New fossil sheds light on the evolution of how dinosaurs breathed

An international team of scientists has used high-powered X-rays at the European Synchrotron to show how an extinct South African 200-million-year-old dinosaur, Heterodontosaurus tucki, breathed. The study, published in eLife, demonstrates that not all dinosaurs breathed in the same way.

In 2016, scientists from the Evolutionary Studies Institute at the University of the Witwatersrand in Johannesburg, South Africa, came to the ESRF, the European Synchrotron in Grenoble, France, the brightest synchrotron light source, for an exceptional study: to scan the complete skeleton of a small, 200-million-year-old plant-eating dinosaur. The dinosaur specimen is the most complete fossil ever discovered of a species known as Heterodontosaurus tucki. The fossil was found in 2009 in the Eastern Cape of South Africa by study co-author, Billy de Klerk of the Albany Museum, Makhanda, South Africa. “A farmer friend of mine called my attention to the specimen”, says de Klerk, “and when I saw it I immediately knew we had something special on our hands.”

Fast forward some years: the team of scientists use scans and new algorithms developed by ESRF scientists to virtually reconstruct the skeleton of Heterodontosaurus in unprecedented detail, and thus show how this extinct dinosaur breathed. “This specimen represents a turning point in understanding how dinosaurs evolved” explains Viktor Radermacher, corresponding author, a South African PhD student and now at the University of Minnesota, US.

Read more on the ESRF website

Image: The skull of the Heterodontosaurus tucki dinosaur.

Credit: ESRF

Dramatic impact of crystallographic conflict on material properties

Many material properties are associated with structural disorder that exhibits local periodicity or correlations. A new form of this phenomenon exhibiting strong disorder-phonon coupling has been shown to arise in response to crystallographic conflict, with dramatic phonon lifetime suppression.

In recent years there has been a rapidly growing understanding that, hidden within the globally periodic structures of many crystals, various forms of disorder may exist that could form ‘locally periodic’ states, which the language of classic crystallography fails to describe. Such phenomena are commonly referred to as ‘correlated disorder’ and in many functional materials, from leading ferroelectric and thermoelectric candidates to photovoltaic perovskites and ionic conductors, this correlated deviation from perfect periodicity plays a pivotal role in governing functionality. As such, understanding the role of disorder, and the correlations that exist within it, is one of the defining challenges for the development of future functional materials.

Read more on the ESRF website

Image: Fig. 1: a) Reciprocal space reconstructions of the (hk2)s plane. All three samples investigated are shown with relevant at. % Mo indicated. Reflections are categorised and indexed in the bottom right quadrant, parent Bragg peaks (black) and diffuse superstructure reflections from two different domains (blue/green). b) Orientational relationship between parent (blue) and superstructure (red) unit cells for one of six possible domains. All atoms in the “shear plane” (highlighted red) move collinearly with the direction of motion indicated by arrows on the plane edge. Alternate planes, demarcated by I, I, III, … , move in antiphase. c) Top-down view showing the 45 relationship between the parent and superstructure. d) Schematic of the atomic motions in a “phonon plane.” Blue dashed and red dotted lines refer to interatomic bonding in the parent and superstructure unit cells, respectively.

Combatting COVID-19 with crystallography and cryo-EM

Crystallography and cryo-electron microscopy are vital tools in the fight against COVID-19, allowing researchers to reveal the molecular structures and functions of the SARS-CoV-2 virus, paving the way for new drugs and vaccines. Since the start of the pandemic, the ESRF has mobilised its crystallography and cryo-electron microscopy expertise and made its new Extremely Brilliant Source available as part of the collective effort to address this critical global health challenge.

When the WHO declared the outbreak of COVID-19 a public health emergency of international concern in early 2020, it signalled the start of a race against time for scientists to understand how the newly identified SARS-CoV-2 virus functioned and to develop treatments for the disease. Structural biologists around the world pitched in, determining the structures of most of the 28 proteins encoded by the novel coronavirus. This remarkable collective effort resulted in over a thousand 3D structural models of SARS-CoV-1 and SARS-CoV-2 proteins deposited in the Protein Data Bank (PDB) public archive in just one year [1]. Researchers and drug developers rely on these models to design antiviral drugs, therapies and vaccines. However, the speed and urgency with which the SARS-CoV-2 protein structures were solved means that errors could inevitably slip in, with potentially severe consequences for drug designers targeting certain parts of the virus’s structure. 

Enter the Coronavirus Structural Task Force, an international team of 25 structural biologists offering their time and expertise to fix errors in structural models of the virus’s proteins in order to give drug designers the best possible templates to work from. Gianluca Santoni, crystallography data scientist in the ESRF’s structural biology group, is part of the task force, whose work is detailed in an article recently published in Nature Structural & Molecular Biology [2]. “Every week, we check the PDB for any new protein structure related to SARS-CoV-2,” he explains. “We push structural biology tools and methods to the limit to get every last bit of information from the data, to evaluate the quality and improve the models where possible.” 

To read more visit the ESRF website

Image: The coronavirus research project ‘COVNSP3’ is based on the use of the ESRF’s cryo-electron microscope facility, led by Eaazhisai Kandiah (pictured)

Credit: ESRF/S. Cande.

X-ray tomography as a new tool to analyse the voids in RRP Nb3Sn wires

Scientists have developed a new tool to investigate the internal features of Nb3Sn superconducting wires, combining X-ray tomographic data acquired at beamline ID19 with an unsupervised machine-learning algorithm. The method provides new insights for enhancing wire performance.

Interest in niobium-tin (Nb3Sn) as a material for superconducting wires has recently been renewed because this material has been selected to replace niobium-titanium as the next step in accelerator magnet technology [1]. The design of these magnets relies on the availability of advanced Nb3Sn wires capable of withstanding extreme mechanical and thermal loads. The Restacked Rod Process (RRP) is considered the most promising technology to produce Nb3Sn wires at industrial scale for future accelerator magnets.

Nb3Sn is a brittle superconducting compound that cannot be drawn directly in the form of a wire. Instead, ductile precursor components are embedded in a copper matrix, drawn, brought to the final shape and then heat-treated, so that Nb3Sn forms in a reactive diffusion process. The result is a composite wire with several Nb3Sn sub-elements surrounded by copper. However, the diffusion process can lead to voids, which can play a role in the electro-mechanical and thermal behaviour of the wire. A team of scientists have developed a novel, non-destructive and non-invasive method to investigate the voids in high-performance RRP Nb3Sn superconducting wires, combining X-ray microtomography data at beamline ID19 with an unsupervised machine-learning algorithm, with a view to providing new insights into the development of these wires.

Read more on the ESRF website

Image:Fig. 1: a) 3D cross-section of a RRP Nb3Sn wire: Nb3Sn sub-elements (red), sub-element voids (light blue), copper voids (white), copper matrix (grey). b) Longitudinal cross-section of a void generated by Sn diffusion due to a leak in the sub-element. The void is highlighted in red inside the sub-element and in blue in the copper matrix, showing the sub-element failure point.

Riverine iron survives salty exit to sea

Iron organic complexes in Sweden’s boreal rivers significantly contribute to increased iron concentration in open marine waters, X-ray spectroscopy data shows. A Lund University study in Biogeosciences characterizes the role of salinity for iron-loading in estuarine zones, a factor which underpins intensifying seasonal algal blooms in the Baltic Sea.

The study ties in with a reported trend of increased riverine iron concentrations over the last decade in North America, northern Europe and in particular, Swedish and Finnish rivers. This, in conjunction with a predicted rise in extreme weather events in Scandinavia due to climate change, provides momentum for more bioavailable iron to enter marine environments such as the Baltic Sea.

“The consequences of increasing riverine iron for the receiving [marine] system depend first and foremost on the fate of iron in the estuarine salinity gradient. We had questions on what factors determine the movement and transport capacity of iron in these boreal rivers,” said Simon Herzog, postdoctoral researcher at Lund University.

The research group investigated the iron discharge in eight boreal rivers in Sweden which drain into the Baltic Sea, a brackish marine system. Water samples were taken upstream and at the river mouths, the latter just before estuarine mixing and stronger saline conditions occur. Spring and autumn specimens enabled the comparative analysis of flow conditions. To determine the type and amounts of iron species, measurements with X-ray absorbance spectroscopy (XAS) were taken at beamline I811 at Max-lab in Lund, Sweden and X-ray Absorption Near-Edge Structure (XANES) spectra at beamline ID26 at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France.

Read more on the MAX IV website

Image: A view of the Ore River in northern Sweden

Credit: Simon Herzog

Making sense of the brain’s circuits

“The brain is one of the most intricate machines that exist, and we still don’t know how it works”, says Carles Bosch Piñol, senior neuroscientist at the Francis Crick Institute in London. His research focuses on understanding how neuronal circuits receive, process and propagate information to drive behaviour. This information is encoded by hierarchical structures of sizes ranging from millimetres (neural circuits) and hundreds of microns (neuronal dendritic trees) to few nanometres (synapses). “We came to the ESRF’s ID16A beamline to find out how these circuits work”, he explains.

Bosch and his colleagues just finished a successful remote experiment. Previous experiments with the same sample provided information on how the neurons in that circuit responded to stimuli, and synchrotron imaging with full-field tomography revealed sub-µm detail on the circuit’s structure. At ESRF they wanted to obtain an even more detailed insight of the structure using X-ray holotomography, which would allow to resolve a very important subset of neuronal cables.

Read more on the ESRF website

Image: Planned acquisition of a neural circuit with holotomography. Diagram showing a top view of the specimen (edges in navy blue) and its regions of interest (in vivo recorded cell bodies in brown, genetically-tagged glomerulus in white). Tiles were planned and priority-ranked (a) with enough overlap so they can be all stitched into a single continuous volume dataset (b). (c-d) Lateral dendrites (green, nucleus in brown) are resolved (c) and can be followed until exiting the tile (d).

Credit: C. Bosch

How a very “sociable” protein can hold clues about Alzheimer’s origin

The origin of the most prevalent form of Alzheimer’s disease, which accounts for 95% of cases, is still not clear despite decades of scientific studies. “Before understanding the pathology, we need to understand the biology”, explains Montse Soler López, scientist leading research on Alzheimer’s disease at the ESRF. “The only thing we are sure about is that the most common form of Alzheimer’s is linked with ageing”, she asserts.

So researchers have been focusing on parts of the body that degrade dramatically with age. Neurons, for example, are long-lived cells, meaning that they don’t renew themselves like other cells do. Neurons lodge mitochondria, which are so-called the “powerhouse of cell” because of their active role generating energy in the body. With time, mitochondria suffer oxidative stress and this leads to their malfunction. It has been recently discovered that people with Alzheimer’s may have an accumulation of amyloids inside mitochondria (previously it was thought amyloids were only outside the neurons). Montse Soler López is trying to find whether there is a link between mitochondrial dysfunction, presence of amyloids and early disease symptoms. “We believe that malfunctioning of the mitochondria can take place 20 years before the person shows symptoms of the disease”.

Read more on the ESRF website

The African fly of death might also save lives

For the first time, an international team of scientists recreated in the lab the molecule that allows the tsetse fly to feed on blood. It’s a powerful yet small anticoagulant with a unique and strong binding to thrombin, the key enzyme of the coagulation pathway. X-ray diffraction measurements at two synchrotron facilities ––ALBA and ESRF–– were instrumental to understand the structure and the mechanism of action of this molecule, which suggests it is also a promising platform for designing improved anticoagulant drugs.

 In the waiting rooms of health care facilities around the world, millions of patients take anticoagulants every day. These are life-saving drugs for the treatment of cardiovascular diseases, which now are also being explored for their benefits to patients with advanced symptoms of COVID-19.

And, as incredible as it may seem, the tsetse fly, responsible for the sleeping sickness disease in humans, is now on the spotlight in the efforts to develop more powerful and safer anticoagulants. 

In a study co-authored by Bárbara Calisto, researcher at the ALBA Synchrotron, an international team of scientists has become the first to recreate in the lab the molecule that the tsetse fly uses to prevent coagulation when it bites to feed. These bites are also the entry channel for the parasite that causes sleeping sickness, a life-threatening disorder, if untreated. And the reason why the tsetse fly has been dubbed as the fly of death in Africa.

Read more on the ALBA website

Image:  Bárbara Calisto at the XALOC beamline of the ALBA Synchrotron

Credit: ALBA

ESRF and UCL scientists awarded Chan Zuckerberg Initiative grant for human organ imaging project

The project, named “Anatomical to cellular synchrotron imaging of the whole human body”, promises to develop a transformational X-ray tomography technology that will enable the scanning of a whole human body with resolution of 25 microns, thinner than a human hair – tens of times the resolution of a CT scanner. Further, it can then zoom into local areas with cellular-level imaging, or one micron – over 100x better resolution than a CT scanner. This imaging project is based on the recent Extremely Brilliant Source (EBS) upgrade to the ESRF that has created the world’s first high-energy fourth-generation synchrotron, which is currently the brightest X-ray source in the world. Feasibility studies have already demonstrated it can resolve unprecedented detail revealing the damage caused by COVID-19 on human lungs, linking from the major airways all the way down to the finest micro-vasculature in an intact lung.

The project is led by an international multidisciplinary team of synchrotron imaging scientists (at UCL and ESRF), mathematicians and computer scientists (at UCL) and medics (at Hannover-biobank, Mainz and Heidelberg), brought together to image deep-tissue in COVID-19-injured organs.

Read more on the ESRF website

Image: Paul Tafforeau, ESRF scientist imaging the complete brain and lung of a COVID-19 victim using HiP-CT at the ESRF-EBS, the world’s brightest X-ray source. By resolving cellular features (ca. one-micron resolution) in local areas we hope to help determine if COVID-19 affects the vasculature in the organs.
Credit: ESRF

Uncovering the secrets of a fish with a super strong jaw

Black drum is a fish from the United States with one of the strongest bite force in the fish world. It can easily crunch through shells, its main source of food. Weight for weight, it has a bite that is as strong as the bite of a crocodile.

The jaw of this fish has scientists fascinated: it is not made of cortical bone, like most jaws, and it has a 3D arrangement of beams. “This is something never seen before in any other animal. It looks like a sponge… how can such a structure, which seems weak, carry all this load?” queries project leader Ron Shahar, veterinarian and engineer at The Hebrew University of Jerusalem in Israel. 

In the quest to find how this structure is built and how it operates, Shahar is joined by Paul Zaslansky, a dentist at the Charité Hospital in Berlin (Germany), as well as physicists Alexander Rack and Marta Majkut at the ESRF.

Read more on the ESRF website

Image: A detailed view of the set-up with the jaw and all the teeth

Credit: A. Rack

Red and black ink from Egyptian papyri unveil ancient writing practices

Scientists led by the ESRF and the University of Copenhagen have discovered the composition of red and black inks in ancient Egyptian papyri from circa 100-200 AD, leading to different hypotheses about writing practices. The analysis shows that lead was probably used as a dryer rather than as a pigment, similar to its usage in 15th century Europe during the development of oil paintings. They publish their results today in PNAS.

The earliest examples of preserving human thought by applying ink on a flexible and durable material, papyrus, are found in ancient Egypt at the dawn of recorded history (c. 3200 BCE). Egyptians used black ink for writing the main body of text, while red ink was often used to highlight headings, instructions or keywords. During the last decade, many scientific studies have been conducted to elucidate the invention and history of ink in ancient Egypt and in the Mediterranean cultures, for instance ancient Greece and Rome.

Read more on The European Synchrotron website

Image: Detail of a medical treatise (inv. P. Carlsberg 930) from the Tebtunis temple library with headings marked in red ink. Credit: The Papyrus Carlsberg Collection and the ESRF.

Opening of ESRF-Extremely Brilliant Source (EBS), a new generation of synchrotron

25 August 2020 – A brilliant new light shines in Grenoble, France, with the opening of the ESRF-Extremely Brilliant Source (ESRF-EBS), the first-of-a-kind fourth-generation high-energy synchrotron. After a 20-month shutdown, scientific users are back at the ESRF to carry out experiments with the new EBS source.

The ring-shaped machine, 844 metres in circumference, generates X-ray beams 100 times brighter than its predecessor’s, and 10 trillion times brighter than medical X-rays. This intense X-ray beam hails a new era for science to understand the complexity of materials and living matter at the nanometric level. ESRF-EBS will contribute to tackling global challenges in key areas such as health, environment, energy and new industrial materials, and to unveiling hidden secrets of our natural and cultural heritage through the non-destructive investigation of precious artefacts and palaeontological treasures. A shining example of international cooperation, EBS has been funded by 22 countries joining forces to construct this innovative and world-unique research infrastructure with an investment of 150 million euros over 2015-2022, lighting the way for more than a dozen projects worldwide, including in the United States and Japan.

“The opening of the first high-energy fourth-generation synchrotron to users is a landmark for the whole X-ray science community. We are all thrilled to envisage the revolutionary science to be carried out and  the new applications that will start to emerge. All ESRF staff should be commended for such an achievement, attained on time and on budget in spite of the current circumstances,” says Miguel Ángel García Aranda, chair of the ESRF council.

Read more on the ESRF website

Image: Panoramic view of the ESRF. Credit: S. Candé.

New nanoimaging method traces metal presence in Parkinson’s brain

Many neurodegenerative diseases like Parkinson’s and Alzheimer’s often exhibit an excess of iron in the brain. Scientists have developed a method to trace the presence of metals in brain at the sub-cellular level, particularly in organelles of neurons vulnerable to these diseases. The results are published in Communications Biology.

The level and distribution of iron in the brain normally contributes to essential cellular functions, including mitochondrial respiration, via its capability to transfer electrons. In vulnerable populations of neurons however, iron dysregulation can have detrimental effects. Genetic defects affecting iron metabolism cause brain diseases, including Parkinson’s and Alzheimer’s, both associated with iron overload. “It is important to be able to explore metal distribution in neurons and glia (non-neuronal cells), with the aim to identify potential causal mechanisms in neurodegeneration”, explains Bernard Schneider, scientist at EPFL and co-author of the study.

Until now, there was no method that could trace the elements with sensitivity and nanometre resolution. A team of scientists from LGL-TPE (Laboratoire de Géologie de Lyon : Terre, Planètes et Environnement), Institut des Sciences de la terre (ISTerre) de Grenoble, the ESRF and the EPFL (École Polytechnique Fédérale de Lausanne) have now combined the techniques of transmission electron microscopy and synchrotron X-ray fluorescence at the ESRF in order to evaluate the element unbalance in Parkinson’s disease.

Read more on the ESRF website

Image : Composition of P/Fe/S in a section of a neuron of the substantia nigra. The neuron and its nucleus are highlighted by dashed lines. Cytoplasmic granules rich in Fe and S are pointed out by arrows. 

Credit: Lemelle, L, et al, Communications Biology, DOI : 10.1038/s42003-020-1084-0.

Researchers find the key to preserving The Scream

Moisture is the main environmental factor that triggers the degradation of the masterpiece The Scream (1910?) by Edvard Munch, according to the finding of an international team of scientists led by the CNR (Italy), using a combination of in situ non-invasive spectroscopic methods and synchrotron Xray techniques. After exploiting the capability of the European mobile platform MOLAB in situ and non-invasively at the Munch Museum in Oslo, the researchers came to the ESRF, the European Synchrotron (Grenoble, France), the world’s brightest X-ray source, to carry out non-destructive
experiments on micro-flakes originating from one of the most well-known versions of The Scream. The findings could help better preserve this masterpiece, which is seldom exhibited due to its degradation. The study is published in Science Advances.


The Scream is among the most famous paintings of the modern era. The now familiar image is interpreted as the ultimate representation of anxiety and mental anguish. There are a number of versions of The Scream, namely two paintings, two pastels, several lithographic prints and a few drawings and sketches. The two most well-known versions are the paintings that Edvard Munch created in 1893 and 1910. Each version of The Scream is unique. Munch clearly experimented to find the exact colours to represent his personal experience, mixing diverse binding media (tempera, oil and pastel) with brilliant and bold synthetic pigments to make ‘screaming colours’. Unfortunately, the extensive use of these new coloured materials poses a challenge for the long-term preservation of Munch’s artworks.

Read more on the ESRF website

Image: ESRF scientist Marine Cotte during the synchrotron experiment at ID21 beamline, at the ESRF, the European Synchrotron, Grenoble, France.

Credit: ESRF/Stef Candé

Out of the blue: X-rays shed light on on ultramarine blue in masterpieces

According to a survey led by Nature in 2016, 70% of scientists admitted they could not reproduce another scientist’s experiments and more than half could not reproduce their own. In order to improve sharing and, in turn, enhancing innovation, the European Union is working on implementing the European Open Science Cloud (EOSC), a kind of “library” of all experimental raw data and methods, available to everyone.

The ESRF is doing its bit by leading the PaNOSC (Photon and Neutron Open Science Cloud) project: “We are in the process of implementing the ESRF Data Policy to organise the data from experiments in an archive, which ultimately everyone will be able to access. The scientific teams will have three years to keep their data closed to the public, and after that any other scientist can try to repeat or do new data analysis of the very same experiment if he or she wishes to”, explains Andy Götz, coordinator of the project. The final goal of PaNOSC and the EOSC is to make data from publicly funded research in Europe Findable, Accessible, Interoperable and Reusable (FAIR).

>Read more on the ESRF website

Image: Alessa Gambardella at a stereomicroscope looking at ultramarine blue in Hendrick per Brugghen’s The Adoration of the Kings (1619)

Credit: Courtesy of Department of Conservation & Science, Rijksmuseum.

Synchrotron X-ray sheds light on some of the world’s oldest dinosaur eggs

An international team of scientists led by the University of the Witwatersrand (South Africa), has been able to reconstruct the skulls of some of the world’s oldest known dinosaur embryos in 3D at the ESRF.

They found that the skulls develop in the same order as those of today’s crocodiles and chickens. The findings are published today in Scientific Reports.
University of the Witwatersrand scientists publish 3D reconstructions of the ~2cm-long skulls of some of the world’s oldest dinosaur embryos in an article in Scientific Reports. The embryos, found in 1976 in Golden Gate Highlands National Park (Free State Province, South Africa) belong to South Africa’s iconic dinosaur Massospondylus carinatus, a 5-meter long herbivore that nested in the Free State region 200 million years ago.

The scientific usefulness of the embryos was previously limited by their extremely fragile nature and tiny size. In 2015, scientists Kimi Chapelle and Jonah Choiniere, from the University of Witwatersrand, brought them to the European Synchrotron (ESRF) in Grenoble, France for scanning. At the ESRF, an 844 metre-ring of electrons travelling at the speed of light emits high-powered X-ray beams that can be used to non-destructively scan matter, including fossils. The embryos were scanned at an unprecedented level of detail – at the resolution of an individual bone cell.

>Read more on the ESRF website

Image: Watercolour painting of the Massospondylus carinatus embryos at 17% through the incubation period, 60% through the incubation period and 100% through the incubation period.
Artwork: Mélanie Saratori.