Egyptian mummy bones explored with X-rays and infrared light

Researchers from Cairo University work with teams at Berkeley Lab’s Advanced Light Source to study soil and bone samples dating back 4,000 years.

Experiments at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) are casting a new light on Egyptian soil and ancient mummified bone samples that could provide a richer understanding of daily life and environmental conditions thousands of years ago.
In a two-monthslong research effort that concluded in late August, two researchers from Cairo University in Egypt brought 32 bone samples and two soil samples to study using X-ray and infrared light-based techniques at Berkeley Lab’s Advanced Light Source (ALS). The ALS produces various wavelengths of bright light that can be used to explore the microscopic chemistry, structure, and other properties of samples.
Their visit was made possible by LAAAMP – the Lightsources for Africa, the Americas, Asia and Middle East Project – a grant-supported program that is intended to foster greater international scientific opportunity and collaboration for scientists working in that region of the globe.

>Read more on the Advanced Light Source (Berkeley Lab) website

Image: From left, Cairo University postdoctoral researcher Mohamed Kasem, ALS scientist Hans Bechtel, and Cairo University associate professor Ahmed Elnewishy study bone samples at the ALS using infrared light.
Credit: Marilyn Sargent/Berkeley Lab

Using European XFEL to shed light on photosynthesis

First membrane protein studied at European XFEL

In a paper now published in Nature Communications an international group of scientists show that the fast X-ray pulse rate produced by the European XFEL can be used to study the structure of membrane proteins such as those involved in the process of photosynthesis. These results open up eagerly awaited experimental opportunities for scientists studying these types of proteins.

Large proteins and protein complexes are difficult to study with traditional structural biology approaches. Large protein complexes, such as those that sit across cell membranes and regulate traffic in and out of cells, are difficult to crystalize and generally only produce small crystals that are hard to analyse. The extremely fast X-ray pulses generated by European XFEL now enable scientists to collect large amounts of data from a stream of small crystals to develop detailed models of the 3D structure of these proteins.

>Read more on the European XFEL website

Image (extract, full illustration in the article): Graphic shows the basic design of a serial femtosecond crystallography experiment at European XFEL. X-ray bursts strike crystallized samples resulting in diffraction patterns that can be reassembled into detailed images.
Credit: Shireen Dooling for the Biodesign Institute at ASU

Machine learning enhances light-beam performance at the ALS

Successful demonstration of algorithm by Berkeley Lab-UC Berkeley team shows technique could be viable for scientific light sources around the globe.

Synchrotron light sources are powerful facilities that produce light in a variety of “colors,” or wavelengths – from the infrared to X-rays – by accelerating electrons to emit light in controlled beams.
Synchrotrons like the Advanced Light Source at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) allow scientists to explore samples in a variety of ways using this light, in fields ranging from materials science, biology, and chemistry to physics and environmental science. Researchers have found ways to upgrade these machines to produce more intense, focused, and consistent light beams that enable new, and more complex and detailed studies across a broad range of sample types. But some light-beam properties still exhibit fluctuations in performance that present challenges for certain experiments.

Image: This image shows the profile of an electron beam at Berkeley Lab’s Advanced Light Source synchrotron, represented as pixels measured by a charged coupled device (CCD) sensor. When stabilized by a machine-learning algorithm, the beam has a horizontal size dimension of 49 microns (root mean squared) and vertical size dimension of 48 microns (root mean squared). Demanding experiments require that the corresponding light-beam size be stable on time scales ranging from less than seconds to hours to ensure reliable data.
Credit: Lawrence Berkeley National Laboratory

Operando X-ray diffraction during laser 3D printing

Additive manufacturing, a bottom-up approach for manufacturing components layer by layer from a 3D computer model, plays a key role in the so-called “fourth” industrial revolution. Selective laser melting (SLM), one of the more mature additive manufacturing processes, uses a high power-density laser to selectively melt and fuse powders spread layer by layer. The method enables to build near full density functional parts and has viable economic benefits. Despite significant progress in recent years, the relationship between the many processing parameters and final microstructure is not well understood, which strongly limits the number of alloys that can be produced by SLM for commercial applications.

>Read more on the Swiss Light Source (PSI) website

Image: Rendered 3D model of the MiniSLM device.

First structure of a DNA crosslink repair ligase determined

Diamond’s Electron Bio-Imaging Facility (eBIC) has been used to generate the first 3D structure of the Fanconi anaemia (FA) core complex, a multi-subunit E3 ubiquitin ligase required for the repair of damaged DNA. The work, led by Dr Lori Passmore from the MRC Laboratory of Molecular Biology and a team of researchers, has been published today in Nature, and their research provides the molecular architecture of the FA core complex and new insights into how the complex functions.

The FA pathway senses and repairs DNA crosslinks that occur after exposure to chemicals including chemotherapeutic agents and alcohol, but also as a result of normal cellular metabolism. The megadalton FA core complex acts as an E3 ubiquitin ligase to initiate removal of these DNA crosslinks, helping to repair the damage caused. The research team used eBIC’s imaging facilities to make a major breakthrough in understanding the FA core complex by determining its structure using an integrative approach including cryo-electron microscopy and mass spectrometry.

Dr Peijun Zhang, Director of eBIC notes that:

Enabling cutting-edge research like this is exactly why we established eBIC, to provide scientists with state-of-the-art experimental equipment and expertise in the field of cryo-electron microscopy, for both single particle analysis and cryo-electron tomography. Determining the structure of the FA core complex for the first time is a fantastic achievement for the MRC research team.

>Read more on the Diamond Light Source website

Image: The FA core complex.
Credit: Phospho Biomedical Animation

Welcome back users!

This month marks the official start of user operation at CHESS and all three partner programs: The NSF funded CHEXS, as well as MacCHESS supported by NIH and NYSTAR, and the Materials Solutions Network at CHESS, or MSN-C, funded by the Air Force Research Lab (AFRL), all welcomed users to new hutches and beamlines. 

Louise Debefve stands outside a hutch on the experimental floor of the Cornell High Energy Synchrotron Source, CHESS. She is preparing the experimental equipment for some of the first data to be collected at CHESS since the completion of the CHESS-U upgrade. The platinum samples that she is about to study at the new beamlines will provide insights into the catalytic function of the element, enabling for example the generation of cleaner energy powering everything from cars to laptops.

But for now, Louise is happy to just be using the X-rays again, a familiar occurrence for the former graduate student, who spent years developing her research of catalysts through the use of X-rays at SSRL. As a postdoc at CHESS, Louise initially found herself right in the middle of the feverish construction of the upgrade, with no X-rays available for research.

>Read more on the CHESS website

Image: Louise Debefve, right, works with Chris Pollock and Ken Finkelstein at the new PIPOXS station.

The mechanism of the most commonly used antimalarial drugs unveiled

For centuries, quinoline has been an effective compound in antimalarial drugs, although no one knew its mode of action in vivo.

Today, a team led by the Weizmann Institute has discovered its mechanism in infected red blood cells in near-native conditions, by using the ESRF, Alba Synchrotron and BESSY. They publish their results in PNAS.

Malaria remains one of the biggest killers in low-income countries. Estimates of the number of deaths each year range from 450,000 to 720,000, with the majority of deaths happening in Africa. In the last two decades, the malaria parasite has evolved into drug-resistant strains. “Recently, the increasing geographical spread of the species, as well as resistant strains has concerned the scientific community, and in order to improve antimalarial drugs we need to know how they work precisely”, explains Sergey Kapishnikov, from the University of Copenhagen, in Denmark, and the Weizmann Institute, in Israel, and leader of the study.

Plasmodium parasite, when infecting a human, invades a red blood cell, where it ingests hemoglobin to grow and multiply. Hemoglobin releases then iron-containing heme molecules, which are toxic to the parasite. However, these molecules crystallise into hemozoin, a disposal product formed from the digestion of blood by the parasite that makes the molecules inert. For the parasite to survive, the rate at which the heme molecules are liberated must be slower or the same as the rate of hemozoin crystallization. Otherwise there would be an accumulation of the toxic heme within the parasite.

>Read more on the ESRF website

Image (taken from BESSY II article): The image shows details such as the vacuole of the parasites (colored in blue and green) inside an infected blood cell.
S. Kapishnikov

Two other institutes, BESSY II at HZB and ALBA Synchrotron, have participated in this research. Please find here their published articles:

> X-ray microscopy at BESSY II reveal how antimalaria-drugs might work

> The mechanism of the most commonly used antimlalarial drugs in near- native conditions unveiled

Multimodal study of ion-conducting membranes

Using multiple x-ray characterization tools, researchers showed how chemical and structural changes improve the performance of a novel ion-conducting polymer (ionomer) membrane from 3M Company.

In fuel cells (which generate clean power from hydrogen fuel) and electrolyzers (water-splitting devices that produce hydrogen fuel), positive and negative electrodes are separated by membranes composed of ion-conducting polymers (ionomers). These membranes prevent contact between the electrodes—thus avoiding catastrophic failure—while allowing selective passage of ions to complete the circuit.

Generally, such membranes are based on a class of perfluorosulfonic acid (PFSA) ionomers with remarkable proton conductivity and stability. Recently, however, companies such as 3M have been developing new ionomers with improved performance. In this work, researchers took a closer look at the structural and chemical properties of these materials at the nanometer scale. The resulting insights provide valuable guidance on design strategies for optimally performing ionomers.

>Read more on the Advanced Light Source website

Image: Resonant x-ray scattering (RXS) and x-ray absorption spectroscopy (XAS) with elemental sensitivity unravel structural features and chemical factors affecting morphology and ion transport in proton-conducting membranes.

NSLS-II celebrates its 5th anniversary

In just five years, 28 beamlines came online, over 1,800 different experiments ran, and nearly 3,000 scientists conducted research at the National Synchrotron Light Source II.

On this day five years ago, the National Synchrotron Light Source II (NSLS-II) achieved “first light”—its first successful delivery of x-ray beams. Signaling the start of operations at NSLS-II—one of the world’s most advanced synchrotron light sources—Oct. 23, 2014 marked a new era of synchrotron science.

“It is astonishing to me how much we have accomplished in just five years,” said NSLS-II Director John Hill. “Every day when I come to work, I am proud of what we have achieved through the expertise, dedication and passion that everyone here brings to NSLS-II.”

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

Image: An aerial view of NSLS-II. The facility is large enough to fit Yankee Stadium inside its half-mile-long ring.


First delivery of single-bunch electron beam to the 1.5 GeV ring

The 22 October at lunchtime, the first single-bunch electron beam was delivered to the 1.5 GeV storage ring at MAX IV and put to use at the FinEstBeAMS beamline.

These are still preliminary trials and the response from FinEstBeAMS will determine the path forward.

Normally the electrons in the storage rings come in so-called multi-bunch formation. You could think of this as several locomotives with many wagons travelling around the ring. In single-bunch mode, there is only one locomotive “on the track”. The abstract of Christian Strålman’s PhD thesis On the Challenges for Time-of-Flight Electron Spectroscopy at Storage Rings gives a good overview of the topic in Swedish.

The single-bunch mode will give the scientists access to a wider portfolio of measurement techniques in several research areas such as atmospheric chemistry, environmental science (in particular renewable energy sources), molecular reaction dynamics, cluster chemistry and physics, materials science, chemistry–chemical reactions at surfaces or in solution and photocatalysis.

>Read more on the MAX IV website

Image (extract):A screenshot of a scope measurement of the current in the ring, where you can clearly see the strong single-bunch signal. See full image here.

Suspending sample droplets with sound waves

TinyLev offers a cheap and portable way to use acoustic levitation at synchrotron beamlines.

Acoustic levitation suspends matter using acoustic radiation pressure to balance the force of gravity. It has potential applications in crystallography, spectroscopy, chemistry, and the study of organisms in microgravity. However, conventional acoustic levitation systems rely on Langevin horns, which are large and expensive pieces of equipment that are complicated to set up. TinyLev, initially developed by researchers at the University of Bristol, is a small single-axis non-resonant acoustic levitator constructed from off-the-shelf components. In work recently published in Scientific Reportsengineers at Diamond led by Dr Pete Docker used the TinyLev system to dispense and contain sample droplets in protein crystallography experiments. Their novel method facilitates efficient X-ray data acquisition in dynamic studies at room temperature.

>Read more on the Diamond Light Source website

Picture: Left: Photograph showing the TinyLev system mounted on the I24 beamline with the X-ray beam path marked with a yellow dashed arrow. Components as labelled: (A) High-magnification viewing system, (B) X-ray scatter-guard, (C) levitating drop, (D) beamstop (out of position), (E) TinyLev Transducer array, (F) backlight (retracted during data collection), (G) sample positioning stage. Right: Model of the acoustic levitation system (E) used in this work annotated with key dimensions and showing the focal point of the transducer array.

Researchers find what makes chocolate melt in your mouth

Scientists use X-rays to see the true nature of chocolate.

The taste of a silky piece of rich chocolate is one of life’s great pleasures, and producing a smooth mouthfeel is an aspiration of every serious chocolatier.  The characteristics that truly set haute chocolate apart can be seen at the microscale thanks to recent, pivotal research performed by researchers from the University of Guelph at the Advanced Photon Source (APS) located at the U.S. Department of Energy’s (DOE) Argonne National Laboratory.

In a series of studies, University of Guelph researcher Fernanda Peyronel used a technique called ultra-small-angle x-ray scattering (USAXS) to investigate a property called fractal dimension, a particular feature of the geometric configuration of tiny particles of chocolate. “Basically, we’re trying to see whether these particles have a more open or a more closed structure and to correlate that to the mouthfeel experienced by consumers,” Peyronel said.

The USAXS technique allows scientists to resolve particles that range in size from a few hundred nanometers to around 10 micrometers — roughly the limit at which our taste buds can distinguish different textures. The beamline at the APS also accommodates detectors for small-angle x-ray scattering as well as large-angle x-ray scattering. These allow scientists to study their systems from less than a nanometer to around 10 micrometers.

>Read more on the APS at Argonne website

Progress on Project Bright beamlines

The complex engineering of scientific instruments is explored in this ‘behind the scenes’ look at the installation of frontends for two new beamlines at the Australian Synchrotron.

Good progress has been made on the installation of supporting infrastructure for the first of the new beamlines for the Australian Synchrotron as part of Project Br–ght.
The work is a series of complex engineering tasks that require precise planning, the expertise of applied mechanical engineering, controls engineering and supporting technicians.
Importantly, the majority of installation works could only be done during periods when the synchrotron was not operational.

Installation of the ‘frontends’ for two new beamlines, Medium Energy X-ray Absorption Spectroscopy (MEX) and Biological Small Angle X-ray Scattering (BioSAX) is now complete with final commissioning tasks on schedule. Completion is expected during the coming Christmas shutdown, according to Senior Engineering Manager Brad Mountford.
The ‘frontend” is the physical conduit that carries powerful synchrotron light from the main storage ring through the shield wall that surrounds the ring.

>Read more on the Australian Synchrotron (ANSTO) website

>Discover the Project BR-GHT here

Developing more nutritious crops to feed a growing world

Using synchrotron light to analyze new varieties of peas could be faster, more environmentally friendly, and help to nourish underfed populations around the world.

With thousands of seed samples produced every growing season, Dr. Tom Warkentin needs fast, accurate and cost-effective techniques to assess the nutritional value of the pea varieties he has developed. Now, thanks to two recent studies, techniques available at the Canadian Light Source (CLS) synchrotron at the University of Saskatchewan show promise for Warkentin and many other plant breeders.

“These studies arose from the question, ‘Can we use the synchrotron to measure the nutrient traits in pea seeds?,’” explained Warkentin, professor of plant science and pulse breeder in the Crop Development Centre at the University of Saskatchewan’s College of Agriculture and Bioresources. “Improving the nutritional value of peas is a higher and higher priority for us in plant breeding so we wanted to look at the standard approaches we’ve been using to measure nutritional traits versus the techniques available at the CLS.”

>Read more on the Canadian Light Source website

Image: Scientists Tom Warkentin, Chithra Karunakaran, Jarvis Stobbs, and David Muir with pea samples at our IDEAS beamline.

NSLS-II scientist named DOE Office of Science Distinguished Fellow

Scientists from the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have garnered two out of five “Distinguished Scientists Fellow” awards announced today by the DOE’s Office of Science.

Theoretical physicist Sally Dawson, a world-leader in calculations aimed at describing the properties of the Higgs boson, and José Rodriguez, a renowned chemist exploring and developing catalysts for energy-related reactions, will each receive $1 million in funding over three years to pursue new research objectives within their respective fields. (…)

José Rodriguez (NSLS-II)

For discoveries of the atomic basis of surface catalysis for the synthesis of sustainable fuels, and for significantly advancing in-situ methods of investigation using synchrotron light sources.”

Rodriguez will devote his funding to the development and construction of new tools for performing extremely rapid, time-resolved measurements to track the reaction mechanisms of catalytic processes as they occur under variable conditions—like those encountered during real-world reactions important to energy applications. These include processes on metal-oxide catalysts frequently used in the production of clean fuels and other “green” chemicals through hydrogenation of carbon monoxide and carbon dioxide, or the conversion of methane to hydrogen.

“At a microscopic level, the structure of a catalyst and the chemical environment around the active sites—where chemical bonds are broken and reformed as reactants transform into new products—change as a function of time, thus determining the reaction mechanism,” said Rodriguez. “We can learn a lot about the nature of the active sites under steady-state conditions, with no variations in temperature, pressure, and reaction rate. But to really understand the details of the reaction mechanism, we need ways to track what happens under transient or variable conditions. This funding will allow us to build new instrumentation that works with existing capabilities so we can study catalysts under variable conditions—and use what we learn to improve their performance.”

>Read more on the NSLS-II website

Dynamic pattern of skyrmions observed

Tiny magnetic vortices known as skyrmions form in certain magnetic materials, such as Cu2OSeO3.

These skyrmions can be controlled by low-level electrical currents – which could facilitate more energy-efficient data processing. Now a team has succeeded in developing a new technique at the VEKMAG station of BESSY II for precisely measuring these vortices and observing their three different predicted characteristic oscillation modes (Eigen modes).

Cu2OSeO3 is a material with unusual magnetic properties. Magnetic spin vortices known as skyrmions are formed within a certain temperature range when in the presence of a small external magnetic field. Currently, moderately low temperatures of around 60 Kelvin (-213 degrees Celsius) are required to stabilise their phase, but it appears possible to shift this temperature range to room temperature. The exciting thing about skyrmions is that they can be set in motion and controlled very easily, thus offering new opportunities to reduce the energy required for data processing.

>Read more on the BESSY II at HZB website

Image: The illustration demonstrates skyrmions in one of their Eigen modes (clockwise).
Credit: Yotta Kippe/HZB