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 on SARS-CoV-2 Rapid Access




Publications

Published articles

2021.12.09 Diamond Light Source (UK) article on their website: Trigger of rare blood clots with AstraZeneca and other COVID vaccines found by scientists

2021.11.06 APS at Argonne National Laboratory (USA) article on their website: Advanced Photon Source Helps Pfizer Create COVID-19 Antiviral Treatment

2021.11.04 ESRF (France) article on their website: EBS X-rays show lung vessels altered by COVID-19 (esrf.fr)

2021.08.11 BESSY II at HZB (Germany) article on their website: HZB coordinates European collaboration to develop active agents against Corona – Helmholtz-Zentrum Berlin (HZB) (helmholtz-berlin.de)

2021.08.10 Canadian Light Source article on their website: Developing antiviral drugs to treat COVID-19 infections

2021.07.06 European XFEL (Germany) article on their website: XFEL: Insights into coronavirus proteins using small angle X-ray scattering

2021.06.21 Diamond Light Source (UK) article on their website: X-ray fluorescence imaging at Diamond helps find a way to improve accuracy of Lateral Flow Tests

2021.06.17 Australian Synchrotron (ANSTO) article on their website: Research finds possible key to long term COVID-19 symptoms

2021.05.11 Swiss Light Source at PSI (Switzerland) article on their website: How remdesivir works against the coronavirus

2021.05.28 SLAC (CA / USA) article from the Stanford Synchrotron Radiation Lightsource (SSRL): Structure-guided Nanobodies Block SARS-CoV-2 Infection | Stanford Synchrotron Radiation Lightsource

2021.05.21 ALS (USA) article on their website: Guiding Target Selection for COVID-19 Antibody Therapeutics

2021.05.21 ESRF (France) article on their website: Combatting COVID-19 with crystallography and cryo-EM (esrf.fr)

2021.05.18 ALS (USA) article on their website: How X-Rays Could Make Reliable, Rapid COVID-19 Tests a Reality | Berkeley Lab (lbl.gov)

2021.04.27 Canadian Light Source (Canada), video on their website Investigating the long-term health impacts of COVID-19 (lightsource.ca)

2021.04.22 Synchrotron Light Research Institute (Thailand), article on their website: SLRI Presented Innovations Against COVID-19 Outbreak to MHESI Minister on His Visit to a Field Hospital at SUT

2021.04.16 Diamond Light Source (UK) article on their website: Massive fragment screen points way to new SARS-CoV-2 inhibitors

2021.04.14 SLAC (CA / USA), article also with news about research at Stanford Synchrotron Radiation Lightsource (SSRL):Researchers search for clues to COVID-19 treatment with help from synchrotron X-rays

2021.04.07 Diamond Light Source (UK), article on their website: First images of cells exposed to COVID-19 vaccine – – Diamond Light Source

2021.04.05 ALS (CA/USA) blog post on Berkeley Lab Biosciences website: New COVID-19 Antibody Supersite Discovered

2021.04.02 PETRA III at DESY (Germany), article and animation on their website DESY X-ray lightsource identifies promising candidate for COVID drugs

2021.03.26 Diamond Light Source (UK), article on their website: New targets for antibodies in the fight against SARS-CoV-2

2021.02.23 Australian Light Source (ANSTO) Australia, article on their website: Progress on understanding what makes COVID-19 more infectious than SARS

2020.12.02 ESRF (France), article and video on their website: ESRF and UCL scientists awarded Chan Zuckerberg Initiative grant for human organ imaging project

2020.11.10 Diamond Light Source (UK), article and video on their website: From nought to sixty in six months… the unmasking of the virus behind COVID-19

2020.10.29 Canadian Light Source (Canada) video on their website: Studying how to damage the COVID-19 virus

2020.10.07 National Synchrotron Light Source II (NSLS-II) at Brookhaven Lab (NY / USA) article on their website: Steady Progress in the Battle Against COVID-19

2020.10.07 Diamond Light Source (UK), article on their website: Structural Biology identifies new information to accelerate structure-based drug design against COVID-19

2020.10.06 MAX IV (Sweden), article on their website: Tackling SARS CoV-2 viral genome replication machinery using X-rays

2020.08.31 SLAC (CA / USA), article also with news about research at Stanford Synchrotron Radiation Lightsource (SSRL): SARS-CoV-2 Spike Protein Targeted for Vaccine

2020.08.27 Diamond Light Source (UK), article on their website: Structural Biology reveals new target to neutralise COVID-19

2020.08.27 Canadian Light Source (Canada) video on their website: Developing more effective drugs

2020.08.25 Australian Synchrotron (ANSTO) (Australia) article on their website: More progress on understanding COVID-19

2020.08.24 DESY (Germany) article on their website: PETRA III provides new insights into COVID-19 lung tissue

2020.08.11 Australian Synchrotron (ANSTO) (Australia) article on their website: Unique immune system of the alpaca being used in COVID-19 research

2020.07.30 Swiss Light Source at PSI (Switzerland) article on their website: COVID-19 research: Anti-viral strategy with double effect

2020.07.29 National Synchrotron Light Source II (NSLS-II) at Brookhaven Lab (NY / USA) article on their website: Ready to join the fight against COVID-19.

2020.07.20 ALBA (Spain) article on their website: A research team from Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC) uses synchrotron light to study the possible effect of an antitumoral drug of clinical use over the viral cycle of SARS-CoV-2 coronavirus. 

2020.07.15 ALS (USA) article on their website: Antibody from SARS Survivor Neutralizes SARS-CoV-2

2020.07.14 Diamond Light Source (UK), article on their website: Engineered llama antibodies neutralise Covid-19 virus

2020.06.17 European XFEL (Germany) article on their website: Pulling Together: A collaborative research approach to study COVID-19

2020.06.15 European XFEL (Germany) article on their website: Open Science COVID19 analysis platform online

2020.06.09 APS at Argonne National Laboratory (USA) article on their website: Novel Coronavirus Research at the Advanced Photon Source

2020.05. Società Italiana di Fisica publishes an article about research done at Elettra Sincrotrone Trieste (Italy) and the Advanced Light Source (CA / USA): Accelerator facilities support COVID-19-related research

2020.05.27 Diamond Light Source (UK), new animation video demonstrating the work that has been done at Diamond’s XChem facilities.

2020.05.19 Advanced Light Source (CA / USA), article about their latest results: X-ray Experiments Zero in on COVID-19 Antibodies

2020.05.15 Swiss Light Source (Switzerland), article about their first MX results: First MX results of the priority COVID-19 call

2020.05.14 MAX VI (Sweden), article about their research: Tackling SARS CoV-2 viral genome replication machinery using X-rays

2020.05.14 CHESS (NY/USA), article: CHESS to restart in June for COVID-19 research

2020.05.14 the LEAPS initiative brings together many of our European members. The initative published this brochure: Research at LEAPS facilities fighting COVID-19

2020.05.12 Diamond Light Source (UK), article about their collaboration in a consortium: UK consortium launches COVID-19 Protein Portal to provide essential reagents for SARS-CoV-2 research

2020.05.11 Advanced Photon Source (IL/USA), article: Studying Elements from the SARS-CoV-2 Virus at the Bio-CAT Beamline

2020.05.07 European XFEL (Germany), article: European XFEL open for COVID-19 related research

2020.05.06 ESRF (France), article: World X-ray science facilities are contributing to overcoming COVID-19

2020.04.29. BESSY II at HZB (Germany), article: Corona research: Consortium of Berlin research and industry seeks active ingredients

2020.04.29. Swiss Light Source and SwissFEL at PSI (Switzerland), interview series on the PSI website: Research on Covid-19

2020.04.23. PETRA III at DESY (Germany), article: X-ray screening identifies potential candidates for corona drugs

2020.04.21. MAX IV (Sweden), article: BioMAX switches to remote operations in times of COVID-19

2020.04.16. SLAC (CA / USA), article also with news about research at Stanford Synchrotron Radiation Lightsource (SSRL): SLAC joins the global fight against COVID-19

2020.04.15 Berkeley National Lab (CA/ USA), article with a focus on the research at the Advanced Light Source (ALS):
Staff at Berkeley Lab’s X-Ray Facility Mobilize to Support COVID-19-Related Research

2020.04.07 Diamond Light Source (UK), article: Call for Chemists to contribute to the fight against COVID-19
Crowdfunding: COVID-19 Moonshot

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

2020.03.25 PETRA III at DESY (Germany), article: Research team will X-ray coronavirus proteins

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

Facility Covid-19 research pages

The Canadian Light Source (Canada) has created a specific page highlighting their COVID-19 research: COVID-19 research at the Canadian Light Source

BESSY II at HZB (Germany) has set up a page where it shows their contributions to the research on SARS-CoV-2 , see here

DESY (Germany) has launched a new page dedicated to Corona Research: https://www.desy.de/news/corona_research/index_eng.html

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

ELETTRA (Italy) has launched a new page dedicated to COVID-19 research: https://www.elettra.eu/science/covid-19-research-at-elettra.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

ALBA (Spain) has set up a dedicated area on their website for information related to COVID-19 (rapid access, publications etc): https://www.albasynchrotron.es/en/covid-19-information/

The ALS (CA/USA) has created a page listing all COVID-19 related research: https://als.lbl.gov/tag/covid-19/




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
  • The Advanced Photon Source (APS) at Argonne National Laboratory in IL / USA  user program is operational to support:

·         Research on SARS-CoV-2 or other COVID-19-related research that addresses the current pandemic.

·         Critical, proprietary pharmaceutical research.

·         Mail-in/remote access work for any research involving low-risk samples and most medium-risk samples (as defined on the APS ESAF form).

·         Limited in situ research (set-up with one person, and ability to carry out majority of experiment safely remotely)
https://www.aps.anl.gov/Users-Information/About-Proposals/Apply-for-Time

PETRA III at DESY in Germany offers also Fast Track Access for Corona-related research:
https://photon-science.desy.de/users_area/fast_track_access_for_covid_19/index_eng.html

Australian Synchrotron at ANSTO makes its macromolecular crystallography beamlines available to structural biologists in response to the COVID-19 pandemic: https://www.ansto.gov.au/user-access

North American DOE lightsource facilities have created a platform to enable COVID-19 research. There you can find ressources and points of contact to request priority access:
Structural Biology Resources at DOE Light Sources

Elettra Sincrotrone Trieste in Italy opens to remote acces following beamlines: XRD1, XRD2, SISSI-BIO and MCX thanks to an CERIC-ERIC initiative:
https://www.ceric-eric.eu/2020/03/10/covid-19-fast-track-access/
http://www.elettra.eu/userarea/user-area.html

The Advanced Light Source (ALS) at LBNL in California / USA has capabilities relevant to COVID-19 and researchers can apply through their RAPIDD mechanism:
https://als.lbl.gov/apply-for-beamtime/

ALBA Synchrotron in Spain offers a COVID-19 RAPID ACCESS on all beamlines:
https://www.albasynchrotron.es/en/en/users/call-information

SOLARIS Synchrotron in Poland gives acces to its Cryo Electron Microscope thanks to an CERIC-ERIC initiative: https://www.ceric-eric.eu/2020/03/10/covid-19-fast-track-access/

Swiss Light Source and Swiss FEL at PSI in Switzerland offer priority access to combating COVID-19:
https://www.psi.ch/en/sls/scientific-highlights/priority-access-call-for-work-on-combating-covid-19

Diamond Light Source in the United Kingdom opened also a call for rapid access:
https://www.diamond.ac.uk/Users.html

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

#SynchroLightAt75 – APS lights the way to 2012 Chemistry Nobel

Thanks in part to research performed at the U.S. Department of Energy’s (DOE) Argonne National Laboratory, the 2012 Nobel Prize in Chemistry was awarded today to Americans Brian Kobilka and Robert Lefkowitz for their work on G-protein-coupled receptors.

G-protein-coupled receptors, or GPCRs, are a large family of proteins embedded in a cell’s membrane that sense molecules outside the cell and activate a cascade of different cellular processes in response. They constitute key components of how cells interact with their environments and are the target of nearly half of today’s pharmaceuticals.

These medicines work by connecting with many of the 800 or so human GPCRs. But to do this well, a drug needs to connect to the protein like a key opens a lock. Improving drugs requires knowing exactly how these proteins work and are structured, which is difficult because the long, slender protein chains are folded in an intricate pattern that threads in and out of the cell’s membrane.

In a study performed at Argonne in 2007, Kobilka, a professor at Stanford University, used intense X-rays produced by the laboratory’s Advanced Photon Source (APS) to make the first discovery of the structure of a human GPCR. This receptor, called the human β2 adrenoreceptor (β2AR), is responsible for a number of different biological responses, including facilitating breathing and dilating the arteries.

Read more on the Argonne National Laboratory website

Image: This is an image of a G-protein-coupled receptor signaling complex whose structure was identified in 2011. The receptor is in magenta while the different G protein subunits are colored green, red and blue. Stanford biochemist Brian Kobilka shared the 2012 Nobel Prize in Chemistry for his work in determining the structure of this activated GPCR using X-rays provided by Argonne’s Advanced Photon Source.

Atomic displacements in High-Entropy Alloys examined

High-entropy alloys of 3d metals have intriguing properties that are interesting for applications in the energy sector. An international team at BESSY II has now investigated the local order on an atomic scale in a so-called high-entropy Cantor alloy of chromium, manganese, iron, cobalt and nickel. The results from combined spectroscopic studies and statistical simulations expand the understanding of this group of materials.

High-entropy alloys are under discussion for very different applications: Some materials from this group are suitable for hydrogen storage, others for noble metal-free electrocatalysis, radiation shielding or as supercapacitors.

The microscopic structure of high-entropy alloys is very diverse and changeable; in particular, the local ordering and the presence of different secondary phases affect significantly the macroscopic properties such as hardness, corrosion resistance and also magnetism. The so-called Cantor alloy, which consists of the elements chromium, manganese, iron, cobalt and nickel mixed in an equimolar proportion, can be considered as a suitable model system for the whole class of these materials.

Local structure studied at BESSY II

Scientists from the Federal Institute for Materials Research (BAM, Berlin), the University of Latvia in Riga, Latvia, the Ruhr University in Bochum and the HZB have now studied the local structure of this model system in detail. Using X-ray absorption spectroscopy (EXAFS) at BESSY II, they were able to precisely track each individual element and their displacements from the ideal lattice positions for this system in the most unbiased manner with the help of statistical calculations and the reverse Monte Carlo method.

Read more on the HZB website

Image: The supercell is randomly filled with the five elements on the fcc-lattice positions; In the starting configuration, all layers are precisely on top of each other. The displacements of all elements in the final configuration have been revealed by a simultaneous fit of the independent experimental spectra with a use of Reverse Monte Carlo simulations.

Credit: © A.Kuzmin / University of Latvia and A. Smekhova / HZ

It sucked to be the prey of ancient cephalopods

The Jurassic cephalopod Vampyronassa rhodanica, thought to be the oldest known ancestor of the modern-day vampire squid (Vampyroteuthis infernalis), was likely an active hunter – a mode of life that is in contrast with its opportunistic descendant. Scientists led by Sorbonne University came to this conclusion after analysing microtomographic data of this rare fossil, acquired at the ESRF and the Muséum national d’Histoire naturelle in Paris. The results are published today in Scientific Reports.

Vampyronassa rhodanica is thought to be one of the oldest relatives of the modern-day vampire squid (Vampyroteuthis infernalis), which is the only remaining living species of its family. This modern form lives in extreme deep ocean environments, often with little oxygen, and feeds on drifting organic matter. Like V. infernalis, the body of V. rhodanica was mostly made of soft tissue. As this rarely fossilises, little is known about the physical characteristics and evolutionary history of this family.

Despite the scarcity of fossil material from this family, Alison Rowe, from Sorbonne University and colleagues were able to study 3 well-preserved V. rhodanica specimens from La Voulte-sur-Rhône (Ardèche, France), dating to more than 164 million years ago. The eight-armed specimens were small, measuring around 10 cm in length, and had elongated oval-shaped bodies with two small fins.

They took them to the ESRF for non-destructive 3-D imaging: “We used synchrotron tomography at the ESRF in order to better identify the outlines of the various anatomical features”, says Rowe. However, the task was challenging, as Vincent Fernández, scientist at the ESRF, explains: “The fossils are on small slabs, which are very difficult to scan. On top of that, soft tissues are preserved but we needed phase contrast imaging to visualise the faint density variation in the data. The coherence of beamline ID19 was therefore very important to perform propagation phase-contrast computed-tomography and track all the minute details, such as the suckers and small fleshy extensions, called cirri”. 

Read more on the ESRF website

Image: Hypothesised reconstruction of Vampyronassa rhodanica

Credit: A. Lethiers, CR2P-SU

#SynchroLightAt75 – X-ray detector technology

X-Ray detectors first developed at Paul Scherrer Institute PSI in the 1990s to aid the search for the Higgs Boson at CERN and then applied to the Swiss Light Source SLS led to the spin-off, Dectris. Today this company employs over 100 people and its cutting-edge detectors are used at synchrotron and free electron laser (FEL) light sources worldwide for diverse applications ranging from protein structure determination to investigations into novel materials.

As the light source community marks #SynchroScienceAt75, we look back on this fascinating chapter in the history of light sources….

From the Higgs boson to new drugs (story published by PSI in 2016)

New ultrafast detector at the Paul Scherrer Institute

A picture-perfect example of how basic research makes solid contributions to the economy is the company DECTRIS in Baden-Dättwil, Switzerland — a spin-off of the Paul Scherrer Institute PSI, founded in 2006 and already highly successful. The detector that became, around ten years ago, the company’s founding product originated in the course of the search for the Higgs boson. Now the newest development from DECTRIS is on the market: an especially precise detector called EIGER, which is used for X-ray measurements at large research facilities. Since the fall of 2015, the newest model of the EIGER series has proven itself at the Swiss Light Source SLS. These days, researchers are writing the first scientific publications about experiments that have been carried out with the new detector. EIGER helps researchers to measure protein molecules better and more precisely than before. That in turn is of great interest for the development of new pharmaceuticals. It’s possible that urgently needed alternatives to antibiotics might be found in this way.

Read more on the PSI website

Image: PSI scientist Justyna Wojdyla and DECTRIS engineer Michel Stäuber with the EIGER X 16M – the spin-off company’s newest and, so far, highest-performance X-ray detector (caption from 2016)

Credit: Scanderbeg Sauer Photography

What role does Elongator play in brain development?

What role does a tRNA modification complex, called Elongator, play in brain development?

SOLARIS Centre users from the Malopolska Centre of Biotechnology (of the Jagiellonian University, together with Australian, Turkish and Canadian colleagues, have found a link between defects in the cellular protein production machinery and neurodevelopmental disorders (NDDs), characterized by an inability to reach cognitive and motor milestones. Key studies in this publication were conducted using Cryo-EM microscopes located at our center.

The speed rate of protein synthesis is crucial to the integrity of the proteome

Scientists showed how genetic mutations in patients affect the Elongator activity and lead to severe clinical symptoms. The study provided the first clinical evidence for missense mutations in the Elongator accessory subcomplex ELP456 to cause neurodevelopmental disorders. Genome-wide analysis allowed identification of pathogenic variants in patients with severe clinical presentation of NDDs. Further modelling of the patient-derived mutations in mice resembled the complex neurodevelopmental phenotype and revealed neuron-specific consequences of the found genetic mutations.

We report patient-derived substitutions in the accessory ELP456 subcomplex to affect different types of neurons than previously known mutations in the catalytic core of the complex” – explains Dr. hab. Sebastian Glatt, the senior author and head of the Max Planck Research Group, that carried out the experimental work in Krakow. This provides a novel concept in the field that depletion of specific tRNA modifications in patient cells may induce specific changes in the cellular proteomes.

Read more on the SOLARIS website

Calculating the “fingerprints” of molecules with artificial intelligence

With conventional methods, it is extremely time-consuming to calculate the spectral fingerprint of larger molecules. But this is a prerequisite for correctly interpreting experimentally obtained data. Now, a team at HZB has achieved very good results in significantly less time using self-learning graphical neural networks.

“Macromolecules but also quantum dots, which often consist of thousands of atoms, can hardly be calculated in advance using conventional methods such as DFT,” says PD Dr. Annika Bande at HZB. With her team she has now investigated how the computing time can be shortened by using methods from artificial intelligence.

The idea: a computer programme from the group of “graphical neural networks” or GNN receives small molecules as input with the task of determining their spectral responses. In the next step, the GNN programme compares the calculated spectra with the known target spectra (DFT or experimental) and corrects the calculation path accordingly. Round after round, the result becomes better. The GNN programme thus learns on its own how to calculate spectra reliably with the help of known spectra.

Read more on the HZB website

Image: The graphical neural network GNN receives small molecules as input with the task of determining their spectral responses. By matching them with the known spectra, the GNN programme learns to calculate spectra reliably.

Credit: © K. Singh, A. Bande/HZB

Karen Appel’s #My1stLight

Karen was a beamline scientist at DESY and is currently a beamline scientist at the European XFEL

My first synchrotron experiment was at beamline L at DORIS at DESY, which at that time just set up the possibility to do micro-focus X-ray fluorescence measurements. The first experiment I was involved in was headed by the group of Prof Schenk at the Institute of Mineralogy of the University of Kiel  and focused on minerals that were formed at high pressures and high temperatures. At that moment, I was a PhD student at the University of Bonn, working on metamorphic rocks and isotope geochemistry of rocks and got involved in the experiment, because I was interested in analytical methods that could be applied to minerals that were formed at high pressures and temperatures. Besides some connections through my earlier studies, my main interest was to learn about this new method of X-ray fluoresence. We investigated the chemical trace element composition (Rare Earth elements) of minerals that were formed during metamorphic processes and commonly show a gradient of the element distribution, which is related to the metamorphic formation process. 

As we were simply providing the samples, we had the chance to have a close look at the instrumentation. Having worked with commercial machines so far, I remember that I was very much impressed by the modular set- up of a beamline and this one-day experience motivated me to apply for a job that was offered from GFZ Potsdam that included a main part in experimental work at beamline L.

Later, as a postdoc, my experiences led me into the van Gogh experiment, where we used the polychromatic mode at beamline L and were able to detect the elemental distributions of a van Gogh painting. Now I am working at the High Energy Density Science instrument at the European XFEL, studying extreme states of matter, allowing me to work as a beamline scientist and also pursue my own scientific interests.

Image (above): Karen and her colleague working at the experimental station at the beamline L of DORIS III.

Credit: DESY

Image: DE: Die Experimentierstation HED (High Energy Density Science) dient der Erforschung von Materie unter extremen Druck- und Temperaturbedingungen oder sehr starken elektromagnetischen Feldern. Zu den wissenschaftlichen Anwendungen gehört die Untersuchung von Zuständen, wie sie im Inneren astrophysikalischer Objekte wie Exoplaneten bestehen, von Phasenzuständen unter extremem Druck, von Plasmen mit hoher Dichte oder von Phasenübergängen komplexer Feststoffe unter dem Einfluss starker Magnetfelder. EN: The HED experiment station will be used to study matter under extreme conditions of pressure, temperature, or electromagnetic fields. Scientific applications will be studies of matter occurring inside astrophysical objects such as exoplanets, of new extreme-pressure phases and solid-density plasmas, and of phase transitions of complex solids in high magnetic fields.

Credit: European XFEL / Jan Hosan

Inauguration of SESAME’s fourth beamline

12 June saw the inauguration of yet another beamline at the SESAME synchrotron light facility near Amman (Jordan). This was the HElmholtz-SEsame Beamline (HESEB) for soft X-ray light designed and constructed by a consortium of five Helmholtz Research Centers of the Helmholtz Association under the lead of DESY. HESEB is a new, state-of-the-art measuring facility for experiments with soft X-ray light that will substantially widen research opportunities for scientists from the region and enable new international collaborations with many institutions, including German institutions. 

Among the dignitaries present to celebrate the event, to cut the ribbon and unveil a commemorative plaque marking the inauguration were H.E. Professor Wajih Owais, Minister of Higher Education and Scientific Research of Jordan, H.E. Mr Bernhard Kampmann, Ambassador of Germany to Jordan, Professor Rolf-Dieter Heuer, President of the SESAME Council, Professor Otmar Wiestler, President of the Helmholtz Association of German Research Centers, and Professor Helmut Dosch, Chair of the Board of Directors at DESY – on behalf of the HESEB Consortium. Also present were the Governor of Balqa Governorate, the President of the Al-Balqa’ Applied University, members of the Jordan Parliament and of the Local Council, a high-level delegation from the Helmholtz Centers, and representatives of the Turkish and United Arab Emirates community and the local community. 

Read more on the SESAME website

Image: Commemorative plaque and the HESEB beamline

Credit: © SESAME 2022

Cutting-edge imaging yields new insights into stroke

Synchrotron’s “superhuman vision” made it easy to detect markers of brain damage.

Hemorrhagic stroke, where a weakened vessel in the brain ruptures, can lead to permanent disability or death. Across the globe, over  15 million people are coping with its effects.

A study by researchers from the University of Saskatchewan (USask) and Curtin University in Australia has moved us one step closer to identifying when the bleeding associated with a hemorrhagic stroke starts – critical information for improving patient outcomes.

Time is of the essence when it comes to stroke; the sooner doctors can start treatment, the better the odds they can limit damage.

Using the Mid-IR beamline at the Canadian Light Source at USask, the team examined brain tissue samples with a special technique called Fourier-transform infrared imaging. The researchers were led by Dr. Lissa Peeling, a neurosurgeon at the Royal University Hospital and an Associate Professor in the Department of Surgery at USask.

The novel approach enabled the researchers to identify changes in the brain specific to hemorrhagic stroke.

Dr. Jake Pushie, a member of Dr. Kelly’s and Dr. Peeling’s research team at USask’s College of Medicine, said the combination of the beamline and infrared imaging made it easy to detect markers of brain damage caused by hemorrhagic stroke.

“In a sense, this is giving us ‘superhuman vision’ to look at these brains and map out what’s happening metabolically,” said Pushie.

With synchrotron technology, the team could see where a bleed originated and the extent of oxidative damage it caused – something impossible to do with a microscope or traditional approaches to imaging. Their findings were published in Metallomics.

Armed with this new approach, and a better understanding of what they are looking for, Pushie and colleagues will now go back through their extensive “library” of stroke tissue samples to gain a clearer picture of the speed at which oxidative damage begins to ramp up.

Read more on the CLS website

Image: Team member Nicole Sylvain, with USask’s College of Medicine, in a lab at the CLS

#SynchroLightAt75 – Rod MacKinnon’s Nobel Prize in chemistry

Rod MacKinnon – Nobel Prize in chemistry 2003 for work on the structure of ion channels  

The structural work of MacKinnon was carried out primarily at the Cornell High Energy Synchrotron Source (CHESS) and the National Synchrotron Light Source (NSLS) at Brookhaven. At the time, CHESS was a first-generation SR source.  The award for MacKinnon’s work was the second recognition of SR work by the Nobel Committee. MacKinnon acknowledges the crucial role that the two synchrotron facilities, Cornell Synchrotron (CHESS/MacCHESS) and NSLS, have played in his research on the protein crystallography of membrane channels.

He said, `Without exaggeration that most of what is known about the chemistry and structure of ion channels has come from experiments carried out at these SR centres’.

Rod MacKinnon

Read more on the Nobel Prize website

Image: View showing the location of CHESS, which is underground at Cornell

Credit: Jon Reis

Gerold Rosenbaum’s #My1stLight

From Gerold Rosenbaum – Advanced Photon Source user

A Playful Use of the Last 10 Minutes of a Run Turns Out to be Very Educational

In 1967, after finishing data collection on the DESY XUV beamline on the polarizer/polarization analyzer I had built for my diploma thesis, there were 15 minutes to go before the synchrotron was to be shut down. Since I always wanted to know how good the vacuum had to be for working in the XUV, I suggested to bleed up the 1-m-long sample chamber to 1/10000 atm or 0.08 torr. The playful use of the last 10 minutes of the run turned out to be an impressive demonstration of the superiority of the continuous spectrum of synchrotron radiation over other XUV sources (paired with a high-resolution monochromator). The very low intensity below 800 Å, even though at the peak of the monochromator spectrum, told me clearly where vacuum-UV starts.

Journal reference: R.P. Godwin, “Synchrotron radiation as a light source,” Springer-Verlag Tracts in Modern Physics 51, p.66, 1969.

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New Director for massive upgrade into Diamond-II

To cement its position as a world-leading research facility, Diamond Light Source recently revealed plans for a large upgrade called Diamond-II and that is set to strengthen the UK’s global scientific leadership. This will be a transformational upgrade that will enable a huge expansion of UK science capabilities as it involves a coordinated programme of development combining state-of-the-art technology in a new machine, five new flagship beamlines and a comprehensive series of upgrades to its Instruments.

To lead this programme, Diamond has appointed Rob Walden, a Chartered Engineer with over 20 years’ experience in delivering business and process improvement programmes in the aerospace manufacturing engineering industry. This was followed by several years as a senior projects advisor in central government where he was involved in, and delivered, nationwide policy projects as well as helping to develop the programme delivery framework for government. Rob was also part of the Cabinet Office’s Gateway Assurance review team and conducted a number of forensic assurance delivery reviews for programmes of national interest. Additionally, he helped to set up the national programme office structure for Highways England and ran two busy Project Management Offices.

Rob joined Diamond Light Source from Sellafield Ltd where he focused on raising the standards of the programme delivery framework, which included the appointment and development of the SRO (Senior Responsible Officer) function for major projects of national interest. Rob comments:

For over 15 years Diamond has been a leading centre for synchrotron science on the world stage, supporting UK business and academia to undertake cutting-edge research in a diverse set of areas and sectors. I am delighted to join a team of such esteemed colleagues as we move into the next chapter in Diamond’s life, the detailed planning of the delivery of Diamond-II to secure long-term funding, pushing the boundaries of scientific research even further and keeping the UK at the forefront of scientific research.

Read more on the Diamond website

Image: Rob Walden, programme director for Diamond-II

Credit: Diamond Light Source

Understanding the structural implications of genetic mutations in heart-muscle disease

Cardiomyopathies are diseases of the heart muscle in which the muscle of the pumping chamber (ventricle) can become enlarged (dilated cardiomyopathy; DCM) or thickened (hypertrophic cardiomyopathy; HCM), potentially leading to heart failure. There are currently no effective treatments but the disease often has a genetic component related to mutations in the heart muscle proteins that are involved in muscle contraction, so some researchers have focused their therapeutic development efforts on correcting these muscle contraction problems based on the structural basis of the defect. A recent study from a team of researchers using the U.S. Department of Energy’s Advanced Photon Source (APS) employed humanized mouse models expressing mutations observed in patients with HCM and DCM to evaluate the structure-function relationships and the changes observed in cardiac muscle contraction with these mutations. The work, published in the Proceedings of the National Academy of Sciences of the United States of America, provides a deeper understanding of the effects of cardiomyopathy-causing gene mutations on heart muscle contraction that could lead to the development of new therapies for this potentially life-threatening disease.

About 70% of patients with inherited HCM have a defect in the gene for the cardiac myosin protein or the cardiac myosin binding protein C. However, recent genetic evidence has suggested that mutations in the cardiac regulatory light chain (RLC) MYL2 gene are more common than previously thought and can be associated with poor outcomes. In order to understand the structural basis for how mutations in the MYL2 gene can cause HCM, or the less commonly occurring DCM, the research team performed muscle structure and force measurement experiments on heart muscle samples from mice that express mutated human RLC proteins, the HCM-D166V mutation associated with hypertrophic cardiomyopathy or the DCM-D94A mutation associated with dilated cardiomyopathy.

Normally, the cardiac regulatory light chain protein acts as a major subunit of the cardiac myosin protein to regulate calcium-mediated interactions with other muscle proteins and the myosin movements that result in the power stroke of muscle contraction. On this basis, the team set out to understand the relationship between these two mutations in the MYL2 gene and associated defects in the function of RLC in cardiomyopathy.

They used the small-angle x-ray diffraction technique at the Biophysics Collaborative Access Team 18-ID x-ray beamline at the APS to compare the spatial orientation of the thick and thin muscle filaments in left ventricular papillary muscle (LVPM) from mice expressing the mutated human RLC to mice expressing the normal, unmutated wildtype human cardiac RLC. (The APS is an Office of Science user facility at Argonne National Laboratory.)

In this model system, small-angle x-ray diffraction can measure interfilament lattice spacing that is proportional to the distance between two adjacent muscle filaments and equatorial intensity ratios that provide information about the number of myosin heads that are attached to actin-containing thin filaments (cross-bridges). By comparing structural results at different concentrations of calcium and simultaneously recording force traces, they were able to get structure-function information for all three muscle types. The intensity ratios at different calcium concentrations showed that contraction of the HCM mutant muscles were the most sensitive to calcium, forming more cross-bridges at submaximal calcium concentrations than either the DCM mutant or the wildtype muscle.

Read more on the APS website

Image: Mechanism of action for HCM-D166V and DCM-D94A mutations. The HCM-D166V model disrupts the SRX state and promotes the SRX-to-DRX transition increasing the number of DRX heads and leading to hypercontractile behavior. The DCM-D94A model stabilizes the SRX state yielding fewer heads available for contraction and leading to clinical hypocontractility. Abbreviations: ELC, myosin essential light chain; RLC, regulatory light chain; DRX, disordered relaxed; SRX, super-relaxed.

#SynchroLightAt75 – The first multi-bend achromat synchrotron light source

At the end of the 1990’s, the MAX-lab management realized that it was necessary to start planning for a possible next step in the development of the laboratory. Although MAX II, one of the first 3rd generation light sources in the world and the flagship of the laboratory, had just recently come into operation, the long lead times made it necessary to start exploring possible further developments already at that stage. This is the saga of MAX IV Laboratory, the world’s first Multi-Bend Achromat (MBA) Synchrotron Radiation Light Source. MBAs strongly focus and guide electrons around the storage ring, creating an ultra-low emittance beam and therefore ultra-bright X-ray radiation.

Read more in this Nuclear Instruments and Methods in Physics Research – section A (NIM-A) publication

Image:  Prof. Ingolf Lindau, Director of MAX-lab 1991–97, shows the facility to the king of Sweden, Carl XVI Gustav, at the inauguration of MAX II, 15 September 1995

Credit:  MAX IV

Introducing Stephen Streiffer

After decades of experience in the DOE lab system and as director of a leading synchrotron light source, he’s back to where he earned his PhD – with a much bigger mission.

Thirty years after earning his PhD at Stanford University, materials scientist Stephen Streiffer will be back on campus next week – this time with an outsized role to play. As Stanford’s new vice president for the Department of Energy’s SLAC National Accelerator Laboratory, he’ll play a key part in advising and supporting the lab as it carries out its scientific mission.

Streiffer comes to Stanford and SLAC after 24 years at Argonne National Laboratory, where he did research at the lab’s Advanced Photon Source, directed APS for eight years and most recently served as chief research officer and deputy lab director for science and technology.

So he’s more than familiar with both the national lab system and the importance of DOE Office of Science user facilities, like APS and SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and Linac Coherent Light Source (LCLS), for both fundamental research and experiments with more immediate practical value.

Read Glennda Chui’s Q & A interview with Stephen on the SLAC website

Image: Stephen Streiffer, the new Stanford vice president for SLAC National Accelerator Laboratory

Credit: Mark Lopez, Argonne National Laboratory