well-preserved mouse, not unlike today’s field mice, that roamed the fields of what is now the German village of Willershausen around 3 million years ago.
The study revealed that the extinct creature, affectionately nicknamed “mighty mouse” by the authors, was dressed in brown to reddish fur on its back and sides and had a tiny white tummy. The results were published today inNature Communications.
The international collaboration, led by researchers at the University of Manchester in the U.K., used X-ray spectroscopy and multiple imaging techniques to detect the delicate chemical signature of pigments in this long-extinct mouse.

>Read more on the SSRL at SLAC Lab website

Image: In this image showing the fossil chemistry of an ancient mouse, blue represents calcium in the bones, green is the element zinc which has been shown to be important in the biochemistry of red pigment and red is a particular type of organic sulfur. This type of sulfur is enriched in red pigment. When combined, regions rich in both zinc and sulfur appear yellow on this image, showing that the fur on this animal was rich in the chemical compounds that are most probably derived from the original red pigments produced by the mouse. (10.1038/s41467-019-10087-2)

Nanoscale sculpturing leads to unusual packing of nanocubes

Cube-shaped nanoparticles with thick shells of DNA assemble into a never-before-seen 3-D “zigzag” pattern that breaks orientational symmetry; understanding such nanoscale behavior is key to engineering new materials with desired organizations and properties.

From the ancient pyramids to modern buildings, various three-dimensional (3-D) structures have been formed by packing shaped objects together. At the macroscale, the shape of objects is fixed and thus dictates how they can be arranged. For example, bricks attached by mortar retain their elongated rectangular shape. But at the nanoscale, the shape of objects can be modified to some extent when they are coated with organic molecules, such as polymers, surfactants (surface-active agents), and DNA. These molecules essentially create a “soft” shell around otherwise “hard,” or rigid, nano-objects. When the nano-objects pack together, their original shape may not be entirely preserved because the shell is flexible—a kind of nanoscale sculpturing.

Now, a team of scientists from the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and Columbia Engineering has shown that cube-shaped nanoparticles, or nanocubes, coated with single-stranded DNA chains assemble into an unusual “zigzag” arrangement that has never been observed before at the nanoscale or macroscale. Their discovery is reported in the May 17 online issue of Science Advances.

>Read more on the NSLS-II website

Image: Brookhaven Lab scientists Fang Lu (sitting), (left to right, standing) Oleg Gang, Kevin Yager, and Yugang Zhang in an electron microscopy lab at the Center for Functional Nanomaterials. The scientists used electron microscopes to visualize the structure of nanocubes coated with DNA.

The interaction between two proteins involved in skin mechanical strength

A research team from the Centro de Investigación del Cáncer of the Universidad de Salamanca has obtained a detailed 3D image of the union between two hemidesmosomal proteins.

The structure of this complex has been unveiled using XALOC beamline techniques, at the ALBA Synchrotron. The results, published in “Structure”, provide insights to understand how these epithelial adhesion structures are formed. Researchers from Centro de Investigación del Cáncer – Instituto de Biología Molecular y Celular del Cáncer of Salamanca, from Centro Universitario de la Defensa in Zaragoza, and from the Netherlands Cancer Institute in Amsterdam have described how two essential proteins interact to each other in order to join epidermis and dermis together. This study reveals at atomic scale how the binding between two hemidesmosomal proteins called integrin α6β4 and BP230 takes place.
Epithelial tissues, such as epidermis, settle on fibrous sheets called basement membrane, formed by extracellular matrix proteins. The junction between epithelia and basement membrane happens through hemidesmosomes, multi-protein complexes located at the membrane of epithelial cells. Integrin α6β4 is an essential protein of the hemidesmosomes, which adheres to proteins of the basement membrane. Inside the cell cytoplasm, plectin and BP230 proteins bind to α6β4 and connect it to the intermediate filaments of the cytoskeleton. Genetic or autoimmune alterations that affect the hemidesmosomal proteins reduce skin resistance and cause diseases such as bullous pemphigoid and various types of epidermolysis bullosa.

>Read more on the ALBA website

Image: Structure of β4(WT)-BP230 complex.

‘A day in the light’ Videos highlight how scientists use light in experiment

In recognition of the International Day of Light (@IDL2019) on May 16, the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) is highlighting how scientists use light in laboratory experiments. From nanolasers and X-ray beams to artificial photosynthesis and optical electronics, Berkeley Lab researchers tap into light’s many properties to drive a range of innovative R&D.
In the three videos displayed below, you will learn how light drives the science of Berkeley Lab’s Advanced Light Source (ALS), a synchrotron that produces many forms of light beams. These light beams are customized to perform a variety of experimental techniques for dozens of simultaneous experiments conducted by researchers from across the nation and around the world.

> Read more on the Advanced Light Source at Berkley Lab website

Image: Shambhavi Pratap, ALS Doctoral Fellow in Residence and a Ph.D. student at the Technical University of Munich, discusses how she studies thin-film solar energy materials using X-rays at the ALS.
Credit: Marilyn Chung/Berkeley Lab


Record-shattering underwater sound

Researchers produced an underwater sound with an intensity that eclipses that of a rocket launch while investigating what happens when they blast tiny jets of water with X-ray laser pulses.

A team of researchers has produced a record-shattering underwater sound with an intensity that eclipses that of a rocket launch. The intensity was equivalent to directing the electrical power of an entire city onto a single square meter, resulting in sound pressures above 270 decibels. The team, which included researchers from the Department of Energy’s SLAC National Accelerator Laboratory, published their findings on April 10 in Physical Review Fluids.
Using the Linac Coherent Light Source (LCLS), SLAC’s X-ray laser, the researchers blasted tiny jets of water with short pulses of powerful X-rays. They learned that when the X-ray laser hit the jet, it vaporized the water around it and produced a shockwave. As this shockwave traveled through the jet, it created copies of itself, which formed a “shockwave train” that alternated between high and low pressures. Once the intensity of underwater sound crosses a certain threshold, the water breaks apart into small vapor-filled bubbles that immediately collapse. The pressure created by the shockwaves was just below this breaking point, suggesting it was at the limit of how loud sound can get underwater.

>Read more on the LCLS at SLAC website

Image: After blasting tiny jets of water with an X-ray laser, researchers watched left- and right-moving trains of shockwaves travel away from microbubble filled regions.
Credit: Claudiu Stan/Rutgers University Newark

Improving engine performance and fuel efficiency

A study conducted in part at the Canadian Light Source (CLS) at the University of Saskatchewan suggests reformulating lubricating oils for internal combustion engines could significantly improve not only the life of the oil but the life of the engine too.
Dr. Pranesh Aswath with the Department of Materials Science and Engineering at the University of Texas at Arlington and his research colleagues focused on the role soot plays in engine wear, and its effect on the stability of engine oil.
He described the research as “one piece of a broader story we’re trying to write” about how the reformulation of engine oils can reduce emissions, decrease wear and increase the longevity of engines.
Soot is a carbon-based material that results from incomplete combustion of fuel in an internal combustion engine, he explained. The soot ends up in crankcase oil where it is trapped by additives, but that leads to reduced engine efficiency and a breakdown of lubricating oil.

>Read more on the Canadian Light Source website

Killing two parasites with one stone

Each year Malaria affects 219 million people, causing almost half a million deaths. Crysptosporidiosis is the leading cause of diarrheal diseases in infants, leading to 200,000 deaths a year. An international team of scientists, led by researchers at the University of Dundee, have discovered a molecule which clears the parasites that cause these two illnesses. Their results are published in PNAS.

Malaria is a well-known disease caused by the parasites Plasmodium falciparum and Plamodium vivax and is the target of many available medications. However, the development of drug resistance has led the scientific community search for new therapeutic molecules which might provide for chemoprotection, prevention of transmission, and the treatment of relapsing malaria.
Like malaria, cryptosporidiosis is also a disease caused parasites, in this case Cryptosporidium hominis and Cryptosporidium parvum. Although it does not have the same ‘visibility as Malaria, Cryptosporidiosis is the leading cause worldwide of moderate-to-severe diarrheal diseases in infants and is estimated to lead to more than 200,000 deaths a year. The disease and is also associated with malnutrition, stunted growth, and cognitive-development problems in children. The currently approved drug, nitazoxanide, has poor efficacy, particularly in the case of immune-compromised patients and malnourished children, where there is no effective treatment.

>Read more on the ESRF website

Image: Binding modes of ligands bound to PfKRS1 and CpKRS. (A) PfKRS1:Lys:2 showing the binding mode of 2 (C atoms, gold) bound to the ATP site of PfKRS1 (PDB ID code 6AGT) superimposed upon PfKRS1:Lys:cladosporin (cladosporin C atoms, slate; PDB ID code 4PG3). (B) PfKRS1:5 showing binding mode of 5 bound to PfKRS1 (PDB ID code 6HCU). (See the full image: here)

17 meter long detector chamber delivered to CoSAXS

The experimental techniques used at the CoSAXS beamline will use a huge vacuum vessel with possibilities to accommodate two in-vacuum detectors in the SAXS/WAXS geometry.

A major milestone was reached for the CoSAXS project when this vessel was recently delivered, installed and tested.
The main method that will be used at the CoSAXS beamline is called Small Angle X-ray Scattering (SAXS). By detecting the scattered rays coming from the sample at shallow angles, less than 4° typically, it is possible to learn about the size, shape, and orientation of the small building blocks that make up different samples and how this structure gives these materials their properties. The materials to be studied can come from various sources and in diverse states, for example, plastics from packaging, food and how it is processed or proteins in solution which can be used as drugs.
The “co” in CoSAXS stands for coherence, a quality of the synchrotron light optimized at the MAX IV machine, that loosely could be translated as laser-likeness. In the specific case of X-ray Photon Correlation Spectroscopy (XPCS), it lets the researchers not only measure the structure of the building blocks in the sample but also their dynamics – how they change in time.

>Read more on the MAY IV Laboratory website

Research on sand near Hiroshima shows fallout debris from A-Bomb blast

X-ray studies at Berkeley Lab provide evidence for source of exotic assortment of melt debris

Mario Wannier, a career geologist with expertise in studying tiny marine life, was methodically sorting through particles in samples of beach sand from Japan’s Motoujina Peninsula when he spotted something unexpected: a number of tiny, glassy spheres and other unusual objects.
Wannier, who is now retired, had been comparing biological debris in beach sands from different areas in an effort to gauge the health of local and regional marine ecosystems. The work involved examining each sand particle in a sample under a microscope, and with a fine brush, separating particles of interest from grains of sediment into a tray for further study.

>Read more on the Advanced LIght Source at L. Berkeley Lab website

Image: Researchers collected and studied beach sands from locations near Hiroshima including Japan’s Miyajima Island, home to this torii gate, which at high tide is surrounded by water. The torii and associated Itsukushima Shinto Shrine, near the city of Hiroshima, are popular tourist attractions. The sand samples contained a unique collection of particles, including several that were studied at Berkeley Lab and UC Berkeley.
Credit: Ajay Suresh/Wikimedia Commons