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.

IMPORTANT: Job opening at Elettra (Italy): Junior Research Associate in Structural Biology for the EXSCALATE4CoV Project

Publications on SARS-CoV-2 Rapid Access




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

2020.04.07. ANSTO’s Australian Synchrotron (Victoria), article:
Aiding the global research effort on COVID-19

2020.04.06. National Synchrotron Light Source II (NSLS-II) at Brookhaven Lab (NY / USA), article:
Brookhaven Lab Mobilizes Resources in Fight Against COVID-19

2020.04.02. BESSY II at HZB (Germany), article:
Corona research: Two days of measuring operation to find the right key

2020.03.31 Diamond Light Source (UK), article:
Jointly with Exscientia and Scripps Research, Diamond aims to accelerate the search for drugs to treat COVID-19

2020.03.27 Argonne National Laboratory with the Advanced Photon Source (APS) and other facilities on-site (IL / USA), article:
Argonne’s researchers and facilities playing a key role in the fight against COVID-19

2020.03.27 ANSTO’s Australian Synchrotron (Victoria), article and video:
Helping in the fight against COVID-19

2020.03.23 Diamond Light Source (UK) releases its first animation explaining:
SARS-CoV-2 Mpro Single Crystal Crystallography

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), 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

2020.03.05. Advanced Photon Source (IL / USA), research publication:
“Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2,” bioRXiv preprint  DOI: 10.1101/2020.03.02.968388
Article on their website (source: Northwestern University):
New Coronavirus Protein Reveals Drug Target




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

Lucy had an ape-like brain, but prolonged brain growth like humans

A study led by the Max Planck Institute for Evolutionary Anthropology reveals that Lucy’s species, Australopithecus afarensis, had an ape-like brain.

However, the protracted brain growth suggests that infants may have had a long dependence on caregivers, as in humans. The study, in collaboration with the ESRF, is published in Science Advances.

The species Australopithecus afarensis, well-known as Lucy’s species, inhabited East Africa more than three million years ago, and occupies a key position in the hominin family tree.. “Lucy and her kind provide important evidence about early hominin behavior. They walked upright, had brains that were around 20 percent larger than those of chimpanzees and may have used sharp stone tools,” explains senior author Zeresenay Alemseged from the University of Chicago, who directs the Dikika field project in Ethiopia, where the skeleton of an Australopithecus afarensis child, known as Dikika child and nicknamed Selam, was found in the year 2000. “Our new results show how their brains developed, and how they were organized,” adds Alemseged.

>Read more on the European Synchrotron website

Image: Brain imprints in fossil skulls of the speciesAustralopithecus afarensis(famous for “Lucy” and the “Dikika child” from Ethiopia pictured here) shed new lighton the evolution of brain growth and organization. The exceptionally preservedendocranial imprint of the Dikika child reveals an ape-likebrain organization, and nofeatures derived towards humans.
Credit: Philipp Gunz, MPI EVA Leipzig.

Ultra-fast switching of helicity of circularly polarized light pulses

At the BESSY II storage ring, a joint team of accelerator physicists, undulator experts and experimenters has shown how the helicity of circularly polarized synchrotron radiation can be switched faster – up to a million times faster than before.

They used an elliptical double-undulator developed at HZB and operated the storage ring in the so-called two-orbit mode. This is a special mode of operation that was only recently developed at BESSY II and provides the basis for fast switching. The ultra-fast change of light helicity is particularly interesting to observe processes in magnetic materials and has long been expected by a large user community.
In synchrotron radiation sources such as BESSY II, electron bunches orbit the storage ring at almost the speed of light. They are forced to emit extremely bright light pulses with special properties by periodic magnetic structures (undulators).

Experiments with polarized light pulses

Elliptical undulators can be used to generate also circularly polarized light pulses, which display a feature called helicity: the polarisation goes either clockwise or counterclockwise. Magnetic structures in materials react differently to circularly polarized light: Depending on the helicity of the X-ray pulses, they more or less absorb this radiation.

>Read more on the BESSY II (HZB) website

Image: This picture shows an X-ray image of the electron beam in TRIB-mode where two orbits co-exist: the regular orbit and the second one winding around it closing only after three revolutions.
Credit: F. Armborst/K. Holldack


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

Researchers use CHESS to map protein motion

Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins.

And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins. And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Their paper, “Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal,”published March 9 in Nature Communications.
As a structural biologist, Nozomi Ando, M.S. ’04, Ph.D. ’08, assistant professor of chemistry and chemical biology, is interested in charting the motion of proteins, and their internal parts, to better understand protein function. This type of movement is well known but has been difficult to document because the standard technique for imaging proteins is X-ray crystallography, which produces essentially static snapshots.

>Read more on the CHESS website
>Read also: Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Image: This slice through the three-dimensional diffuse map shows intense peaks resulting from lattice vibration, as well as cloudy features caused by internal protein motions.

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