Lightsource research on SARS-CoV-2

Coronaviruses are a family which includes the common cold, SARS, MERS and the current outbreak of the disease COVID-19, caused by the SARS-CoV-2 virus.
Several facilities of our collaboration have started research about SARS-CoV-2 virus or launched open calls for rapid access. This post will be updated regularly.

Publications

Diamond Light Source (UK) has created a specific website “Coronavirus Science” with platforms for various audiences: scientific community, general public and the media: https://www.diamond.ac.uk/covid-19.html

The Photon Division of PSI (Switzerland) have collated many information linked to their institute on coronavirus-relevant research (recent publications, rapid access…): https://www.psi.ch/en/psd/covid-19

2020.03.25 CERN Courrier (Switzerland) article about synchrotron research on SARS-CoV-2, written by Tessa Charles (accelerator physicist at the University of Melbourne currently based at CERN, completed her PhD at the Australian Synchrotron):
Synchrotrons on the coronavirus frontline

2020.03.19 BESSY II at Helmholtz-Zentrum Berlin (Germany), research publication:
Coronavirus SARS-CoV2: BESSY II data accelerate drug development

2020.03.19 BESSY II at Helmholtz-Zentrum Berlin (Germany), technique explanation webpage:
Protein crystallography at BESSY II: A mighty tool for the search of anti-viral agents

2020.03.16 Diamond Light Source (UK), latest article on their “Coronavirus Science” website:
Main protease structure and XChem fragment screen

2020.03.12. Elettra Sincrotrone (Italy), article on their website:
New project to fight the spread of Coronavirus has been approved

2020.03.05. Advanced Photon Source (IL / USA), article on their website:
APS Coronavirus Research in the Media Spotlight

Rapid access

Scientists can apply for rapid access at following facilities (only member facilities of Lightsources.org are referenced, the most recent published (or updated) call is mentioned first).

  • The National Synchrotron Light Source II (NSLS-II) in NY / USA is offering a streamlined and expedited rapid access proposal process for groups that require beam time for structural biology projects directly related to COVID-19. The Center for Biomolecular Structure team is supporting remote macromolecular crystallography experiments at Beamlines 17-ID-1 (AMX) and 17-ID-2 (FMX) in this research area. To submit a macromolecular crystallography proposal for COVID-19 related research, use the following form:
    https://surveys.external.bnl.gov/n/RapidAccessProposal.aspx

Image: Electron density at the active site of the SARS-CoV-2 protease, revealing a fragment bound
Credit: Diamond Light Source

Ten years at the service of the society and its challenges

On 22nd March 2010, ALBA was inaugurated becoming one of the most important scientific infrastructures of Spain.

Since then, its synchrotron light has been a great ally for numerous advances in a huge range of scientific fields, such as biomedicine, materials science, nanotechnology or archaeology. The ALBA Synchrotron represents a formidable return of knowledge, development and well-being for society.
Cerdanyola del Vallès, 23rd March 2020 10 years have passed since the inauguration of ALBA, the Spanish synchrotron light source. InMarch 2010, it was celebrated the launch of an unprecedented scientific project whose aim was becoming an essential tool for science and technology. Ten year later, ALBA has far exceeded its initial expectations, also being an international reference among worldwide light sources. It is currently under a continuous growth process byinstalling new equipment and updating its instrumentation to meet both present and future scientific challenges. In particular, ALBA is helping in the fight against COVID-19 to advance in the knowledge of the virus and in the development of vaccines and treatments.

The number of synchrotron light users in Spain has reach, from the initial 200 at the time of the project approval, to more than 5,000 users, almost half of them international; as well as more than 50 private national and international companies. In total, ALBA has provided synchrotron light for research groups belonging to 1,850 institutions from 45 different countries. The result has been more than 1,500 experiments performed that have been reflected in around 1,100 scientific publications.
Currently, the ALBA Synchrotron has 8 beamlines and 5 more are under construction, all equipped with different techniques for analyzing matter at an atomic and molecular level thanks to the high quality of the synchrotron light produced. Since the beginning, 37,722 hours of light have been generated. In this time, the electrons inside the accelerators would travel 2.7 million times the distance from Earth to the Sun!

>Read more on the ALBA website.

Super laser delivered to European XFEL

High Energy laser will enable study of exoplanet interiors.

A keenly awaited piece of high-tech equipment has been delivered to European XFEL. The high repetition rate, high-energy laser, DiPOLE 100-X, was developed in the UK by scientists and engineers at the Science and Technology Facilities Council’s Central Laser Facility (CFL) as part of the UK contribution to the facility. This unique laser, developed within the framework of the HiBEF user consortium, will be used at the instrument for High-Energy Density (HED) science at European XFEL to generate extreme temperatures and pressures in materials. The atomic structure and dynamics of these extreme states of materials can then be studied using the extremely bright and intense X-ray pulses produced by the European XFEL. This experimental set-up will enable scientists to create conditions similar to the interior of exoplanets with temperatures of up to 10,000°C, and pressures of up to 10,000 tons per square centimeter – similar to the weight of 2000 adult elephants concentrated onto the surface of a postage stamp!

>Read more on the European XFEL website

Image: The HED instrument at European XFEL.
Credit: European XFEL/Jan Hosan

Enhanced tandem solar cells set new standard in converting light into electricity

A collaboration between U of T Engineering and King Abdullah University of Science and Technology has created two-layered solar cells that successfully combine traditional silicon with new perovskite technology .

Researchers from University of Toronto Engineering and King Abdullah University of Science and Technology (KAUST) have overcome a key obstacle in combining the emerging solar-harvesting technology of perovskites with the commercial gold standard — silicon solar cells. The result is a highly efficient and stable tandem solar cell, one of the best-performing reported to date.
“Today, silicon solar cells are more efficient and less costly than ever before,” says Professor Ted Sargent (ECE), senior author on a new paper published today in Science. “But there are limits to how efficient silicon can be on its own. We’re focused on overcoming these limits using a tandem (two-layer) approach.”

>Read more on the Canadian Light Source website

Picture: Left to right: Postdoctoral fellows Erkan Aydin (KAUST), Yi Hou (University of Toronto) and Michele De Bastiani (KAUST) are part of an international team that has designed a new type of tandem solar cell. The device combines industry standard silicon manufacturing with new perovskite technology.
Credit: Andrea Bachofen-Echt / KAUST

Beyond graphene: monolayer arsenene observed for the first time

An article recently published in 2D Materials shows the first experimental evidence of the successful formation of arsenene, an analogue of graphene with noteworthy semiconducting properties.

This material shows a great potential for the development of new nanoelectronics. Crucial sample preparation and electron spectroscopy experiments were performed at the Bloch beamline at MAX IV.

The discovery of graphene, the single-layer carbon honeycomb material worth the Nobel Prize in Physics in 2010, surely has had a revolutionary impact on research. It triggered a whole new field of study within two-dimensional (2D) materials. However, its application in developing new 2D electronics has been hindered by its lack on an intrinsic band gap. Researchers therefore started to turn their attention to other elements in the periodic table and set their eyes on group V, to which arsenic belongs.
“The aim of the study was to show that arsenene can be formed. Our article is the first to report this”, says Roger Uhrberg, professor at Linköping University and spokesperson for the Bloch beamline at MAX IV. Arsenene, a single-layer buckled honeycomb structure of arsenic, had been previously predicted by various theoretical studies, but this is the first experimental observation that verifies its existence.

>Read more on the MAX IV website

Image: A view of the Bloch beamline at MAX IV. The Bloch beamline consists of two branchlines, and is dedicated to high resolution photoelectron spectroscopy, encompassing angle-resolved (ARPES), spin resolved (spin-ARPES) and core-level spectroscopy.

Plastic from Wood

X-ray analysis points the way to lignin-based components made to measure

The biopolymer lignin is a by-product of papermaking and a promising raw material for manufacturing sustainable plastic materials. However, the quality of this naturally occurring product is not as uniform as that of petroleum-based plastics. An X-ray analysis carried out at DESY reveals for the first time how the internal molecular structure of different lignin products is related to the macroscopic properties of the respective materials. The study, which has been published in the journal Applied Polymer Materials, provides an approach for a systematic understanding of lignin as a raw material to allow for production of lignin-based bioplastics with different properties, depending on the specific application.

Read more on the PETRA III at DESY website (opens in a new tab)”>>Read more on the PETRA III at DESY website

Image: Lignin is a promising raw material (left) for thermoplast (right) production.
Credit: KTH Stockholm, Marcus Jawerth

Expertise in characterising materials for lithium ion batteries

Pioneering work on materials for energy production, such as lithium ion batteries, has made ANSTO a centre of specialist capabilities and expertise.

(…)
In addition to the research on lithium-ion batteries; the team also investigates other types of batteries that can reversibly host ions, such as sodium and potassium ion batteries. 
Dr Christophe Didier, a post-doc working with Peterson at the ACNS and shared with Peterson’s University of Wollongong collaborators, published work in Advanced Energy Materials providing structural insights into layered manganese oxide electrodes for potassium-Ion batteries.
“In this case, we were able to use X-rays on an operating battery at the Australian Synchrotron,  because potassium has a lot more electrons than lithium.”
These results again confirm the importance of understanding the detailed structural evolution that underpins performance that will inform the strategic design of electrode materials for high-performance potassium ion batteries. “We do have many collaborators but we are always interested in new projects.  Because we are knowledgeable in the materials themselves, we can contribute to the selection of suitable materials as well as leading the characterisation effort.

>Read more on the Australian Synchrotron (ANSTO) website

Image: Powder diffraction instrument scientist, Dr Qinfen Gu at the Australian Synchrotron.

Water improves material’s ability to capture CO2

With the help of the Advanced Light Source (ALS), researchers from UC Berkeley and ExxonMobil fine-tuned a material to capture CO2 in the presence of water.

About 65% of anthropogenic greenhouse gas emissions comes from the combustion of fossil fuels in power plants. So far, efforts to capture CO2 from power-plant flue gases and sequester it underground have mainly focused on coal-fired power plants. However, in the United States, natural gas has surpassed coal in the amount CO2 released, despite the fact that natural gas emits approximately half as much CO2 per unit of electricity. Therefore, new materials are urgently needed to address this situation.

Not all combustion is alike

Compared to coal-fired power plants, natural gas combined cycle (NGCC) plants produce flue gases with low CO2 concentrations. This reduces the carbon footprint, but increases the technical difficulty of CO2 capture. Also, materials capable of adsorbing such low concentrations of CO2 often require high temperatures to release it for sequestration, an important part of the cycle that offsets initial low-carbon benefits. NGCC emissions also have a higher concentration of O2, which has a corrosive effect on adsorbent materials, and both NGCC and coal flue streams are saturated in water, which can both degrade materials and reduce efficiency. Thus, an effective NGCC CO2-capture material must selectively bind low-concentration CO2 under humid conditions while being thermally and oxidatively stable.

>Read more on the Advanced Light Source website

Image: Single-crystal x-ray diffraction enables the precise determination of the positions of the atoms in metal–organic frameworks (MOFs), highly porous materials capable of soaking up vast quantities of a specific gas molecule, such as CO2. This structure represents 2-ampd–Zn2(dobpdc), a MOF with the same structure as 2-ampd–Mg2(dobpdc), the subject of this study. Light blue, blue, red, gray, and white spheres represent Zn, N, O, C, and H atoms, respectively.

Diabetes discovery challenges known research

Yale University scientists and colleagues who used the CLS share findings that could lead to a new therapeutic approach to treating diabetes.

A discovery by an international group of scientists challenges known research on diabetes and may open the door to new therapeutic approaches for the disease that affects nearly 500 million people globally.
Their research focused on pyruvate kinase, an enzyme that is involved in communication at the cell level through a process known as protein phosphorylation, which changes the shape of a protein and alters how that protein behaves.
The study is a piece of a larger project that has researchers looking at how different signals, like insulin levels, are interpreted in the liver.
“We set out to understand and characterize insulin signalling in a laboratory model, and we found some activities in that model that were contrary to the textbooks,” said Jesse Rinehart, associate professor in the Department of Cellular & Molecular Physiology at the Yale University School of Medicine.
The team’s findings were published in Cell Reports and have opened up a new area of insight and exploration in an already highly active field of research.

>Read more on the Canadian Light Source website

Image: Gassaway et al. identified a phosphorylation site on pyruvate kinase linking it to cyclin dependent kinase (CDK) function in the liver. This new site is part of a CDK pathway stimulated by insulin resistance in vivo. Structural and biochemical characterization reveled that pyruvate kinase phosphorylation does not alter enzymatic activity. Instead phosphorylation dictates cellular compartmentalization. This image depicts the “hand” of CDK reaching out to sequester PKL in the hepatocyte nucleus.
Credit: J. Rinehart and B. Gassaway.

Imaging how anticancer compounds move inside the cells

Chemotherapeutics are key players in the clinical setting to fight most types of cancer, and novel chemicals hold the promise to facilitate new and unique intracellular interactions that modulate the cell machinery and destroy the tumour cells. Equally necessary are new tools that enable the unequivocal location and quantification of such molecules in the intracellular nano-space, so that their therapeutic action is fully understood.

Researchers from IMDEA Nanociencia, the ALBA Synchrotron, the European Synchrotron Radiation Facility (ESRF) and the National Centre for Biotechnology (CNB) have developed a new family of organo-iridium drug candidates about a hundred times more potent than the clinically used drug cisplatin.
In order to understand the therapeutic potential of the compound, it is mandatory to accurately localize its fate within the cell ultrastructure with minimal perturbation. To this aim researchers have correlated on the same cell, for the first time, two 3D X-ray imaging techniques with a resolution of tenths of nanometers: cryo soft X-ray tomography, at MISTRAL beamline at ALBA Synchrotron, and cryo X-ray fluorescence tomography, at ID16A beamline at ESRF. These techniques help elucidate the 3D architecture of the whole cell and to reveal the intracellular location of different atomic elements, respectively.

>Read more on the ALBA website

Cryo-electron microscopy for industry coming soon to SOLARIS

The SOLARIS Centre and the Malopolska Centre of Biotechnology (Jagiellonian University) won a two-stage competition for the purchase of an electron microscopy for industrial research.

Funding was awarded by the National Information Processing Institute (OPI PIB) as part of the EU’s Smart Growth Operational Programme.

“We have been trying to purchase a microscope because Polish companies keep asking us about the possibility to carry out measurements using the Cryo-EM technique” – says Michał Młynarczyk, Finance and Administration Deputy Director at SOLARIS. “We expect that the total time allocated for the commercial study will be at least 40% of operational time. The remaining time will be available for academic researchers” –  continues the director.

“We are keen to enable Polish companies to access this exciting new technology, which is developing very fast and is currently becoming the most important one used in structural biology. The achievable results facilitate to understand the cellular mechanisms behind human diseases, the design of new drugs, the optimization of existing drug molecules. The technique is also successfully applied in nanotechnology and other fields” – adds Sebastian Glatt, Max Planck Research Group leader at the Malopolska Centre of Biotechnology – the main partner of SOLARIS in the implementation of this project.

>Read more on the SOLARIS website

Shaping attosecond waveforms

Scientists show how to control attosecond light pulses at a free-electron laser.

Chemical reactions and complex phenomena in liquids and solids are determined by the movement and rearrangement of electrons. These movements, however, occur on an extremely short timescale, typically only a few hundred attoseconds (1 attosecond =10-18 s or one quintillionth of a second).  Only light pulses of a comparable duration can be used to take snapshots of the dynamics of electrons. An international team of researchers led by Guiseppe Sansone from the University of Freiburg and including scientists from European XFEL have now, for the first time, been able to reliably generate, control and characterize such attosecond light pulses from a free-electron laser.

“These pulses enable us to study the first moment of the electronic response in a molecule or crystal,” explains Sansone. “With the ability to shape the electric field enables us to control electronic movements – with the long-term goal of optimising basic processes such as photosynthesis or charge separation in materials.”

>Read more on the European XFEL website

Image: Scientists have been able to shape the electric field of an attosecond light pulse.
Credit: Jürgen Oschwald and Carlo Callegari

ALS reveals vulnerability in cancer-causing protein

A promising anticancer drug, AMG 510, was developed by Amgen with the help of novel structural insights gained from protein structures solved at the Advanced Light Source (ALS).

Mutations in a signaling protein, KRAS, are known to drive many human cancers. One specific KRAS mutation, KRAS(G12C), accounts for approximately 13% of non-small cell lung cancers, 3% to 5% of colorectal cancers, and 1% to 2% of numerous other solid tumors. Approximately 30,000 patients are diagnosed each year in the United States with KRAS(G12C)-driven cancers.

Despite their cancer-triggering significance, KRAS proteins have for decades resisted attempts to target their activity, leading many to regard these proteins as “undruggable.” Recently, however, a team led by researchers from Amgen identified a small molecule capable of inhibiting the activity of KRAS(G12C) and driving anti-tumor immunity. Protein crystallography studies at the ALS provided crucial information about the structural interactions between the potential drug molecule and KRAS(G12C).

>Read more on the Advanced Light Source website

Image: A structural map of KRAS(G12C), showing the AMG 510 molecule in the binding pocket. The yellow region depicts where AMG 510 covalently attaches to the KRAS protein.
Credit: Amgen

New detector accelerates protein crystallography

In Feburary a new detector was installed at one of the three MX beamlines at HZB.

Compared to the old detector the new one is better, faster and more sensitive. It allows to acquire complete data sets of complex proteins within a very short time.

Proteins consist of thousands of building blocks that can form complex architectures with folded or entangled regions. However, their shape plays a decisive role in the function of the protein in the organism. Using macromolecular crystallography at BESSY II, it is possible to decipher the architecture of protein molecules. For this purpose, tiny protein crystals are irradiated with X-ray light from the synchrotron source BESSY II. From the obtained diffraction patterns, the morphology of the molecules can be calculated.

>Read more on the BESSY II at HZB website

Image: 60s on the new detector were sufficient to obtain the electron density of the PETase enzyme.
Credit: HZB

X-ray microscopy at BESSY II: Nanoparticles can change cells

Nanoparticles easily enter into cells. New insights about how they are distributed and what they do there are shown for the first time by high-resolution 3D microscopy images from BESSY II.

For example, certain nanoparticles accumulate preferentially in certain organelles of the cell. This can increase the energy costs in the cell. “The cell looks like it has just run a marathon, apparently, the cell requires energy to absorb such nanoparticles” says lead author James McNally.
Today, nanoparticles are not only in cosmetic products, but everywhere, in the air, in water, in the soil and in food. Because they are so tiny, they easily enter into the cells in our body. This is also of interest for medical applications: Nanoparticles coated with active ingredients could be specifically introduced into cells, for example to destroy cancer cells. However, there is still much to be learned about how nanoparticles are distributed in the cells, what they do there, and how these effects depend on their size and coating.

>Read more on the BESSY II at Helmholtz-Zentrum Berlin website

Image: 3D architecture of the cell with different organelles:  mitochondria (green), lysosomes (purple), multivesicular bodies (red), endoplasmic reticulum (cream).
Credit: Burcu Kepsutlu/HZB

Five U.S. light sources form data solution task force

New collaboration between scientists at the five U.S. Department of Energy light source facilities will develop flexible software to easily process big data.

Light source facilities are tackling some of today’s biggest scientific challenges, from designing new quantum materials to revealing protein structures. But as these facilities continue to become more technologically advanced, processing the wealth of data they produce has become a challenge of its own. By 2028, the five U.S. Department of Energy (DOE) Office of Science light sources, will produce data at the exabyte scale, or on the order of billions of gigabytes, each year. Now, scientists have come together to develop synergistic software to solve that challenge.
With funding from DOE for a two-year pilot program, scientists from the five light sources have formed a Data Solution Task Force that will demonstrate, build, and implement software, cyberinfrastructure, and algorithms that address universal needs between all five facilities. These needs range from real-time data analysis capabilities to data storage and archival resources.
“It is exciting to see the progress that is being made by all the light sources working together to produce solutions that will be deployed across the whole DOE complex,” said Stuart Campbell, leader of the data acquisition, management and analysis group at the National Synchrotron Light Source II (NSLS-II), a DOE Office of Science user facility at DOE’s Brookhaven National Laboratory.

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

>Explore the other member facilities of the task force and read about their latest science news: Advanced Light Source (ALS), Advanced Photon Source (APS), Stanford Synchrotron Radiation Lightsource (SSRL), Linac Coherent Light Source (LCLS).

Image: Members of the task force met at NSLS-II for a project kickoff meeting in August of 2019.