Safely studying dangerous infections just got a lot easier

An extremely fast new 3D imaging method can show how cells respond to infection and to possible treatments

To combat a pandemic, science needs to move quickly. With safe and effective vaccines now widely available and a handful of promising COVID-19 treatments coming soon, there’s no doubt that many aspects of biological research have been successfully accelerated in the past two years.

Now, researchers from Lawrence Berkeley National Laboratory (Berkeley Lab) and Heidelberg University in Germany have cranked up the speed of imaging infected cells using soft X-ray tomography, a microscopic imaging technique that can generate incredibly detailed, three-dimensional scans.

Their approach takes mere minutes to gather data that would require weeks of prep and analysis with other methods, giving scientists an easy way to quickly examine how our cells’ internal machinery responds to SARS-CoV-2, or other pathogens, as well as how the cells respond to drugs designed to treat the infection.

“Prior to our imaging technique, if one wanted to know what was going on inside a cell, and to learn what changes had occurred upon an infection, they’d have to go through the process of fixing, slicing, and staining the cells in order to analyze them by electron microscopy. With all the steps involved, it would take weeks to get the answer. We can do it in a day,” said project co-lead Carolyn Larabell, a Berkeley Lab faculty scientist in the Biosciences Area. “So, it really speeds up the process of examining cells, the consequences to infection, and the consequences of treating a patient with a drug that may or may not cure or prevent the disease.”

Taking cellular freeze frames

Larabell is a professor of anatomy at UC San Francisco and director of the National Center for X-Ray Tomography, a facility based at Berkeley Lab’s Advanced Light Source (ALS). The facility’s staff developed soft X-ray tomography (SXT) in the early 2000s to fill in the gaps left by other cellular imaging techniques. They currently offer the SXT to investigators worldwide and continue to refine the approach. As part of a study published in Cell Reports Methods late last year, she and three colleagues performed SXT on human lung cell samples prepared by their colleagues at Heidelberg University and the German Center for Infection Research.

Read more on the Berkeley Lab website

Image: Digital images of cells infected with SARS-CoV-2, created from soft X-ray tomography taken of chemically fixed cells at the Advanced Light Source

Credit: Loconte et al./Berkeley Lab

Metal-Organic Frameworks can capture toxic air pollutants

The air that we breathe

According to the World Health Organisation1 (WHO), 92% of people worldwide live in places with poor air quality, and outdoor air pollution causes 4.2 million deaths a year, with another 3.8 million caused by indoor air pollution.

Figures published by Public Health England2 showed that the health and social care costs of air pollution in England alone were £42.88 million in 2017 and could reach £5.3 billion by 2035.

There are many different types of air pollution, which arise from a wide range of sources. In the UK, five types are of particular concern: 

  1. The mixture of liquid droplets and solid particles found in the air is called particulate matter (PM). Some PM comes from natural sources (e.g., pollen, sea spray and desert dust), but it also includes dust from car exhausts, brakes and tyres and smoke. PM is classified according to size, with PM2.5 (particles less than 2.5 micrometres across) able to reach and damage the lungs and other organs.
  2. Volatile organic compounds (VOCs) are a range of organic molecules that display similar behaviour in the atmosphere. These include vapours from household products such as air fresheners, cleaning products and perfumes, as well as petrol and solvents.
  3. Ammonia (NH3) gas is mainly released from agricultural sources such as slurry, other rotting farm waste and fertilisers.
  4. Nitrogen oxide (NOx) gases, including nitrogen dioxide (NO2), are mainly created by burning fossil fuels. 
  5. Sulphur dioxide (SO2) is an acidic gas that can irritate airways, particularly in people with asthma.

SO2 and NO2 are both reactive, corrosive gases. Removing them from the air is challenging but would have enormous benefits for human health. 

Can we clean up our act with MOFs?

Metal-Organic Frameworks (MOFs) are sponge-like materials that can adsorb and hold “guest” molecules. By fine-tuning their properties – pore size and geometry, framework topology and chemical functionality – they can be tailored for specific applications, including gas adsorption, separation, catalysis, substrate binding and delivery. MOFs containing open metal sites (OMSs), in particular, can provide highly selective adsorption of target gases. 

However, stable MOFs with OMSs are rare, as are MOF materials that can reversibly adsorb SO2 and NO2. While there are already over 100,000 known MOFs (and over half a million structures have so far been predicted), screening each one individually for its suitability for this application would be time-consuming and costly. A far better approach is to improve our understanding of the mechanism of active sites within capture materials so that we can design or discover new functional MOF materials. This in itself is a challenging task, as host-guest interactions are often dynamic processes, where multiple binding sites of similar energies affect the movement of guest molecules in the pores.

Using synchrotron techniques, an international team of researchers has described the synthesis, crystal structure and gas adsorption and separation properties of a unique {Ni12}- wheel-based MOF that exhibits high isothermal uptake of SO2 and NO2.

Using single crystal X-ray diffraction (SCXRD) at the Advanced Light Source in California and infrared (IR) single crystal micro-spectroscopy at Diamond’s B22 beamline, the team performed dynamic breakthrough experiments that confirmed the selective retention of SO2 and NO2 at low concentrations under dry conditions. Their results show, at a crystallographic resolution, a detailed molecular mechanism with reversible coordination of SO2 and NO2 at the six open Ni(II) sites on the {Ni12}-wheel and at oxygen atom and ligand sites. 

Read more on the Diamond website

Image: Artist’s impression of the unique {Ni12}- wheel-based MOF in action, exhibiting high isothermal uptake of SO2 and NO2.

Credit: Dr Sihai Yang

More to life than light

The #LightSourceSelfies video campaign highlights the dedication and enthusiasm that is felt by those working in this field. To maintain a sense of physical and mental wellbeing, it is also important to make time for non-work related things like family, hobbies and interests. This montage, with contributors from the ESRF, ALS, MAX IV and Diamond, gives a flavour of the wide range of activities that those in the light source community enjoy when they are not working.


Experimental time at light sources is very precious. When a synchrotron or X-ray Free Electron Laser (XFEL) is in operating mode the goal is to allocate as many experimental shifts to external scientists and in-house research as possible. This includes night shifts! So, how do light source users survive the night shifts? #LightSourceSelfies brings you top tips from scientists based at, or using, 5 light sources in our collaboration – the ESRF, Advanced Light Source (ALS), ANSTO’s Australian Synchrotron, CHESS and the PAL XFEL.

A recipe for successful science

Synchrotrons and free electron lasers (FELs) look stunning. The experimental equipment is state-of-the-art, which makes being a light source user both exhilarating and nerve racking. A key ingredient for success is excellent support from the beamline staff on the experimental station you are using. As Kuda Jakata, a postdoc who supports users at the ESRF in Grenoble, France, says in this #LightSourceSelfie, “The light sources community, they are very helpful people and they actually want to push boundaries and so they work hard and they do a lot of really interesting science.”

#LightSourceSelfies Monday Montage!

Unexpected Transformations Reinforce Roman Concrete

Researchers used the Advanced Light Source (ALS) to study binding phases in Roman architectural concrete, revealing reactions and profound transformations that contribute to the material’s long-term cohesion and durability.

The findings add to our growing understanding of cementing processes in Roman concretes, informing resilient materials of the future.

Marie Jackson, a research associate professor at the University of Utah, has devoted much of her career to understanding the scientific mysteries underlying the exceptional durability of Roman concretes. The ALS has been essential to her and her colleagues’ studies, helping to reveal the chemical and microstructural evolution of the materials.

Concrete is made of rock aggregates and a binder. Modern concretes typically use Portland cement—made by burning a mixture of limestone and clay at high temperature—as binder. Roman concretes, in contrast, consist of coarse volcanic rock (or brick) aggregate bound with mortar made from hydrated lime and reactive tephra—the particles ejected from explosive volcanic eruptions.

In this study, Jackson, along with collaborators Admir Masic and Linda Seymour of the Massachusetts Institute of Technology and Nobumichi Tamura of the ALS, examined mortar samples from the Tomb of Caecilia Metella in Rome. The team hoped that the 2,050-year-old monument would provide insights into how Roman builders’ selections of reactive volcanic rock influenced the material characteristics of the very robust concrete.

Read more on the ALS website

Image: The Tomb of Caecilia Metella on the Via Appia Antica in Rome. The edifice is one of the most refined concrete and dimension stone structures of the latest Roman Republican era.

Credit: Emmanuel Brunner

Preparing yourself for setbacks

Experimental time at light sources is precious. It can also be unpredictable as Ro-Ya Liu, a Beamline Scientist at NSRRC in Taiwan, discovered during her first synchrotron experiment at the Photon Factory in Japan. As setbacks go it was a pretty dramatic one, as you’ll discover in this #LightSourceSelfie. Quinn Carvalho, a PhD student at Oregon State University and a user at the Advanced Light Source (ALS) in California, advises light sources users to, “Go into anything with a healthy mentality of optimism, but a realistic sense of what will go wrong. Things will go wrong and you will have to overcome those, so being able to face failure and embrace it and learn from it is much more valuable than fearing it, I think.”

A scientist’s life: At the edge of what is known

Quinn Carvalho is a PhD student at Oregon State University and a user at the Advanced Light Source (ALS) at Lawrence Berkeley National Lab in California. Quinn and his colleagues are using spectroscopic techniques to develop design strategies for electrocatalysts that will provide the resources we need for a carbon-free world. In his #LightSourceSelfie, Quinn shares what excites him about his research and his experiences on the support provided by beamline staff at the ALS. Reflecting on what drives him as a research scientist, Quinn explains, “That moment when you realise that you’re the first person to observe, measure and describe a physical phenomenon is one of the greatest sensations I’ve experienced as a professional and something that motivates me still to this day.”

Beginning your light source journey

Scientists who use synchrotrons such as the Advanced Light Source in California and CHESS at Cornell University, along with staff scientists at Free Electron Lasers in South Korea (the PAL-XFEL) and California (LCLS at SLAC), reflect on how they felt the first time they used a light source facility to conduct research experiments.  The expertise available from the staff scientists who work on the beamlines is also highlighted in this #LightSourceSelfie video.

Secrets of skyrmions revealed

Why skyrmions could have a lot in common with glass and high-temperature superconductors

Spawned by the spins of electrons in magnetic materials, these tiny whirlpools behave like independent particles and could be the future of computing. Experiments with SLAC’s X-ray laser are revealing their secrets.

Scientists have known for a long time that magnetism is created by the spins of electrons lining up in certain ways. But about a decade ago, they discovered another astonishing layer of complexity in magnetic materials: Under the right conditions, these spins can form little vortexes or whirlpools that act like particles and move around independently of the atoms that spawned them.

The tiny whirlpools are called skyrmions, named after Tony Skyrme, the British physicist who predicted their existence in 1962. Their small size and sturdy nature – like knots that are hard to undo – have given rise to a rapidly expanding field devoted to understanding them better and exploiting their strange qualities.

“These objects represent some of the most sophisticated forms of magnetic order that we know about,” said Josh Turner, a staff scientist at the Department of Energy’s SLAC National Accelerator Laboratory and principal investigator with the Stanford Institute for Materials and Energy Sciences (SIMES) at SLAC.

Read more on the SLAC website

Images: Top: Images based on simulations show how three phases of matter, including skyrmions – tiny whirlpools created by the spins of electrons – can form in certain magnetic materials. They are stripes of electron spin (left); hexagonal lattices (right); and an in-between phase (center) that’s a mixture of the two. In this middle, glass-like state, skyrmions move very slowly, like cars in a traffic jam – one of several discoveries made in recent studies by scientists at SLAC, Stanford, Berkeley Lab and UC San Diego. Bottom: Patterns formed in a detector during experiments that explored fundamentals of skyrmion behavior at SLAC’s Linac Coherent Light Source X-ray free-electron laser.

Credit: Esposito et al., Applied Physics Letters, 2020

A new approach creates an exceptional single-atom catalyst for water splitting

Anchoring individual iridium atoms on the surface of a catalytic particle boosted its performance in carrying out a reaction that’s been a bottleneck for sustainable energy production.

A new way of anchoring individual iridium atoms to the surface of a catalyst increased its efficiency in splitting water molecules to record levels, scientists from the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University reported today.

It was the first time this approach had been applied to the oxygen evolution reaction, or OER ­–part of a process called electrolysis that uses electricity to split water into hydrogen and oxygen. If powered by renewable energy sources, electrolysis could produce fuels and chemical feedstocks more sustainably and reduce the use of fossil fuels. But the sluggish pace of OER has been a bottleneck to improving its efficiency so it can compete in the open market.

The results of this study could ease the bottleneck and open new avenues to observing and understanding how these single-atom catalytic centers operate under realistic working conditions, the research team said.

They published their results today in the Proceedings of the National Academy of Sciences.

Read more on the SLAC website

Image: An illustration depicts a new system developed at SLAC and Stanford that anchors individual iridium atoms to the surface of a catalyst, increasing its efficiency at splitting water to record levels. The eight-sided support structures, shaded in blue, each contain a single iridium atom (large blue spheres). The iridium atoms grab passing water molecules (floating above and to the left of them), and encourage them to react with each other, releasing oxygen molecules (above and to the right). This reaction, known as the oxygen evolution reaction or OER, plays a key role in producing sustainable fuels and chemicals.

Credit: Greg Stewart/SLAC National Accelerator Laboratory

A powerful infrared technique broadens its horizons

Infrared light has the right energy range to probe many interesting material properties, including the vibrational modes of molecules and the way electrons interact with external photons. As devices get smaller and faster, the ability to study the way light and matter interact at the nanoscale will become crucial for the development of quantum and microelectronic technologies.

A powerful infrared method for probing such phenomena is called scattering-type scanning near-field optical microscopy (s-SNOM), which uses the tip of an atomic force microscope (AFM) to focus infrared light down to about 10 nm, below the wavelength of the light itself (i.e., below the diffraction limit). However, because of the elongated geometry of the AFM tip, oriented perpendicular to the sample, s-SNOM is less sensitive to features of interest that lie parallel to the sample surface.

“Probing in-plane responses at the subwavelength scale has been a long-time hurdle for the technique,” said Ziheng Yao, a former ALS doctoral fellow and co-first author of a Nature Communications paper that reports on a way around this hurdle. “With our results, we can get not only the the top view of the object, but also the side views.”

At ALS Beamline 2.4, the researchers used s-SNOM to study samples of sapphire and LiNbO3, two well-characterized, prototypical materials suitable for a proof-of-concept demonstration. Both have a property (the dielectric function) that varies along different in-plane crystal axes.

Read more on the ALS website

Image: Schematic of the s-SNOM nanospectroscopy setup and the crystal orientation of the sample (a, b, and c axes). Red arrow indicates the in-plane component of the incident light, kin-plane. Rotating the sample changes θ, the angle between kin-plane and the c-axis. Inset: Image of the gold disk on sapphire (m-cut Al2O3). Sdark and Sbright are the two locations were spectra were collected. Scale bar = 1 µm.

Credit: Xinzhong Chen and Ziheng Yao/Stony Brook University

When vibrations increase on cooling: Anti-freezing observed

An international team has observed an amazing phenomenon in a nickel oxide material during cooling: Instead of freezing, certain fluctuations actually increase as the temperature drops. Nickel oxide is a model system that is structurally similar to high-temperature superconductors. The experiment, which was carried out at the Advanced Light Source (ALS) in California, shows once again that the behaviour of this class of materials still holds surprises.

In virtually all matter, lower temperatures mean less movement of its microscopic components. The less heat energy is available, the less often atoms change their location or magnetic moments their direction: they freeze. An international team led by scientists from HZB and DESY has now observed for the first time the opposite behaviour in a nickel oxide material closely related to high-temperature superconductors. Fluctuations in this nickelate do not freeze on cooling, but become faster.

Read more on the HZB website

Image: The development of this speckle pattern over time reveals microsocopic fluctuations in the material.

Credit: © 10.1103/PhysRevLett.127.057001

Main Attraction: Scientists Create World’s Thinnest Magnet

The development of an ultrathin magnet that operates at room temperature could lead to new applications in computing and electronics – such as high-density, compact spintronic memory devices – and new tools for the study of quantum physics.

The ultrathin magnet, which was recently reported in the journal Nature Communications, could make big advances in next-gen memory devices, computing, spintronics, and quantum physics. It was discovered by scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley.

“We’re the first to make a room-temperature 2D magnet that is chemically stable under ambient conditions,” said senior author Jie Yao, a faculty scientist in Berkeley Lab’s Materials Sciences Division and associate professor of materials science and engineering at UC Berkeley.

“This discovery is exciting because it not only makes 2D magnetism possible at room temperature, but it also uncovers a new mechanism to realize 2D magnetic materials,” added Rui Chen, a UC Berkeley graduate student in the Yao Research Group and lead author on the study.

Read more on the ALS website

Image: Illustration of magnetic coupling in a cobalt-doped zinc-oxide monolayer. Red, blue, and yellow spheres represent cobalt, oxygen, and zinc atoms, respectively.

Credit: Berkeley Lab

Scientists uncover a different facet of fuel-cell chemistry

Solid oxide fuel cells (SOFCs) are a promising technology for cleanly converting chemical energy to electrical energy. But their efficiency depends on the rate at which solids and gases interact at the devices’ electrode surfaces. Thus, to explore ways to improve SOFC efficiency, an international team led by researchers from Berkeley Lab studied a model electrode material in a new way—by exposing a different facet of its crystal structure to oxygen gas at operating pressures and temperatures.

“We began by asking questions like, could different reaction rates be achieved from the same material, just by changing which surface the oxygen reacts with?” said Lane Martin, a faculty scientist in Berkeley Lab’s Materials Sciences Division. “We wanted to examine how the atomic configuration at specific surfaces of these materials makes a difference when it comes to reacting with the oxygen gas.”

Thin films of a common SOFC cathode material, La0.8Sr0.2Co0.2Fe0.8O3 (LSCF), were epitaxially grown to expose a surface that was oriented along a diagonal crystallographic plane. Electrochemical measurements on this atypical surface yielded oxygen reaction rates up to three times faster than those measured on the usual horizontal plane.

To better understand the mechanisms underlying this improvement, the researchers used Advanced Light Source (ALS) Beamline 9.3.2 to perform ambient-pressure spectroscopy experiments at high temperatures and in varying pressures of oxygen. The results, combined with first-principles calculations, revealed that different crystallographic planes stabilize different surface chemistries, even though the bulk chemistry of the films is identical.

Read more on the ALS website

Image: A model SOFC cathode material adsorbs oxygen molecules (purple spheres) at vacancy sites, an important step in the electrochemical reaction taking place in fuel cells. Ambient-pressure experiments at the ALS allowed measurement of the surface chemical and electronic interactions at high temperature so that researchers could “see” the adsorption of oxygen at it happens. Light blue = La, dark blue = Sr, red = lattice O or O2 molecules, purple = adsorbed O2 molecules.

Credit: Abel Fernandez/UC Berkeley