Protecting communities from toxic mine waste

Imagine an abandoned mine site, surrounded by dead trees and dotted with dark, red ponds with no signs of aquatic life. This is the result of mine waste left in the environment that gets weathered by water and air. With exposure to the elements over time, the waste produces toxic substances such as arsenic and lead.

“It is a major environmental problem facing the mining industry in Canada and worldwide,” said Aria Zhang, who studied a method for covering mine tailings as part of her Master’s degree at the University of Waterloo. “Once these toxins are released, it’s difficult to control. It pollutes the soil and seeps into lakes and groundwater. It can threaten people’s drinking water supply, agricultural production, and the ecosystem.”

Under the supervision of professors David Blowes and Carol Ptacek, and hydrogeochemist Jeff Bain, Zhang assessed the effectiveness of a cover of layers of soil, sand, and gravel placed over mine waste near Timmins, Ontario in 2008.

The cover was intended to inhibit the chemical reaction that produces toxins and prevent them from leaching into the environment. However, there were concerns within the remediation industry about how effective covers would be in containing toxins from the waste — which was deposited on this site between 1968 and 1972.

At old mine sites, metals like lead, arsenic, and copper have precipitated into unstable solids,” said Zhang. “It’s similar to limescale buildup in a kettle if there is hard water. They are sensitive to chemical changes, which means they could dissolve again under a cover and potentially get released into the environment.”

Using experimental techniques at the Canadian Light Source at the University of Saskatchewan and the Advanced Photon Source at Argonne National Laboratory in Illinois, Zhang and colleagues determined the remediation approach had been successful. They found that the cover did not destabilize toxic minerals at the site and was preventing more toxins from developing. Their findings were recently published in Applied Geochemistry.

Read more on Canadian Light Source website

A closer look at how cells package DNA

Cryo-imaging reveals how cells efficiently store the genome

Our cells use an ensemble of histone proteins to fold and package the DNA genome into the nucleus. Histones also determine whether to expose DNA to enzymes to allow processes like gene expression, replication, and repair to occur. Although many in vitro studies have explored the mechanism histones use to fold and package DNA into higher-order structures called chromatin, less is known about chromatin organisation inside the nucleus of intact cells, and understanding this phenomenon could be key to understanding multiple DNA-associated processes. Recent advances in cryo-electron tomography have enabled scientists to observe these structures within the nucleus of rapidly cryopreserved cells. Reporting in Nature Communications, scientists at the University of Oxford collaborated with the electron Bio-Imaging Centre (eBIC) at the Diamond Light Source to capture chromatin in the nucleus of immune T cells, revealing that DNA is folded into more flexible and heterogenous fibres than previously modelled. Their experiments lay the groundwork for future studies into the roles of chromatin in health and disease.

Packing the essentials

Have you ever rushed to pack clothes into a suitcase and skipped the folding step only to find the suitcase wouldn’t close? Though it may have been a struggle, it doesn’t compare to the challenge our cells face when they pack 2 metres of DNA into a nucleus 200,000 times smaller in width. Here an efficient folding mechanism is key, and histone proteins direct the operation.

A complex of histone proteins act as a spool around which 147 base pairs of DNA can wind like thread. Multiple histone spools called nucleosomes can be found along the length of a DNA molecule and coil its strands into so-called chromatin. When chromatin is purified and observed using electron microscopy, scientists have observed that nucleosomes are spaced apart at regular intervals like beads on a string. These beads can then cluster together to form thicker chromatin fibres that pack the DNA into an even smaller volume.

Beyond efficiently folding DNA to fit inside the nucleus, histones play vital roles in regulating gene expression, DNA replication, and repair by loosening or tightening their grip on DNA and controlling its exposure to enzymes. An in-depth understanding of the folding mechanism could help researchers understand how chromatin affects multiple processes within the nucleus.

Read more on the Diamond website

The ESRF Council appoints next Director General

The ESRF Council has appointed Jean Daillant as the next Director General of the ESRF, the European Synchrotron.

A soft matter physicist, Jean Daillant has been Director General of the SOLEIL synchrotron since 2011. Under his guidance, SOLEIL has become a leading facility among the medium-energy synchrotron radiation sources. He is the current Chair of LEAPS, the League of European Accelerator-based Photon Sources, which aims to promote scientific excellence and strengthen the cooperation between synchrotron and X-ray free electron laser facilities to support an innovative and sustainable European Research Area. He also holds the role of Spokesperson of the Analytical Research Infrastructures in Europe (ARIE).

Jean Daillant will take over on 1 September 2024 from Francesco Sette, who, during a close to sixteen-year mandate, has overseen the implementation of the entire Upgrade Programme of the ESRF to become the world’s first and leading fourth-generation high-energy synchrotron radiation source.

“The Council extends a heartfelt welcome to Jean in his new role as Director General, and is looking forward to collaborating with him to steer the ESRF towards a bright future amidst challenging circumstances,” states Prof. Helmut Dosch, Chair of the ESRF Council.

Francesco Sette says: “I congratulate Jean on his appointment and welcome him on board on behalf of all of us at the ESRF. I wish him a lot of success in leading the ESRF in the years to come, keeping the facility at the forefront of X-ray science.”

Jean Daillant says: “I feel deeply honoured to be joining the ESRF to serve as Director General. Succeeding Francesco, who has so successfully lead the facility for many years, is a challenge I am taking on with humility. EBS provides extraordinary opportunities for scientific creativity that I will be most excited to develop further, together with the ESRF staff and the wider scientific community.”

Read more on ESRF website

New hope for fighting malaria: Decoding human antibodies

Using CMCF beamline, researchers from Hospital for Sick Children decode how human antibodies protect us against malaria

Researchers from The Hospital for Sick Children (SickKids) recently decoded how human antibodies protect us from the malaria parasite, which kills more than 600,000 people worldwide annually. The CMCF facility at the Canadian Light Source at the University of Saskatchewan helped them identify the precise structures involved in identifying and fighting off the disease.

“The key question that we hoped to address was what made a protective antibody protect? What makes it tick, what makes it better than some that might not be so protective and might not be so potent?” says SickKids researcher Elaine Thai.

They were able to see that protective antibodies lock on to a vulnerable point on the malaria parasite in a specific form, making it easier to neutralize the infection.

The results, published in Cell Reports, point to a way forward to better treatments and vaccines.

While there are two vaccines approved today, they can only be used on the very young, have limited protective power, and the effects fade over time. Researchers can take the maps created by projects like this to engineer better tools for healthcare.

Read more on Canadian Light Source website

Grape pomace, a waste of viticulture, is effective for nematode pest control on crops

Researchers from Universidad de Castilla la Mancha, Universidad Autónoma de Madrid and the Institute of Agricultural Sciences – CSIC proved the potential of wine production residues as biopesticides in agriculture, thus reducing the waste management problem and contributing to a circular economy. Their work shows that recycled biochar from grape pomace is effective to reduce the parasitic nematode infection of tomato plants in pots. Biochar characterization by synchrotron light infrared spectroscopy was performed at MIRAS beamline of the ALBA Synchrotron.

Cerdanyola del Vallès, 22nd November 2023 The large amount of grape waste generated after wine production can be transformed into a valuable product such as biochar, a form of charcoal. A new published study shows that biochar soil amendments can help to control the infection of a group of plant parasitic nematodes: the root-knot nematodes.

Nematodes are a big group of invertebrates also known as roundworms. They are among the most widespread pests and can be found in almost every crop worldwide, causing annual global agriculture losses of approximately $125 billion. In particular, root-knot nematodes parasite plants penetrating the roots and inducing knots or galls. The plant becomes their host and will nourish them until life cycle completion.

Root-knot nematode infection is difficult to eradicate and usually requires the use of toxic nematicides that are banned in most countries. In this sense, the research team, formed by scientists from the Universidad de Castilla la Mancha (UCLM), Universidad Autónoma de Madrid (UAM) and the Institute of Agricultural Sciences (ICA-CSIC), proposes the use of biochar as an environmentally friendly and economic alternative.

To run the studies, tomato plants were infected withMeloidogyne javanica, a root-knot nematode, and grown in hydroponic system over a clay sandy substrate mixed with different proportions of biochar. After several days of post-inoculation, nematode infection progression was analysedThe infective and reproductive traits of a Meloidogyne javanica population in tomato were significantly reduced (egg masses and eggs per plant) for the biochar pyrolyzed at 350ºC.

In parallel, researchers performed a complete characterization of biochar after a thermal treatment (pyrolysis at 350ºC and 700ºC) by determining their elemental composition and analysing the particulate structure. To do so they use, among other techniques, infrared spectroscopy at MIRAS beamline of ALBA. The analysis with synchrotron light enabled scientist to visualize the large changes in the biomolecular composition of biochar, occurring during grape pomace pyrolysis.

Read more on ALBA website

Research on the structure of human cold receptor TRPM8

Researchers from the Laboratory of Protein Structure at the International Institute of Molecular and Cell Biology in Warsaw, led by Prof. Marcin Nowotny, used the KRIOS cryoelectron microscope located at the SOLARIS National Synchrotron Radiation Centre to study the human TRPM8 protein.

The structure they obtained will enable a better understanding of the binding mechanism of small-molecule compounds affecting the activity of this ion channel. It will facilitate the design of new small-molecule compounds that can be used as therapeutics to treat numerous diseases associated with TRPM8 protein, such as neuropathic pain, irritable bowel syndrome, oropharyngeal dysphagia, chronic cough, and hypertension. As an example, in collaboration with scientists from Italy led by Dr. Carmine Talarico of Dompé Farmaceutici SpA, they have performed modeling of the binding of icilin, a small-molecule compound showing 200 times stronger TRPM8 channel activation than menthol. 

Read more on SOLARIS website

Image:  Structure of human cold receptor TRPM8

Credit: Mariusz Czarnocki-Cieciura

Adding calcium to soils can help increase organic matter, trap more carbon

armers add calcium to their soil for many reasons related to increasing crop yields — including regulating pH and improving soil structure.

Using the Canadian Light Source (CLS) at the University of Saskatchewan, scientists from Cornell University and Purdue University have identified a previously undiscovered mechanism triggered by calcium when it’s added to soil. Their finding could lead to more strategic use of the mineral in agriculture.

Researchers already knew that calcium impacts the way organic matter is stabilized in soil. What wasn’t known was whether calcium had an effect on which microbes were involved and how they acted. Microbes are microscopic organisms that live in the air, soil, and water; in soil, they process soil organic matter and help promote plant growth.

“We showed that by adding calcium to soil, we changed the community of microbes in the soil and the way they process organic matter,” says lead researcher Itamar Shabtai, an assistant scientist with the Connecticut Agricultural Experiment Station. “They processed it in a more efficient manner – more carbon was retained in the soil and less was lost to the atmosphere as CO2.”

Carbon, which makes up about half of the organic matter in soil, is incredibly important to almost all soil properties, says Shabtai, who carried out the research as part of his postdoctoral fellowship at Cornell. “Soils that contain more carbon are generally healthier. They are better able to hold on to water in drought conditions. Soils with higher amounts of organic carbon are also are able to deliver nutrients more efficiently to plants and promote plant growth, and they’re more resistant to erosion.”

Read more on Canadian Light Source website

From beams to bytes: navigating data management for users of PaN facilities

Embark on a journey “From Beams to Bytes” with this 7:53-minute video, tailored for users of Photon and Neutron (PaN) facilities in Europe.

Through a blend of animations and interviews from insiders, we guide you through the essential steps of creating a data management plan for your experiment.

Watch the video on the PaNOSC EOSC YouTube channel

🔗 Useful links and references from the video:

2:18: example of DMP tools: Research Data Management Organiser (RDMO), Data Stewarship Wizard (DSW), DMPonline, DMPTool, EasyDMP, OpenDMP. See…

2:50: public repositories of PaN facilities:…

3:10: EOSC data search https://search.marketplace.eosc-porta… and Zenodo

3:40: the NeXus format

4:45: metadata framework: Soler, N. (2023). ExPaNDS Guidance Note: Key Recommendation Elements for FAIR Photon and Neutron Data Management. Zenodo. and

4:50: orcid, PIDINST, PaNET

5:05: VISA…

7:03: workflow feature of PaN

Watch the assembly of the Grand Tube at the APS

The Advanced Photon Source (APS) Upgrade will result in X-ray beams that are up to 500 times brighter than those generated by the original APS. But that’s only half the story. The upgrade team is also building seven new beamlines, constructing critical infrastructure to enable two more beamlines to be built, and updating many other experiment stations around the ring. 

Work on the beamlines is ramping up. One of the most visible recent projects has been the assembly of the Grand Tube at beamline 9-ID. The Grand Tube is a 70-foot-long enclosure that will enable a new X-ray technique called Coherent Surface Scattering Imaging (CSSI). This will allow scientists to image extremely small materials in three dimensions on a scale previously unattainable. 

The Grand Tube, weighing 100,000 pounds, arrived at Argonne in four sections and took three weeks to assemble. The video below shows the scale of the enclosure and the process of putting it together on the APS experiment floor.

Watch the Grand Tube assemly video here

Ptychographic computed X-ray tomography reveals structure of porous membranes on the nano scale

Article published in Communications Materials presents significant findings and discusses the possibilities offered by this technique combined with synchrotron light sources

Porous materials play key roles in a variety of contexts, from transporting water and nutrients in biological systems to storing oil and water in reservoirs of rock. And synthetic polymer membranes are essential to separation processes, as in the case of chromatography. They have well-established applications in water desalination, hemodialysis, and gas separation, and these uses are expanding into processes that filter out pollutants from contaminated water. Their benefits include energy efficiency, smaller carbon footprint, and compact design that provides a large area of membrane in a small volume.

Membranes that can fulfill technological objectives have complex porous structures that ensure the required selectivity, mechanical stability, and characteristics for rapid transport; the effectiveness and performance of these membranes is defined by characteristics such as porosity and interconnectivity, which can be particularly difficult to measure when they are brought down to the nano scale.

The limitations of electron microscopy and advantages of ptychographic X-ray computed tomography

Techniques such as scanning electron microscopy (SEM), atomic force microscopy (AFM), and transmission electron microscopy (TEM) have helped scientists better understand the transport mechanisms in these applications and develop membranes for different purposes. But even though they are powerful, these techniques also have significant limitations: the samples must be dehydrated and covered with a metallic layer, and must also remain in a vacuum during analysis, which can affect the structure of these membranes and hinder analysis under near-real conditions.

Furthermore, when the pores of the material reach the nano scale, the total sample volume must be significantly reduced in order to attain the resolution necessary for analysis. Within this context, X-ray tomography has emerged as a good alternative. This method not only offers non-destructive visualization, but samples can be analyzed in ambient conditions with significantly larger total sample volumes.

Conventional X-ray tomography, which analyzes different absorption in different parts of a sample, faces challenges related to resolution limits when analyzing less dense materials (such as membranes). But as new fourth-generation synchrotron light sources have recently come online and ptychographic X-ray tomography has been developed, images of these materials can be obtained with nanometric resolution.

Ptychographic X-ray computed tomography (PXCT) is a powerful phase-contrast imaging technique that uses a series of two-dimensional projections of the object from different angles to reconstruct its three-dimensional structure in high resolution, revealing information about porosities and interconnectivity.

Read more on CNPEM website

CHESS celebrates construction milestone with Wilson West open house

On Wednesday, November 15, CHESS had an open house for members of the Cornell community in the new Wilson West expansion project. The project recently received its temporary certificate of occupancy, which marks a milestone in the construction project.

Wilson West houses a new large experimental hall to accommodate the upcoming High Magnetic Field X-ray Beamline. Guests were invited to tour the new building, including future beamline caves, server rooms, electronics and vacuum labs, sample preparation rooms, and an ADA-accessible chemistry room.

The new milestone marks a point in the project when efforts will begin to move from building construction to installing highly specialized experimental equipment.

Read more on CHESS website

Image: The high bay area of the new Wilson West building

Laser-Induced Crystallisation Offers a Quicker Route to Smart Windows

Synchrotron studies show laser annealing is a simpler route to thermochromic VO2 thin films

Smart windows change their properties in response to external factors, with glazing that can switch between transparent and opaque depending on temperature, light levels or an applied voltage. They can be used for privacy and visual effects or to improve energy efficiency. Smart windows using thermochromic materials, for example, can change to block infrared transmission as temperatures rise, remaining transparent to visible light. The thermochromic properties of vanadium dioxide (VO2) offer great potential for energy-saving smart windows. However, depositing VO2 films and coatings through sputtering, chemical or physical vapour deposition can be time-consuming and requires complex and expensive equipment. Solution-based methods are a simpler option, but usually require using a furnace to heat the materials above around 400°C to achieve the necessary crystalline structure, limiting the materials that can be used as a substrate. In work recently published in Applied Surface Science, an international team of researchers crystallised VO2 thin film using laser annealing, substantially reducing the annealing time and crystallisation temperature. Their results showed that the thermochromic properties were comparable with those of furnace-treated samples and that pulsed laser annealing of VO2 could be exploited for a range of applications, including smart windows, metamaterials and flexible electronics.

“Vanadium dioxide is a thermochromic material,” said lead author Maria Basso, a PhD candidate at the University of University of Padova in Italy.

We can tune the material so that at a given temperature – the transition temperature – it continues to transmit visible light but starts to reflect the near-IR. By depositing this phase-change material as a thin film on windows, we can create smart windows as a passive way to improve the energy efficiency of a building. Since they don’t need an active energy input, they’re a low-energy way of keeping a room cooler. In this research, we crystallised the material in an unconventional way. Using a laser allowed us to induce the crystallisation locally, without using a furnace, which could be extended to substrates that are sensitive to temperature, e.g. plastics.

Read more on Diamond Light Source website

Synchrotron Radiation News Volume 37 – call schedule

Synchrotron Radiation News (SRN) is a bimonthly magazine that publishes latest news related to research on synchrotron facilities, meeting reports, upcoming conferences, and new products. SRN invites contributions to Volume 37.

Please find SRN’s call schedule below, and direct any questions or requests to contribute to Andrea Taylor, SRN Commissioning Editor, at

Researchers visualise in 3D how SARS-CoV-2 replicates in cells

The use of different microscopy and tomography techniques, including synchrotron light, unveils how lung cells are modified along the infection in cell culture models. The work is the result of the European consortium CoCID (Compact Cell Imaging Device) with the participation of CSIC groups and the ALBA Synchrotron.

The covid-19 pandemic has affected more than 770 million people and has caused the death of nearly seven million people around the world. Its huge impact on health and global economy has promoted research in the field since 2020, although it is still necessary to understand how this infection makes progress with the aim of finding specific solutions to this pathogen. Now, a team from the Spanish National Research Council (CSIC) and the ALBA Synchrotron publishes in the journal ACS Nano the results obtained after three-dimensional analysis of the interior of an infected cell.

Members of the National Centre of Biotechnology (CNB-CSIC) and the ALBA Synchrotron, the only synchrotron light source in Spain located in Cerdanyola del Vallès (Barcelona), have imaged in three dimensions the interior of human lung epithelium cells, the primary target of the virus, and the severe structural changes caused by SARS-CoV-2 infection.

Pablo Gastaminza, CNB-CSIC researcher and main author of the work, explains the alterations they found: “when comparing an uninfected cell with an infected one, we can see that the virus multiplication machinery forms vesicles and tubules as well as remarkable signs of stress on cellular organelles such as mitochondria and the endoplasmic reticulum.”

The study is part of the collaboration established within the European CoCID (Compact Cell Imaging Device) consortium. It combines the use of molecular biology, virology and three types of microscopy techniques. One of them is the so-called soft X-ray cryo-tomography (Cryo-SXT), a technology available only in four places all over the world, including the MISTRAL beamline at the ALBA Synchrotron. This technique allows “to generate three-dimensional maps of the ultrastructure of complete cells, reconstructing their total volume and providing extra information to other techniques like electron microscopy,” according to Eva Pereiro, head of the MISTRAL beamline at ALBA.

Read more on ALBA website

Image: Three-dimensional images of a fragment of a control cell (left) and a cell infected with SARS-CoV-2 (right). The cell nucleus is highlighted in purple, healthy mitochondria in green, and mitochondria modified by the infection in red, the vacuoles in light blue, the viral factory in yellow and the viral particles in blue. 

Credit: ALBA Synchrotron/CNB-CSIC

A beautiful machine integrated within a peaceful forest setting

On World Science Day for Peace and Development, we’re heading to a forest in Switzerland!

Maël Clémence is a PhD student at the Swiss X-ray Free-Electron Laser  (SwissFEL), which is located at the Paul Scherrer Institut (PSI) in Villigen, Switzerland. His #LightSourceSelfie journey starts in the forest on top of the facility where he explains that the SwissFEL was designed to be fully integrated with the natural environment. Maël then uses a popular mode of transport to travel to the facility entrance. He recalls his childhood fascination with light, what led him to fall in love with physics, and his path to the SwissFEL.

For his PhD studies, Maël is utilising the machine’s ultraintense, ultrashort X-ray pulses to study and investigate quantum properties of magnetic materials in extreme conditions. Being at the SwissFEL has enabled Maël to gain a deeper understanding of this beautiful machine and the huge amount of skill and dedication that is required by the teams responsible for building and maintaining it.

The word ‘teamwork’ best describes his job as, on good days and bad, everyone pulls together and supports each other.

You’ll discover one of Maël’s favourite free time activities at the close out of his #LightSourceSelfie. Happy viewing!        

Find out more about the SwissFEL here

Combination of techniques for effective pharmaceutical formulation

The environment in your gastrointestinal tract affects the properties and effectiveness of medicines. Researchers have used MAX IV to investigate a technique for studying these changes. They found that the structural properties of the anti-inflammatory drug Indomethacin changed in the presence of common biomolecules.

The fluid in your gastrointestinal tract is a complex soup of biomolecules. When you take a pharmaceutical drug, the biomolecules may stick to its surface and alter how it’s dissolved and taken up by the body at a certain pH. Such effects need to be understood and taken into account when producing pharmaceuticals. But it’s not always easy to investigate. In the present paper, the authors tested the accessible technique of Low-Frequency Raman spectroscopy, in which inelastic scattered light is used to analyse the sample. They then controlled the accuracy using X-ray methods.

Read more on MAX IV website