Monitoring Avian Flu Evolution Using SLAC’s Synchrotron

Monitoring Avian Flu Evolution Using SLAC’s Synchrotron

In the game of evolution, viruses are among the most adaptable players, constantly changing in response to their environments. Researchers in immunology and structural biology regularly monitor these changes, especially those that could pose a threat to public health. Scientists use X-ray facilities like the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory to examine the underlying structures of individual proteins, which influence a virus’ behavior and ability to spread between species. 

Since the first recorded case of highly pathogenic avian influenza H5N1 – commonly known as avian flu or bird flu – in 1996, Ian Wilson, professor of structural biology at Scripps Research, and his colleagues have been closely tracking the evolution of several key proteins using SSRL. 

Recently, Wilson’s team investigated the evolution of a protein that plays a crucial role in H5N1’s ability to transmit between species. Their analysis found that the protein is susceptible to a mutation that could help the virus attach to human cells, potentially increasing the risk of human transmission. The findings – published in Proceedings of the National Academy of Sciences – underscore the need for ongoing monitoring of H5N1’s evolution. 

“Facilities like SSRL enable research on infectious diseases and pandemic threats, accelerating our ability to respond to global health emergencies,” said Aina Cohen, division director of Structural Molecular Biology at SSRL. “Discoveries made in areas like drug development, vaccine design and diagnostics can lead to more effective treatments, earlier disease detection and stronger preventive measures.” 

Studying proteins with SSRL 

Though H5N1 viruses are prevalent in birds and some mammals around the world, transmission to and between humans is rare. However, this could change as the virus continues to mutate. Wilson’s team focuses on H5N1’s hemagglutinin (HA) protein, which enables the virus to attach to receptors on the surfaces of host cells. If this protein mutates from its current receptor specificity – which favors avian-type receptors – to one that effectively binds to human-type receptors, the potential for transmission to humans could rise significantly. 

“Monitoring changes in receptor specificity – the way a virus recognizes host cells – is crucial because receptor binding is a key step toward transmissibility,” Wilson said. “That being said, receptor mutations alone don’t guarantee that the virus will transmit between humans.” 

To build a timeline of the HA protein’s evolution, Wilson’s team analyzes proteins from samples collected in various years. These studies do not use live virus samples; instead, the research team generates proteins using data from the Global Initiative on Sharing All Influenza Data. The team then crystallizes these proteins and sends the crystallized samples to SSRL. 

At SSRL’s Beam Line 12-1, the Scripps team collects data remotely with assistance from on-site scientists at SLAC. By analyzing how X-rays diffract when passing through the protein crystals, researchers can reconstruct the protein’s 3D structure, gaining insights into the behavior of various HA proteins.

“The bright X-ray microbeams produced by SSRL, combined with a high level of experimental automation and user-friendly experimental control interface, make Beam Line 12-1 a premiere resource for these types of experiments,” Cohen said. “With decades of experience, SSRL staff support our users, helping them achieve the highest quality data.” 

Read more on SLAC website

Concept for self-sustained oxygen mask wins competition

Concept for self-sustained oxygen mask wins competition

Researchers at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) have developed a concept for a self-sustained oxygen mask that uses the ability of microalgae to convert carbon dioxide into oxygen. This could form the basis for a portable microalgae-biomaterial hybrid device that enables prolonged oxygen supply and water absorption. With this concept, the HZDR team is one of the winners in a competition organized by the journal Nature Reviews Bioengineering. The task was to develop medical innovations for resource-limited regions.  

Life-saving medical devices such as oxygen masks are often dependent on limited or expensive resources, such as medical oxygen. In addition, many important devices and treatments require expensive and complex components, which hinders their development and local manufacturing. Solutions that work in resource-poor and disadvantaged regions of the world are, therefore, urgently needed. This is why the journal Nature Reviews Bioengineering has called on young bioengineers to find a simple solution to this problem.

Oxygen masks are usually dependent on an external oxygen supply, whether in the form of oxygen tanks or capsules. For the competition “The ultimate bioengineering challenge”, Xuan Peng, Xinne Zhao and Željko Janićijević from the Department of Nano-Microsystems for Life Sciences at HZDR´s Institute of Radiopharmaceutical Cancer Research have designed the idea for a self-sustained oxygen mask made of lightweight, biocompatible materials that enables prolonged oxygen supply and water collection in resource-poor areas.

The main challenge in designing a self-sustained oxygen mask was to reduce carbon dioxide and water vapor while increasing the oxygen content in the inhaled air. The scientists’ idea is based on photosynthesis, in which light energy (from the Sun) is converted into chemical energy. This energy is then used to build up energy-rich organic substances from carbon dioxide and water and release oxygen. For photosynthesis, they use microalgae, which are considered excellent converters of carbon dioxide to oxygen and can survive even under harsh environmental conditions. 

Read more on HZDR website

Image: Schematic illustration of how a self-sustained oxygen mask works.

Credit: HZDR / A. Grützner

Do Robots Dream of Electron Beams?

Do Robots Dream of Electron Beams?

NSLS-II scientists are changing how many experiments run by employing a coordinated team of AI-powered robots

UPTON, N.Y. — To build the experimental stations of the future, 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, are learning from some of the challenges that face them today. As light source technologies and capabilities continue to advance, researchers must navigate increasingly complex workflows and swiftly evolving experimental demands.

To meet these challenges, a team of NSLS-II scientists is training a team of AI-driven collaborative robots. These agile, adaptable systems are being developed to quickly shift between tasks, adjust to different experimental setups, and respond autonomously to real-time data. By taking on work using learning processes rather than preprogrammed steps, much like a human researcher, these robots are helping scientists realize a future where these systems can be deployed on demand, empowering them to explore new possibilities and fully harness the facility’s cutting-edge capabilities to investigate everything from battery technologies to quantum materials.

The team has successfully demonstrated this technology by rapidly deploying a prototype of one of these robotic systems to run an autonomous experiment overnight. The setup included different-sized samples that were randomly placed in the experimental environment without any preprogrammed knowledge of their location. The simulated experiment proceeded for eight hours without errors, showcasing the potential for user-friendly, AI-driven robotic integration in scientific research. Their results were recently published in Digital Discovery.

“We’re envisioning a new path forward,” said Phillip Maffettone, a computational scientist in NSLS-II’s Data Science and Systems Integration (DSSI) division and lead author of the study. “This approach isn’t just about speeding up current experiments; it’s a roadmap for the next generation of beamlines — modular, intelligent, and deeply integrated with AI. We’re designing a system that dynamically adapts to user needs.”

Building an automation foundation

NSLS-II currently operates 29 beamlines, with three more under construction and several others in development. The range, complexity, and volume of experiments conducted across these beamlines presents a challenge: designing a system that can automate existing workflows while remaining flexible enough to adapt to new types of experiments and new beamlines as they come online.

The synchrotron community has already found a lot of success in automating macromolecular X-ray crystallography (MX) experiments using robotics. MX beamlines can now perform automated and semi-automated experiments that routinely reach 99.96% reliability, which has increased the throughput of MX experiments. At NSLS-II alone, almost 13,000 samples were mounted at the Highly Automated Macromolecular Crystallography (AMX) beamline over the past four months. The robotic systems used at these beamlines are very effective for MX samples, and the robots have inspired scientists to think about what a more modular system could look like as they developed ideas for new beamline designs.

Daniel Olds is the lead beamline scientist at the upcoming High Resolution Powder Diffraction (HRD) beamline at NSLS-II. The beamline’s design enables users to take fast, in situ measurements that reveal real-time material behaviors such as battery cycling, catalytic reactions, and phase transitions — an approach that demands an innovative, adaptable system tailored to custom sample environments.

“We’re tackling a challenge faced by many researchers: how do we get the most science out of a limited window of beam time?” Olds said. “With so many formats and such little time, managing these experiments becomes a high-stakes logistical sprint.”

To envision what future experiments could look like, Maffettone, Olds, and a team of scientists from DSSI studied current experiments that would benefit most from flexible automation. They focused on the Pair Distribution Function (PDF) beamline, where visiting scientists, particularly those studying battery materials, often arrive with hundreds of unique samples. These can range from powders in narrow capillaries to flat “coupons” and even full pouch cell batteries like those used in electric vehicles. Some must be measured while charging and discharging in real time.

Instead of working in a single geometry or setup, a “smart” robot would be able to quickly learn how to handle a wide variety of sample types that differ in shape, size, and weight, just as a human scientist would. This kind of adaptability would reduce downtime, enable continuous beamline operation, and free researchers to focus more on insights than logistics.

Take capillary samples, for example. These are typically mounted on T-shaped brackets that hold 10 to 30 capillaries each. Once loaded and aligned with the beam, the capillaries are scanned sequentially as the bracket moves vertically, allowing different regions of each sample to be measured and averaged for more reliable data. Scans are fast, with each bracket taking just five to 10 minutes, leaving users little time between sample changes. Currently, switching from a capillary containing battery material to an actual operando battery setup also requires stopping the experiment, opening the protective hutch, and manually swapping samples. An automated system could streamline these processes, but only if it’s intuitive and flexible.

For energy research in particular, this shift could be transformative. Progress in energy storage depends on the ability to screen new materials and quickly test them under real-world conditions with limited scheduled time at the beamline. Adaptive robotics at NSLS-II would dramatically accelerate that process, helping researchers develop the next generation of high-performance batteries for applications ranging from earbuds to electric vehicles.

This is only one example of the many types of experiments in several different fields that this kind of system is hoping to accelerate. As Maffettone explained, “The dream is to have smart robots that users can request on a per-beam-time basis. These applications are designed to be quickly deployed, removed, and redeployed based on the needs of the experiment while also being able to integrate AI-agent-driven automation techniques. Because of this, the robots we use would need to be light and portable, have a modular build, and plug into an accessible software infrastructure.”

Read more on NSLS-II website

Image: NSLS-II computational scientist Phillip Maffettone simulated an experimental setup to test AI-driven robotic automation.

Credit: Kevin Coughlin/Brookhaven National Laboratory

Bioinspired controlled crystallisation: Towards sustainable artificial coral reefs

Bioinspired controlled crystallisation: Towards sustainable artificial coral reefs

Inspired by nature, scientists have replicated some aspects of the biomineralisation process used by marine organisms like corals, enabling them to control crystal phases in materials. This advancement could lead, among others, to artificial coral reefs that seamlessly integrate into marine environments without disrupting the ecosystem. Their results are out in Advanced Functional Materials.

Artificial coral reefs are often made of concrete or steel to provide stable structures for a marine habitat. However, they can also foster biofilm formation, promoting bacterial growth that may influence water chemistry.

Now a team led by Boaz Pokroy at Technion Israel Institute of Technology is working on artificial coral reefs that are as close to their natural counterparts as possible by reproducing the biomineralisation process typical of coral reefs and other marine organisms.

“For many years, we’ve extensively studied many marine organisms, such as the coralline alga Jania sp., sea urchins, starfish or brittle stars, and have unveiled the steps these organisms take to create a super hard skeleton through the process of biomineralisation”, explains Pokroy.

The natural process of biomineralisation starts as an amorphous phase before transforming into crystalline stable structures.

A key player in in this process is amorphous calcium carbonate (ACC), a precursor that can crystallise into different forms of calcium carbonate, including calcite, aragonite, and vaterite. The stability of ACC is influenced, among other factors, by impurities like magnesium, which affects the final crystal structure and properties. Traditionally, controlling this transformation required chemical additives and environmental adjustments.

Pokroy and his team used lasers to selectively transform ACC into different mineral phases. Laser power, scanning speed and the composition of the substrate are factors that affect the process of formation of distinct crystalline phases.

As the next step, the powders were analysed using synchrotron high-resolution powder X-ray diffraction (HR-PXRD) to identify the phases formed. “The experiments on beamline ID22 at the ESRF were crucial to characterise the different phases and track the impurities in the sample”, explains Hadar Shaked, scientist at Technion and first author of the publication. “With EBS providing higher flux, we were able to scan hundreds of samples in a very short time”, adds Pokroy.

Engineering bio-inspired materials

This method represents a significant advancement in bio-inspired material science, offering a way to engineer complex mineral structures with the same spatial accuracy seen in biological systems. “Whilst crystallisation from an amorphous phase was already possible through heating, it is the first time that we have full control of the process, which is key in engineering new structures as we wish”, says Shaked.

Dubbed ‘writing crystallography’, this approach opens exciting possibilities not only for artificial coral reefs but also for advanced additive manufacturing, semiconductors or single-layer patterning, where precise phase control is essential.

Read more on ESRF website

How an old drug could make a comeback against antibiotic resistance

How an old drug could make a comeback against antibiotic resistance

In the quest for solutions to modern antibiotic resistance, researchers at Goethe University Hospital in Frankfurt, together with their colleagues from European Synchrotron, the ESRF (Grenoble, France) and the EMBL Heidelberg are turning back to the past—and finding hope in an old, often-overlooked drug. Using X-ray nanofluorescence at the ESRF, they have uncovered how the rarely used antibiotic nitroxoline can fight back against drug-resistant bacteria. Their findings, published in Nature Communications, could spark renewed medical interest in the forgotten drug as a potential weapon against hard-to-treat infections.

Five years ago at Goethe University Hospital in Frankfurt, a patient in the intensive care unit was battling with a stubborn urinary tract infection. Despite multiple rounds of antibiotics, nothing seemed to make a difference. Then, as a last resort, doctors turned to an old drug from the 1960s—nitroxoline, typically reserved for uncomplicated urinary tract infections (UTIs). To their surprise, it worked.

Doctor and researcher Stephan Göttig was investigating this drug. “I realised that the potential of nitroxoline is huge towards multidrug-resistant Gram-negative bacteria, so we started studying its spectrum and mechanism”, he explains.

Targeting hospital pathogens

Nitroxoline is only used in a handful of countries today, after the rise of newer antibiotics and lack of clinical research. In Germany, where Göttig and the first author of the paper, Elisabetta Cacace were based (Cacace has now moved to ETH Zurich), it is an approved drug and it is still commonly prescribed for uncomplicated UTIs. However, it is not included in the WHO’s essential medicines list nor is it FDA approved in the US. “New pharmaceutical compounds are difficult to market, so it is useful to repurpose existing antibiotics”, explains Cacace.

Göttig and Cacace investigated more than a thousand isolates of different Gram-negative bacteria that nitroxoline could potentially fight against. Gram-negative bacteria have an outer membrane that can block many antibiotics and even some immune system components. They focused on Enterobacteriaceae, a group of bacteria that includes notorious hospital pathogens such as Klebsiella pneumoniae and Escherichia coli.

Read more on ESRF website

Plant leaves inspire design of improved fuel cell

Plant leaves inspire design of improved fuel cell

Hydrogen fuel cells convert hydrogen and oxygen into electricity, heat, and water. Because this conversion process doesn’t generate any carbon emissions, fuel cells are seen as a valuable source of green energy that could be key in addressing climate change.

However, there’s an obstacle standing in the way of their use in large-scale applications – powering electric trucks for long-haul transport, for example, or replacing diesel generators to provide electricity in remote, northern communities. Current fuel cells have reached a ceiling in the amount of electricity they can generate because their internal structure cannot adequately manage all of the water that cells create as a byproduct.

Researchers from the University of Toronto’s Department of Mechanical and Industrial Engineering looked to a novel source when they were brainstorming for ideas to improve the design of the channels — called “flow fields” — that direct water inside the cell. PhD student Eric Chadwick says that, instead of starting from scratch, he turned to nature for inspiration (“biomimicry”). “Rather than trying to come up with a brand-new design, I decided to look toward nature, as often some organism has already, through evolution, optimized a process.”

In this case, the process was moving water in a single direction. He found evidence of this on the skin of lizards and the leaves of certain plants. “Lizards living in dry, arid climates have scales that have evolved to trap condensation from air and channel it to their eyes and mouth,” says Chadwick. “Similarly, on certain types of leaves the veins catch water and move it to tips of the leaves so that it falls down, so the roots can absorb it.” He and his team incorporated these patterns from nature into the channels within their new cell, to more effectively move water from the porous layer inside the cell to the outside of the cell.

Using the Canadian Light Source at the University of Saskatchewan, Chadwick and his colleagues found the nature-inspired design resulted in a 30% increase in the peak power density they could reach in the fuel cell, compared to existing designs. The new cell design showed a more even distribution of water within the cell, with no build up, which also meant more even distribution of the reactants (oxygen and hydrogen) – “so the fuel cell is using the catalyst (platinum) more effectively.” The researchers also found that, because the new design removed excess liquid water from the porous layer, the channels served as additional pathways for more reactant to get to the catalyst layer.

With the high-energy X-rays at the CLS, Chadwick and the team were able to generate richly detailed, cross-sectional images of their new fuel cell while it was operating. “We were able see exactly where the water is going, how much is remaining in the cell, with the different designs we tested,” says Chadwick. In the old design, we used to have this heterogeneous distribution of water. Now we have a much more homogeneous layer of water, which in turn means we have a much more homogenous distribution of the reactants and we’re using the catalyst in the fuel cell much more effectively and evenly.”

Read more on CLS website

Image: Plant leaves inspire design of improved fuel cell

Green hydrogen: A cage structured material transforms into a performant catalyst

Green hydrogen: A cage structured material transforms into a performant catalyst

Clathrates are characterised by a complex cage structure that provides space for guest ions too. Now, for the first time, a team has investigated the suitability of clathrates as catalysts for electrolytic hydrogen production with impressive results: the clathrate sample was even more efficient and robust than currently used nickel-based catalysts. They also found a reason for this enhanced performance. Measurements at BESSY II showed that the clathrates undergo structural changes during the catalytic reaction: the three-dimensional cage structure decays into ultra-thin nanosheets that allow maximum contact with active catalytic centres. The study has been published in the journal ‘Angewandte Chemie’.

Hydrogen can be produced by electrolysis of water. If the electrical energy required for this process comes from renewable sources, this hydrogen is even carbon neutral. This ‘green’ hydrogen is seen as an important building block for the energy system of the future and is also needed in large quantities as a raw material for the chemical industry. Two reactions are crucial in electrolysis: hydrogen evolution at the cathode and oxygen evolution at the anode (OER). However, the oxygen evolution reaction in particular slows down the desired process. To speed up hydrogen production, more efficient and robust catalysts for the OER process need to be developed.

Clathrates, a structure build of cages

Currently, nickel-based compounds are considered to be good and inexpensive catalysts for the alkaline oxygen evolution reaction. This is where Dr. Prashanth Menezes and his team come in. ‘The contact between the active nickel centres and the electrolyte plays a crucial role in the efficiency of a catalyst,’ says the chemist. In conventional nickel compounds, this surface area is limited. ‘We therefore wanted to test whether nickel-containing samples from the fascinating class of materials known as clathrates could be used as catalysts’.

The materials are made of Ba8Ni6Ge40 and were produced at the Technical University of Munich. Like all clathrates, they are characterised by a complex crystalline structure of polyhedral cages, in this case, formed by germanium and nickel, enclosing barium. This structure gives clathrates special properties that make them interesting as thermoelectrics, superconductors or battery electrodes. However, until now, no research group had considered of investigating clathrates as electrocatalysts.

Read more on HZB website

Image: The illustration shows schematically how nanothin sheets of nickel compounds are released from the clathrate structure, providing an extremely large surface area for the oxygen evolution reaction. 

Credit: Hongyuan Yang/HZB/TUB

A pioneering spectrometer for hard X-rays

A pioneering spectrometer for hard X-rays

Researchers at the European XFEL have developed a new device for X-ray measurements at high photon energies–a so-called Laue spectrometer. It enables X-ray light with photon energies of over 15 kiloelectronvolts to be detected with improved efficiency and highest precision. This is important for researching technically significant materials that, for example, transport electricity without losses or ensure that chemical processes run more efficiently.

To unravel the secrets of the world of atoms, molecules and materials in general, scientists often use special measurement devices known as spectrometers. They work by recording the light that objects emit. From the way in which the objects do that, researchers learn a lot about the physical processes that take place in the materials. Particularly revealing is the research with X-ray light, which penetrates deeply in matter and provides information specific to each atomic species. This light is invisible to our eyes, but can be detected and measured using special spectrometers.

The main components of these devices are usually extremely precisely cut crystals made of silicon or germanium. Traditionally, the X-ray spectrometers work in what is known as Bragg geometry: The X-ray light hits the crystal and is then diffracted by the atomic planes parallel to the surface, similarly as mirrors reflect visible light. From the direction and intensity of the scattered radiation, the researchers can draw conclusions about the electronic properties of the materials they are analysing.

A unique characteristic of European XFEL is the ability to provide X-ray light with very high energy. However, as the energy of the X-rays increases, the interaction with the crystals becomes smaller, making the measurements challenging. In this high photon energy regime, a large proportion of the X-ray light simply passes through the crystal unused, which is why the performance of X-ray spectrometers using these analysers, known as Johann or Von Hamos spectrometers, decreases rapidly with increasing X-ray energy. They usually only work well up to a photon energy of around 15 kiloelectronvolts (keV).

Read more on European XFEL website

Image: Contrary to regular spectrometer the new Laue spectrometer is diffracting the X-ray beams (red arrows) by atomic layers perpendicular to the surface.

PETRA III peers deep into plant tumours

PETRA III peers deep into plant tumours

Analysis of leaf galls formed by mites show how they alter the plants’ metabolism of metals

They can be a nightmare for farmers and gardeners: galls, abnormal plant growths caused by various organisms, can damage crops and other plants. Researchers have used PETRA III to analyse galls caused by mites that infest the leaves of various trees and bushes. What they found is incredible: The mites alter the plants’ metabolism of trace metals in the newly formed galls to better suit their needs, aggregating metals needed for their nutrition and protection while sequestering the excessive ones. The results, published in the journal New Phytologist, could help scientists to better understand these evolutionarily fascinating interactions between plants and specialised herbivores and perhaps eventually help avoid damage to economically important plants.

A gall can be formed on every part of a plant: leaf, root, trunk, flower. Insects and mites can induce complex galls by hijacking the plant’s cellular functions and extensively reprogramming expression of its genes. The new tissue serves to feed and protect the gall-inducing insect or mite. The mites from the family Eriophyidae make brightly coloured, spike-shaped “nail” galls, within which they spend multiple generations from spring to autumn each year. A female mite infests the emerging leaves in springtime, and the leaf grows with galls filled with numerous male and female mites. During winter, the female mites emerging from the galls hide in winter buds to initiate another life cycle in the spring.

“The gall is a sort of ordered tumour,” says Filis Morina, a plant scientist based at the Biology Centre of the Czech Academy of Sciences in České Budĕjovice who is first author of the study. “This is like a hijacking of the plant’s cellular functions because the mite completely manipulates what happens to the leaf. The leaf otherwise would never make such a shape as a nail gall.”

Although they are essential for both the plant and the mites, the role of the metals in the interaction between the two had remained elusive. To reveal this, the authors used a technique called tomography – more commonly used in medical imaging – and the X-rays of the DESY X-ray light source PETRA III to peer into the gall.

“In scanning X-ray fluorescence tomography, you scan the sample line by line, and you rotate the sample between the lines,” says DESY scientist Gerald Falkenberg, who leads the PETRA III P06 beamline and performed the research with the team. The result is a three-dimensional see-through map of the structures and contents of the galls.

“The P06 beamline at PETRA III allowed us to look down with subcellular detail as to where elements that are decisive for the development of the mite and the gall are distributed,” says Hendrik Küpper, who led the research with Morina at the Biology Centre CAS. The team found that mites induce accumulation of zinc, iron and copper in the nutritive tissue, while manganese and calcium accumulate in large secretory cells. The mites had changed the distribution of metals as well as their function. Using complementary spectroscopic, biochemical and genetic techniques, the team could finally map different metals with gene expression, metabolic profile and oxidation–reduction reactions regulated by the mite in the gall.

To further understand the changes in manganese metabolism, the team used a technique called XANES (X-ray absorption near edge spectroscopy) tomography to get a map of manganese absorption spectra in different gall compartments. This allowed for identification and mapping of the classes of manganese-binding compounds, linking distribution of the metal and its function in individual cells in the galls.

Read more on DESY website

Image: Nail galls on a leaf

Credit: Wikimedia Comms

High-resolution imaging provides clues to lung disease

High-resolution imaging provides clues to lung disease

Researchers have imaged lung tissue affected by Idiopathic Pulmonary Fibrosis (IPF) with nanometre resolution. They managed to capture differences in the distribution of trace elements compared to a healthy lung. The result is a step towards better understanding the body at the nanoscale and managing this and other currently untreatable diseases.

The distribution of chemical elements in our cells can say a lot about their function and processes. To see this distribution, we need a method with a resolution that is high enough to see details inside cells. The method should also be sensitive to differences in chemical content. The structures inside the cell are on the nanometre scale, and Nano X-ray Fluorescence (Nano-XRF) offers a powerful imaging method that fulfils both criteria. The technique is relatively young and has been used in the research community for about 10–15 years.

“Nano-XRF is becoming more prominent as synchrotron facilities are advancing. Its growing use is linked to improvements in synchrotron technology, such as brighter beams and better focusing, that now allow nanometre-scale spatial resolution and higher sensitivity, enabling applications that were not possible before,” says Bryan Falcones, a postdoc at the Department for Lung Biology at Lund University and visiting research fellow at MAX IV.

Read more on MAXIV website

New strategy for targeting cancer-causing protein previously considered “undruggable”

New strategy for targeting cancer-causing protein previously considered “undruggable”

A cancer-causing protein long thought to be resistant to medication could soon be the target of new drugs, thanks to the work of Quebec researchers who used synchrotron light to find and exploit its weak spot.

Dr. Steven LaPlante, a professor at Quebec’s Institut National de la Recherche Scientifique (INRS), and his team studied a type of protein called Ras, “which is highly related to a good percentage of the cancers that are out there,” especially those of the head, neck and urinary tract. Ras proteins act as a molecular “switch,” flipping between active and inactive modes; they play a critical role in cell signaling and growth regulation and are often mutated in cancers. Major pharmaceutical companies have studied Ras for years, trying to develop new medications, says LaPlante, but have only recently begun to make some breakthroughs.

LaPlante, who worked in the a pharmaceutical industry before joining INRS, said he wanted to take a new approach to the problem, “to start everything from scratch, like making a nice cake – you start from scratch and when you do that, you really have control over how to optimize every segment (of the process) and make a really good cake.”

Using the Canadian Light Source (CLS) at the University of Saskatchewan, LaPlante and his team gathered atomic-level, 3D information about the protein; they discovered a “pocket” in it that appears to be an ideal target for molecular drug treatment. But, he added, it is “a cryptic pocket – it’s there sometimes and not there other times,” depending on the state of the protein.

The researchers found that, when the Ras protein is in its mutated, cancer-causing state, “molecules snuggle inside the pocket.” “Using crystallography, we were able to look at the mutant proteins to better understand what their structures are,” says LaPlante. Their work was recently published in the journal ACS Omega.

Read more on CLS website

A faster route to green hydrogen

A faster route to green hydrogen

Acidic conditions are a challenge. If you want to produce hydrogen by electrolysis and use a low-cost catalyst such as cobalt, the process doesn’t function as well if the aqueous environment is acidic – working in alkaline conditions is easier. Researchers at the Paul Scherrer Institute PSI have now discovered the reason for this: the surface of the catalyst changes with the pH value of the environment. Their study, published in the journal Nature Chemistry, provides important clues to enable efficient and cost-effective production of hydrogen for the energy transition in the future.

The simplest and most environmentally friendly method for producing hydrogen is electrolysis: with an electric current, water (H2O) is split into its components, hydrogen (H2 ) and oxygen (O2). Oxygen is produced at the positive pole, the anode; hydrogen is produced at the negative pole, the cathode. Water splitting can be carried out in an alkaline environment (pH>7), an acidic one (pH<7), or a neutral one (pH=7). Different types of electrolysers operate at different pH values, that is, in different aqueous environments.

In splitting water, the formation of oxygen is the step that requires the most energy, effectively the bottleneck of the reaction. To make it possible to do this more efficiently and cost-effectively, catalysts such as the metal cobalt are used. However, electrolysis with cobalt only works satisfactorily in an alkaline environment; the reason for this was previously unknown.

A PSI research group in the Center for Energy and Environmental Sciences have now found out the cause: depending on the pH value, the catalyst’s surface changes. In acidic conditions, active sites where oxygen can be produced require more energy to form – as a result, electrolysis becomes slow and uneconomical. “We assume that this is the case not only with cobalt, but also with other metals that likewise perform less well in acidic conditions – such as manganese, iron, and nickel,” says Jinzhen Huang, a postdoctoral researcher in Emiliana Fabbri’s and Thomas Schmidt’s research group and first author of the study.

Cobalt as a low-cost alternative

At present, the noble metals iridium and ruthenium are usually used as catalysts for splitting water. Their activity changes only slightly depending on the pH value and therefore also work well in acidic environments. However, cobalt and other so-called transition metals are significantly cheaper and more abundant on Earth, which makes them particularly attractive for large-scale applications. “Replacing the noble metals with cobalt and other lower-cost metals is a major challenge,” Emiliana Fabbri explains. “Our findings are important steps on the way to that goal.”

Read more on PSI website

Image: Close-up of a glass vial containing a cobalt-based catalyst powder, captured in the lab at the Paul Scherrer Institute PSI. Researchers at the PSI Center for Energy and Environmental Sciences have discovered why this catalyst performs more efficiently in alkaline environments during hydrogen production.

Credit: Paul Scherrer Institute PSI/Mahir Dzambegovic

A milestone for laser plasma acceleration

A milestone for laser plasma acceleration

A DESY team substantially improved the properties of a laser-plasma accelerated electron beam opening up new areas of applications

Laser plasma acceleration is a potentially disruptive technology: It could be used to build far more compact accelerators and open up new use cases in fundamental research, industry and health. However, on the path to real-world applications, some properties of the plasma-driven electron beam as delivered by current prototype accelerators still need to be refined. DESY’s LUX experiment has now made significant progress in this direction: Using a clever correction system, a research team was able to significantly improve the quality of electron bunches accelerated by a laser plasma accelerator. This brings the technology a step closer to concrete applications, such as a plasma-based injector for a synchrotron storage ring. The research group presents their results in the journal Nature.Conventional electron accelerators use radio waves which are directed into so-called resonator cavities. The radio waves transfer energy to the electrons as they fly past, increasing their velocity. To achieve high energies, many resonators have to be connected in series making the machines large and costly. Laser-plasma acceleration is promising a novel compact alternative. Short, intense laser pulses are shot into a small hydrogen-filled capillary generating a plasma – an ionised gas. When the laser pulse passes through the plasma, it creates a wake similar to the wake of a high-speed boat travelling though water. This wake can accelerate a bunch of electrons to enormous energies within a few millimetres.

To date, the innovative technology has had some drawbacks. “The electron bunches produced are not yet uniform enough,” explains Andreas Maier, lead scientist for plasma acceleration at DESY. “We would like each bunch to look precisely like the next one.” Another challenge concerns the energy distribution within a bunch. Figuratively speaking, some electrons fly faster than others which is unsuitable for practical applications. In modern accelerators, these problems have long been solved by using clever machine control systems.

Using a two-stage correction, the DESY team has now succeeded in significantly improving the properties of the electron bunches produced by their laser-plasma accelerator. To achieve this, electrons accelerated by the LUX plasma accelerator are sent through a chicane consisting of four deflecting magnets. By forcing the particles to take a detour, the pulses are stretched in time and sorted according to their energy. “After the particles have passed the magnetic chicane, the faster, higher-energy electrons are at the front of the pulse,” explains Paul Winkler, first author of the study. “The slower, relatively low-energy particles are at the back.”

The stretched and energy-sorted bunch is then sent into a single accelerator module similar to those used in modern radiofrequency-based facilities. In this resonator, the electron bunches are slightly decelerated or further accelerated. “If you time the beam arrival carefully to the radio frequency, the low-energy electrons at the back of the bunch can be accelerated and the high-energy electrons at the front can be decelerated,” explains Winkler. “This compresses the energy distribution.” The team was able to reduce the energy spread by a factor of 18 and the fluctuation in the central energy by a factor of 72. Both values are smaller than one permille making them comparable to those of conventional accelerators.

“This project is a fantastic example of the collaboration between theory and experiment,” says Wim Leemans, Director of the Accelerator Division at DESY. “The theoretical concept was recently proposed and has now been implemented for the first time.” Most of the components used were from existing DESY stocks. The project team had to invest a great effort in setting up the correction stage and synchronising the extremely rapid processes. “But once that was done things went surprisingly well,” says Winkler. “On the very first day when everything was set up, we switched on the system and immediately observed an effect.” After a few days of fine-tuning, it was clear that the correction system was working as intended.

Read more on DESY website

Image: Energy compression of a laser-plasma accelerated electron bunch in an active radiofrequency cavity: High-energy electrons at the beginning of the pulse are decelerated while low-energy electrons at the end of the bunch are accelerated. Image: Science Communication Lab for DESY

Cross-Facility Collaboration | Panel Discussion

Cross-Facility Collaboration | Panel Discussion

Do you participate in cross-facility collaborations? Are you interested in cross-facility collaborations, but encountering some roadblocks? Hear from staff at light sources around the world about how they work together on MLExchange, SciCat, PaNOSC, LEAPS, and more. Then, we’ll learn about existing resources and brainstorm ways to collaborate in the future.

Date: Tuesday, April 22, 2025

Time: 16:00 UK/BST or 17:00 Germany/CEST or 8:00 California/PDT

In-person:Diamond Light Source (Room: MR G59), Didcot, Oxfordshire, UK

Virtually: Zoom

Contact cindylee@lbl.gov and events@diamond.ac.uk with any questions.

REGISTER

Share your collaboration experiences with the panel in advance of the discussion by filling out this survey.

Panelists and Collaborations:

  • Sharif Ahmed, Diamond Light Source: Sharif Ahmed is the Principal Beamline Scientist for the DIAD beamline. His software collaborations focus on developing user-centric capabilities that enable novel measurement methods and easy “results” generation. Collaborations include MLExchange with Dylan McReynolds and the ALS Computing Group, the Ada Lovelace Centre, and The Faraday Institute. 
  • Andy Gotz, European Synchrotron Radiation Facility (ESRF): Andy Gotz is the coordinator of the Photon and Neutron Open Science Cluster (PaNOSC) collaboration which developed out of the PaNOSC and ESCAPE projects. He also chairs the Tango Controls collaboration for control systems (similar to EPICS) used by a number of synchrotrons and laser facilities.
    • Collaboration requires constant effort by a dedicated few to ensure it grows and is nurtured
    • Collaborations are often set up to achieve a higher purpose goal like “Open Science” but require concrete measurable outcomes with impact on the ground to be really useful
    • Collaborations can be strengthened through strong support from top management and being part of the facility objectives
    • Collaborations help facilities to achieve more with less resources and to learn from experience of other facilities
  • Cara Laasch, Stanford Synchrotron Radiation Lightsource (SSRL): Cara Laasch is the User Research Administration Manager at SSRL. Previously, she moderated the U.S. Department of Energy (DOE) Light & Neutron Sources Remote Access Forum. This was organized by the Remote Access Working Group, providing a connection point for the five DOE light sources.
  • Dylan McReynolds, Advanced Light Source (ALS): Dylan McReynolds is the Data Infrastructure Lead at the ALS. His collaborations include MLExchange with Sharif Ahmed, SciCat,  ILLUMINE and Bluesky. Dylan sits on the Bluesky Technical Steering Committee. He is a co-creator of the Tiled data service project, a multi-facility Bluesky collaboration.  
  • Elke Plönjes, Deutsches Elektronen-Synchrotron (DESY): Elke Plönjes is the Group Leader for Beamlines and Optics at the FLASH free electron laser. She is the Scientific Coordinator of the LEAPS-INNOV project, where League of European Accelerator-based Photon Sources (LEAPS) institutes are working with companies to develop new technologies.
  • Tim Snow, Diamond Light Source: Tim Snow is the Data Analysis Scientist working alongside the I22 beamline. His collaborations include MLExchange and SciCat.
  • Nick Terrill, Diamond Light Source: Nick Terrill is the Principal Beamline Scientist responsible for the SAXS instruments I22 and labSAXS as well as the SAXS Sample Environment Development Lab (SEDL). His work on sample environments and sample holders has facilitated collaboration across light sources.
  • Moderator: Cindy Lee, Senior Communications Specialist, Advanced Light Source (ALS)

Co-organizer: Silvana Westbury, Project Manager, Lightsources.org

Newly created molecules block cytokine storm

Newly created molecules block cytokine storm

Cytokine storms are potentially life-threatening overreactions of the immune system provoked by viral infection and other “threats.” Two key players are cytokines interleukin-6 (IL-6) and interleukin-1 (IL-1). Currently available inhibitors of IL-6 and IL-1 relieve the cytokine storm associated with rheumatoid arthritis, but not with COVID-19. 

Now, scientists from the University of Washington have computationally designed protein inhibitors that may prevent the COVID-19-related cytokine storm. X-ray crystallography revealed a near-perfect match between the computational designs and their real-life counterparts, which blocked the cytokine storm in a human heart organoid. This suggests that computational design has the power to create entirely new proteins that function as viable therapeutics against the cytokine storm associated with COVID-19. 

Researchers used the resources of the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory. 

Cytokine storm became a household term during the COVID-19 pandemic. Also known as cytokine release syndrome (CRS), this process happens when the immune system grossly overreacts to a threat and produces too many inflammatory immune cells. A cytokine storm can also be triggered by certain autoimmune diseases and CAR-T cell therapy.

The major players in a cytokine storm are cytokines IL-6 and IL-1. They bind to receptors on the surface of inflammatory immune cells, among others, sending signals to the cell’s DNA. These signals may activate the cell, amplify production of more inflammatory cells, or recruit cells to various locations. During a cytokine storm associated with COVID-19, too many inflammatory cells are activated and directed to the lungs and heart, where they can destroy tissue and cause fatal organ failure.

Binding is essential to the signal being sent; if there is no binding, there is no signal, and no cytokine storm. A few drugs on the market currently inhibit IL-6 and IL-1 binding, but they are better suited for long-term conditions like rheumatoid arthritis rather than short-term, acute events like COVID-19. To fill the void, a team of scientists led by 2024 Nobel Prize winner David Baker set out to design proteins from scratch that could effectively inhibit IL-6 and IL-1 binding. 

Both IL-6 and IL-1 rely on a third protein—GP130 in the case of IL-6, and an accessory protein in the case of IL-1—to send a signal when they bind with their receptors. The scientists used Rosetta, a proprietary protein design program, to create inhibitors that would occupy (a) binding sites on the IL-6 receptor, (b) the site on GP130 where IL-6 and its receptor would bind, and (c) the site on IL-1 where it would bind to both its receptor and the accessory protein.  

After generating their initial designs, the scientists tweaked them to improve the structure and amino acid sequence, then chose the top 100,000 candidates to test experimentally. First, they expressed the designs as real-life proteins in yeast cells. Then they optimized binding affinity by mutating each of the amino acids in the proteins. Finally, they used E. coli to express the optimized proteins. 

Read more on APS website

Image: Advances in computational design tools now enable functional proteins to be created from scratch.

Advancing Polarization-Sensitive Photodetection: The Potential of Naturally Anisotropic Tin Monochalcogenides

Advancing Polarization-Sensitive Photodetection: The Potential of Naturally Anisotropic Tin Monochalcogenides

A team of scientists from Wrocław University of Science and Technology, in cooperation with researchers from the URANOS beamline, conducted a series of experiments on layered semiconductors SnS and SnSe using photoemission spectroscopy. Their investigation revealed characteristic features of the electronic band structure, which influence the optical properties of these materials and their potential for near-infrared polarization-sensitive photodetectors.

Polarization-sensitive photodetectors play a crucial role in detecting changes in light polarization, which has applications ranging from liquid crystal technology to biological studies. Existing designs rely on complex optical components, but this study demonstrates that the natural anisotropy of tin monochalcogenides can significantly simplify device construction. This could lead to more efficient and compact photodetectors with polarization resolution.

The unique properties of SnS and SnSe stem from their distorted orthorhombic crystal structure, which introduces directionality in electronic band dispersion. This, in turn, affects their optical characteristics, enabling selective absorption of polarized light. The study also highlights the impact of lone electron pairs on the energy levels of these materials (determining parameters such as work function and ionization potential), which is crucial for the design of heterostructures and metal contacts. Compared to black phosphorus (BP), another anisotropic vdW crystal, SnS and SnSe offer superior stability in ambient conditions, making them more practical for real-world applications.


Read more on SOLARIS website