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 

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.

New approach for solving protein structures from tiny crystals

Technique opens door for studies of countless hard-to-crystallize proteins involved in health and disease

Using x-rays to reveal the atomic-scale 3-D structures of proteins has led to countless advances in understanding how these molecules work in bacteria, viruses, plants, and humans—and has guided the development of precision drugs to combat diseases such as cancer and AIDS. But many proteins can’t be grown into crystals large enough for their atomic arrangements to be deciphered. To tackle this challenge, scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and colleagues at Columbia University have developed a new approach for solving protein structures from tiny crystals.

The method relies on unique sample-handling, signal-extraction, and data-assembly approaches, and a beamline capable of focusing intense x-rays at Brookhaven’s National Synchrotron Light Source II (NSLS-II)—a DOE Office of Science user facility—to a millionth-of-a-meter spot, about one-fiftieth the width of a human hair.

>Read more on the NSLS-II at Brookhaven Lab website

Image: Wuxian Shi, Martin Fuchs, Sean McSweeney, Babak Andi, and Qun Liu at the FMX beamline at Brookhaven Lab’s National Synchrotron Light Source II, which was used to determine a protein structure from thousands of tiny crystals.

Coelacanth reveals new insights into skull evolution

A team of researchers, in conjunction with the National Museum of Natural History in Paris, presents the first observations of the development of the skull and brain in the living coelacanth Latimeria chalumnae.

The study, published in Nature, uses data from beamline ID19 and provides new insights into the biology of this iconic animal and the evolution of the vertebrate skull.
The coelacanth Latimeria is a marine fish closely related to tetrapods, four-limbed vertebrates including amphibians, mammals and reptiles. Coelacanths were thought to have been extinct for 70 million years, until the accidental capture of a living specimen by a South African fisherman in 1938. Eighty years after its discovery, Latimeria remains of scientific interest for understanding the origin of tetrapods and the evolution of their closest fossil relatives – the lobe-finned fishes.

>Read more on the European Synchrotron website

Image: Overall anterolateral view of the skull of the coelacanth foetus imaged on beamline ID19. The brain is in yellow.
Credit: H. Dutel et al.

Low background noise crucial for single particle imaging experiments

Model experiment brings scientists a step closer to SPI at European XFEL

Taking snapshots of single molecules with X-rays has long been a dream for many scientists. Such experiments have successfully been computationally modelled, but have never been practically demonstrated before.
In a model experiment carried out at the European Synchrotron Radiation Facility (ESRF), European XFEL scientists, together with international collaborators, have now come one step closer to successfully carrying out so-called single particle imaging experiments (SPI) at X-ray laser facilities such as European XFEL. In a paper published today in the journal from the International Union of Crystallography (IUCrJ), scientists demonstrate experimentally that, in principle, a 3D structure can indeed be obtained from many tens of thousands of very weak images, using X-rays with similar properties as produced at X-ray free-electron lasers such as European XFEL.

>Read more on the European XFEL website

Image: Reconstruction of the 3D electron density. (a) Reconstruction from the result derived by EMC. The electron density projected along an axis perpendicular to the drawing plane is shown here. (b) Reconstruction from the reference Fourier volume. Again, the projected electron density is shown. (c) 3D iso-surface rendering of the reconstructed electron density shown in panel (a). The threshold of the iso-surface has been set to 0.2, given a normalized density with values between 0 and 1. (d) Scanning electron micrograph from the original sample.
Image source

First ever images of fuel debris fallout particles from Fukushima

Unique synchrotron visualisation techniques offer new forensic insights into the provenance of radioactive material from the Fukushima nuclear accident to understand the sequence of events related to the accident.

In April 2017, a joint team comprising the University of Bristol, the Japan Atomic Energy Agency (JAEA) and Diamond, the UK’s national synchrotronlight source, undertook the first experiment of its kind to be performed at Diamond.  A small radioactive particle (450μm x 280μm x 250 μm) from the Fukushima Daiichi nuclear accident in 2011 underwent a comprehensive and independent analysis of its internal structure and 3D elemental distribution, to establish the source of the material and the potential environmental risks associated with it.  

>Read more on the Diamond Light Source website

Image: Fukushima Particles research group (L-R): Cristoph Rau (I13), Yukihiko Satou, (researcher from the Collaborative Laboratories for Advanced Decommissioning Science, Japan Atomic Energy Agency), with Tom Scott and Peter Martin (University of Bristol).

Secrets of the deadly white-tail virus revealed

The inner workings of a lethal giant freshwater prawn virus have been revealed by an international team of researchers using data gathered at Diamond Light Source. The results reveal a possible new class of virus and presents the prospect of tackling a disease that can devastate prawn farms around the world.

The detailed structure of a virus that can devastate valuable freshwater prawn fisheries has been revealed by an international team using image data collected in the Electron Bio-Imaging Centre (eBIC) based at Diamond Light Source. The researchers produced high-resolution images of virus like particles, VLP’s, composed of virus shell proteins which they compared with lower resolution images of the complete virus purified from prawn larvae. They found strong similarities between the two suggesting that the more detailed VLP images are a good representation of the intact virus. This research, exposing the inner workings of the MrNV, could make it easier to develop ways of combating the economically important disease, but also suggests that it belongs in a new, separate, group of nodaviruses.
The researchers used the rapidly developing technique of cryo-electron microscopy, cryoEM, which has the ability to produce very high-resolution images of frozen virus particles. Images so detailed that the positions of individual atoms could be inferred. Recent breakthroughs in this technique have transformed the study of relatively large biological complexes like viruses allowing researchers to determine their structures comparatively quickly. The data to produce the MrNV structure described here was captured in two days at the eBIC facility.

>Read more on the Diamond Light Source website

Image: 3D model of the MrNV
Credit: Dr David Bhella

Scientists produce 3-D chemical maps of single bacteria

Researchers at NSLS-II used ultrabright x-rays to generate 3-D nanoscale maps of a single bacteria’s chemical composition with unparalleled spatial resolution.

Scientists at the National Synchrotron Light Source II (NSLS-II)—a U.S. Department of Energy (DOE) Office of Science User Facility at DOE’s Brookhaven National Laboratory—have used ultrabright x-rays to image single bacteria with higher spatial resolution than ever before. Their work, published in Scientific Reports, demonstrates an x-ray imaging technique, called x-ray fluorescence microscopy (XRF), as an effective approach to produce 3-D images of small biological samples.

“For the very first time, we used nanoscale XRF to image bacteria down to the resolution of a cell membrane,” said Lisa Miller, a scientist at NSLS-II and a co-author of the paper. “Imaging cells at the level of the membrane is critical for understanding the cell’s role in various diseases and developing advanced medical treatments.”
The record-breaking resolution of the x-ray images was made possible by the advanced capabilities of the Hard X-ray Nanoprobe (HXN) beamline, an experimental station at NSLS-II with novel nanofocusing optics and exceptional stability.
“HXN is the first XRF beamline to generate a 3-D image with this kind of resolution,” Miller said.

>Read more on the NSLS-II at Brookhaven National Laboratory website

Image: NSLS-II scientist Tiffany Victor is shown at the Hard X-ray Nanoprobe, where her team produced 3-D chemical maps of single bacteria with nanoscale resolution.

New approach to breast cancer detection

Phase contrast tomography shows great promise in early stages of study and is expected to be tested on first patients by 2020.

An expert group of imaging scientists in Sydney and Melbourne are using the Imaging and Medical Beamline (IMBL) at the Australian Synchrotron as part of ongoing research on an innovative 3D imaging technique to improve the detection and diagnosis of breast cancer.

The technique, known as in-line phase-contrast computed tomography (PCT), has shown advantages over 2D mammography with conventional X-rays by producing superior quality images of dense breast tissue with similar or below radiation dose.
Research led by Prof Patrick Brennan of the University of Sydney and Dr Tim Gureyev at the University of Melbourne with funding from the NHMRC and the support of clinicians in Melbourne including breast surgeon Dr Jane Fox, is now focused on demonstrating the clinical usefulness of the technique.
Together with Associate Professor Sarah Lewis and Dr SeyedamirTavakoli Taba from the University of Sydney heading clinical implementation, the technique is expected to be tested on the first patients at the Australian Synchrotron by 2020.

>Read more on the Australian Synchrotron website

Image: CT reconstruction of 3D image of mastectomy sample revealing invasive carcinoma

Diamond shines its light on moon rocks

Nearly 50 years after our first steps on the Moon, rock samples from the Apollo missions still have a lot to tell us about lunar formation, and Earth’s volcanoes.

An international collaboration involving scientists in Tenerife, the US and the UK, are using Diamond, the UK’s national synchrotron light source, to investigate Moon rocks recovered during the Apollo Missions in a brand new way.
Dr. Matt Pankhurst of Instituto Volcanológico de Canarias and NASA lunar principle investigator explains: “We have used a new imaging technique developed at Diamond to carry out 3D mapping of olivine – a common green mineral found in the Earth’s sub-surface and in these Moon rock samples. These maps will be used to improve understanding of the Moon’s ancient volcanic systems and help to understand active geological processes here on Earth.
With this new technique, our team may be able to recover from these Moon rock samples information such as what the patterns of magma flow within the volcanic system were, what the magma storage duration was like, and potentially even identify eruption triggers. The data will be analysed using state-of-the-art diffusion modelling which will establish the history of individual crystals.”

>Read more on the Diamond Light Source website

Image:
Dr Matt Pankhurst studies one of the moon rock samples from the Apollo 12 & 15 missions at Diamond Light Source

Unprecedented 3D images of neurons in healthy and epileptic brains

Results open new perspectives for the study of neurodevelopment and neurodegenerative diseases.

A comprehensive understanding of the brain, its development, and eventual degeneration, depends on the assessment of neuronal number, spatial organization, and connectivity. However, the study of the brain architecture at the level of individual cells is still a major challenge in neuroscience.
In this context, Matheus de Castro Fonseca, from the Brazilian Biosciences National Laboratory (LNBio), and collaborators [1] used the facilities of the Brazilian Synchrotron Light Laboratory (LNLS) to obtain, for the first time, three-dimensional images in high resolution of part of the neuronal circuit, observed directly in the brain and with single cell resolution.

The researchers used the IMX X-Ray Microtomography beamline, in combination with the Golgi-Cox mercury-based impregnation protocol, which proved to be an efficient non-destructive tool for the study of the nervous system. The combination made it possible to observe the points of connectivity and the detailed morphology of a region of the brain, without the need for tissue slicing or clearing.
The mapping of neurons in healthy and unhealthy tissues should improve the research in neurodegenerative and neurodevelopmental diseases. As an example of this possibility, the work presents, for the first time in 3D, the neuronal death in an animal model of epilepsy.

The researchers are now working to extend the technique to animal models of Parkinson’s disease. The intention is to better understand the cellular mechanisms involved in the onset and progression of the disease. In the future, with the inauguration of the new Brazilian synchrotron light source, Sirius, the researchers believe that it will be possible to obtain images at the subcellular level, that is, images of the interior of the neurons.

>Read more on the Brazilian Synchrotron Light Laboratory website

Image: X-ray microtomography of the cerebral cortex showing the segmentation of individual neurons. Each color represents a single neuron or a group of neurons.

World record: Fastest 3D tomographic images at BESSY II

An HZB team has developed an ingenious precision rotary table at the EDDI beamline at BESSY II and combined it with particularly fast optics.

This enabled them to document the formation of pores in grains of metal during foaming processes at 25 tomographic images per second – a world record.

The quality of materials often depends on the manufacturing process. In casting and welding, for example, the rate at which melts solidify and the resulting microstructure of the alloy is important. With metallic foams as well, it depends on exactly how the foaming process takes place. To understand these processes fully requires fast sensing capability. The fastest 3D tomographic images to date have now been achieved at the BESSY II X-ray source operated by the Helmholtz-Zentrum Berlin.

Dr. Francisco Garcia-Moreno and his team have designed a turntable that rotates ultra-stably about its axis at a constant rotational speed. This really depends on the highest precision: Any tumbling around the rotation axis or even minimal deviations in the rotation speed would prevent the reliable calculation of the 3D tomography. While commercially available solutions costing several hundred thousand euros allow up to 20 tomographic images per second, the Berlin physicists were able to develop a significantly cheaper solution that is even faster. ”My two doctoral students at the Technische Universität Berlin produced the specimen holders themselves on the lathe”, says Garcia-Moreno, who not only enjoys working out solutions to tricky technical problems, but possesses a lot of craftsman skill himself as well. Additional components were produced in the HZB workshop. In addition, Garcia-Moreno and his colleague Dr. Catalina Jimenez had already developed specialized optics for the fast CMOS camera during the preliminary stages of this work that allows even for simultaneous diffraction. This makes it possible to record approximately 2000 projections per second, from which a total of 25 three-dimensional tomographic images can be created.

>Read more on the BESSY II at Helmholtz-Zentrum Berlin (HZB) website

Image: Experimental setup is composed of a fast-rotation stage, an IR heating lamp (temperature up to 800 °C), a BN crucible transparent to X-rays, a 200-μm thick LuAG:Ce scintillator, a white-beam optical system, and a PCO Dimax CMOS camera. The incident (red) and transmitted (green) X-ray beams as well as the light path from the scintillator to the camera (blue) are shown.
Credit: HZB

3D X-ray tomography scoops up information about ice cream

There’s nothing quite like an ice cream on a hot day, and eating it before it melts too much is part of the fun.

Ice cream is a soft solid, and its appeal is a complex combination of ‘mouthfeel’, taste and appearance, which are all strongly affected by the underlying microstructure. We know that changes in the microstructure of ice cream occur at storage temperatures above -30°C, so they will occur during shipping, and in freezers at the supermarket and at home. In their ongoing quest to create the perfect ice cream, an international team of researchers brought samples to Diamond to investigate the temperature dependence of these microstructural changes, and the underlying physical mechanisms that control microstructural stability.

>Read more on the Diamond Light Source website

Advanced imaging technique used to study triggers of tree mortality

Researchers are using advanced imaging technologies similar to those used in hospitals, including micro-computed tomography on the Imaging and Medical beamline (IMBL) at the Australian Synchrotron, to determine how vulnerable our trees are to drought and heatwaves.
A new scientific review published In Nature outlines progress towards understanding the likely risks from droughts and heatwaves that combine to kill millions of trees around the world with spectacular effects on the environment.

Recent drought and heatwave conditions in northern Australia have killed more than 7000ha of mangrove forests, leaving these essential ecosystems stark, grey skeletons of trees. In California, the prolonged drought period has killed more than 100 million trees that increase the intensity of wildfires and impact on the region’s beauty, tourism and environmental health.
Dead trees, of course, cannot store carbon out of the air and the enormous numbers of dead trees release large quantities of stored carbon back into the air as they are burned or decay, further amplifying the effects of rising carbon dioxide.

>Read more on the Australian Synchrotron website

Image: IMBL robot positions the tree for imaging.

A surprising twist on skyrmions

Magnetic tomography has been used to reconstruct a tornado-like 3D magnetic skyrmion structure.

Vortex structures are common in nature, reaching from swirls in our morning coffee to spiral galaxies in the universe. Vortices are been best known from fluid dynamics. Take the example of a tornado. Air circulates around an axis, forming a swirl, and once formed, the twisted air parcels can move, deform, and interact with their environment without disintegrating. A skyrmion is the magnetic version of a tornado which is obtained by replacing the air parcels that make up the tornado by magnetic spins, and by scaling the system down to the nanometre scale. Once formed, the ensemble of twisted spins can also move, deform, and interact with their environment without breaking up ‒ the ideal property for information carriers for memory and logic devices.

What makes a tornado stable is not only coming from its twist, but also due to its three-dimensional properties, i.e., the wind current has extra twist along the column of turbulent flow. This leads to a tight bundling of the vortex sheets at different heights along the tornado column. Similarly, such a 3D structure can also occur in magnetic skyrmions, guaranteeing their topological stability. Up to now, skyrmions have been most commonly treated as two-dimensional objects, and their exciting tornado-like structure remained unexplored. In fact, the 3D characterization of magnetic structures is a rather challenging task. A team of researchers, led by the University of Oxford and Diamond Light Source, have used the energy-dependence of resonant elastic X-ray scattering (REXS) on beamline I10 at Diamond to measure the microscopic depth dependence of ‘skyrmion tornados’ in Cu2OSeO3. In their work, published in Proceedings of the National Academy of Sciences, they reveal a continuous change from Néel-type winding at the surface to Bloch-type winding in the bulk with increasing depth. This not only demonstrates the power of REXS for microscopic studies of surface-induced reconstructions of magnetic order, but also reveals the hidden energetics that makes magnetic skyrmions such a stable state – a crucial finding for skyrmion device engineering.

>Read more on the Diamond Light Source website

Figure: Illustration of a ‘Skyrmion tornado’. The skyrmion order changes from Néel-type at the surface to Bloch-type deeper in the sample. On the right hand side, the corresponding stereographic projections of these two boundary skyrmion patterns are shown.

Synchrotron X-rays reveal identity of 1.5 million-year-old Tuscan big cat

The identity of a mysterious fossil felid found in central Italy has been revealed thanks to synchrotron techniques.

Scientists used X-ray tomography to virtually extract the fossil from its rock encasing and describe decisive anatomical details for the first time. Previously thought to be an extinct Eurasian jaguar, this new study concluded by identifying the felid as Acinonyx pardinensis, one of the most intriguing extinct carnivores of the Old World Plio-Pleistocene. The study is published in Scientific Reports.

The team of physicists and palaeontologists from the University of Perugia, the University of Verona and the University of Rome Sapienza, in collaboration with the European Synchrotron, ESRF, scanned the partial skull of the specimen, still embedded in the rock. The analysis of images and 3D models obtained revealed a mosaic of cheetah-like teeth and Panthera-like features leading to a reconsideration of the ecological role of this species.

>Read more on the European Synchrotron website

Image: Dawid Iurino with the Acinonyx pardinensis skull from Monte Argentario, on the set-up of ESRF ID17 beamline.
Credit: Marco Cherin