Understanding the protein responsible for regulating heartbeats

A new research project uses the Canadian Light Source to help researchers understand the protein responsible for regulating heartbeats. Errors in this crucial protein’s structure can lead to potentially deadly arrhythmias, and understanding its structure should help researchers develop treatments. This protein, calmodulin (CaM), regulates the signals that cause the heart to contract and relax in almost all animals with a heartbeat.

“Usually you find some differences between versions of proteins from one species to another,” explains Filip Van Petegem, a professor in the University of British Columbia’s Department of Biochemistry and Molecular Biology. “For calmodulin that’s not the case—it’s so incredibly conserved.”

It also oversees hundreds of different proteins within the body, adjusting a broad array of cellular functions that are as crucial to our survival and health as a steady heartbeat.

>Read more on the Canadian Light Source website

Image: A surface representation of the disease mutant CaM (D95V, red) in complex with the piece of the voltage-gated calcium channel (blue).

The secret to Rembrandt’s impasto unveiled

Rembrandt van Rijn revolutionized painting with a 3D effect using his impasto technique, where thick paint makes a masterpiece protrude from the surface. Thanks to the ESRF, three centuries later an international team of scientists led by the Materials Science and Engineering Department of TU Delft and the Rijksmuseum have found how he did it.

Impasto is thick paint laid on the canvas in an amount that makes it stand from the surface. The relief of impasto increases the perceptibility of the paint by increasing its light-reflecting textural properties. Scientists know that Rembrandt, epitome of the Dutch Golden Age, achieved the impasto effect by using materials traditionally available on the 17thcentury Dutch colour market, namely lead white pigment (a mixture of hydrocerussite Pb3(CO3)2.(OH)2 and cerussite PbCO3), and organic mediums (mainly linseed oil). The precise recipe was, however, unknown until today.

>Read more on the European Synchrotron (ESRF) website

Image: Scientist Marine Cotte on beamline ID21.
Credit: Steph Candé.

Identification of a new genetic mutation associated with intellectual disability

Study contributes to the understanding of mechanisms involved in neurodevelopmental disorders

Once a disease-related protein or enzyme is identified as a therapeutic target, the study of its three-dimensional structure – the positions of each of its atoms and their interactions – allows a deeper understanding of its mechanisms of action.

This is possible not only for these substances produced by microorganisms, such as viruses or bacteria, capable of attacking our body. It is also possible, for example, to understand molecules normally produced by the human body itself, but which had their structure and function altered due to some genetic mutation.

Thus, in an article recently published in Nature Chemical Biology, Juliana F. de Oliveira, of the Brazilian Biosciences National Laboratory (LNBio), and collaborators elucidates the mechanism of action of a new genetic mutation in the UBE2A gene identified in patients with intellectual disability.

The UBE2A gene is located on the X chromosome and encodes the protein of the same name that participates in the process of “labeling” defective proteins inside the cell. This labeling is done by adding and protein called ubiquitin to the defective proteins as if it were a label. Next, under normal conditions, the defective proteins are sent for degradation.

>Read more on the Brazilian Synchrotron Light Laboratory (LNLS) website

Image: Overlap of the patient’s UBE2A protein structure (blue) with the normal protein (gray) evidences similarity between them. On the right, it is shown in detail the only altered amino acid in the patient’s protein due to the genetic mutation.

Tomography beamline at SESAME is officially launched

On 1st January 2019, the European Horizon 2020 project BEAmline for Tomography at SESAME (BEATS) was launched with the objective to design, procure, construct and commission a beamline for hard X-ray full-field tomography at the SESAME synchrotron in Jordan.

The European grant is worth 6 million euros and will span a four-year period from beginning 2019 to end 2022.
Led by the ESRF, the European synchrotron (France), BEATS involves leading research facilities in the Middle East (SESAME and the Cyprus Institute), and European synchrotron radiation facilities ALBA-CELLS (Spain), DESY (Germany), the ESRF (France), Elettra (Italy), INFN (Italy), PSI (Switzerland), SESAME (Jordan) and SOLARIS (Poland). The initiative is funded by the European Union’s Horizon 2020 research and innovation programme.

Nine partner institutes will join forces to lay the groundwork for the efficient and sustainable operation of the SESAME research infrastructure. Through the development and consolidation of the scientific case for a beamline for tomography, and actions to fortify the scientific community, the partners will pay particular attention to the R&D and technology needs of the SESAME Members. Built upon the OPEN SESAME project, BEATS will address the issue of sustainability of operation by preparing medium- to long-term funding scenarios for the tomography beamline and the facility.

>Read more on the European Synchrotron (ESRF) website

Beam us up

The upgrade of the U.S. Department of Energy’s Advanced Photon Source at Argonne National Laboratory will make it between 100 and 1,000 times brighter than it is today.

That factor is such a big change, it’s going to revolutionize the types of science that we can do,” said Stephen Streiffer, Argonne Associate Laboratory Director for Photon Sciences and Director of the APS. We’ll be able to look at the structure of materials and chemical systems in the interior of things — inside a turbine blade or a catalytic reactor — almost down to the atomic scale. We haven’t been able to do that before. Given that vast change, we can only dream about the science we’re going to do.”
In December, DOE approved the technical scope, cost estimate and plan of work for an upgrade of APS.
The APS upgrade has been in the works since 2010. The upgrade will reveal a new machine that will allow its 5,500 annual users from university, industrial, and government laboratories to work at a higher spatial resolution, or to work faster with a brighter beam (a beam with more X-rays focused on a smaller spot) than they can now.

>Read more on the Advanced Photon Source at Argonne National Laboratory website

Image: A closeup of the magnets that will drive the upgraded APS beams.

Illuminating nanoparticle growth with X-rays

Ultrabright x-rays at NSLS-II reveal key details of catalyst growth for more efficient hydrogen fuel cells

Hydrogen fuel cells are a promising technology for producing clean and renewable energy, but the cost and activity of their cathode materials is a major challenge for commercialization. Many fuel cells require expensive platinum-based catalysts—substances that initiate and speed up chemical reactions—to help convert renewable fuels into electrical energy. To make hydrogen fuel cells commercially viable, scientists are searching for more affordable catalysts that provide the same efficiency as pure platinum.

“Like a battery, hydrogen fuel cells convert stored chemical energy into electricity. The difference is that you’re using a replenishable fuel so, in principle, that ‘battery’ would last forever,” said Adrian Hunt, a scientist at the National Synchrotron Light Source II (NSLS-II), a U.S. Department of Energy (DOE) Office of Science User Facility at DOE’s Brookhaven National Laboratory. “Finding a cheap and effective catalyst for hydrogen fuel cells is basically the holy grail for making this technology more feasible.”

>Read more on the NSLS-II website

Image: Brookhaven Lab scientists Mingyuan Ge, Iradwikanari Waluyo, and Adrian Hunt are pictured left to right at the IOS beamline, where they studied the growth pathway of an efficient catalyst for hydrogen fuel cells.

Know your ennemy

Light source identifies a key protein interaction during E. coli infection

Escherichia coli is a common source for contaminated water and food products, causing the condition known as gastroenteritis with symptoms that include diarrhea, vomiting, fever, loss of energy, and dehydration. In fact, for children or individuals with weakened immune systems, this bacterial infection in the gut can be life-threatening.

One of the microbes responsible for gastroenteritis, known formally as enteropathogenic E. coli (EPEC), causes infections by directing a pointed, needle-like projection into the human intestinal tract, releasing toxins that make people sick.

“Enteropathogenic E. coli can fire toxic proteins from inside the bacterium right into the cells of your gut lining,” says Dustin Little, a post-doctoral researcher in the Brian Coombes lab at McMaster University’s Department of Biochemistry and Biomedical Sciences.

>Read more on the Canadian Light Source website

Image: Dustin Little and Brian Coombes in the lab.
Credit: Dustin Little. 

H2020 project PaNOSC officially started

The project PaNOSC, Photon and Neutron Open Science Cloud, is one of five cluster projects funded under the European H2020 programme.

The project, which will run until December 2022, is coordinated by the ESRF and brings together six strategic European research infrastructures.

Large-scale research infrastructures produce a huge amount of scientific data on a daily basis. For their storage and future (re)use, data need to managed according to the FAIR principles, i.e., be Findable, Accessible, Interoperable and Re-usable. The adaptation and development of both policies and technologies are key to making FAIR data a reality and to serving the broad set of stakeholders who will benefit from a coherent ecosystem of data services.

Under the headline “European Open Science Cloud (EOSC)”, projects covering a wide range of scientific disciplines from physics, astronomy, and life sciences, to social sciences and humanities, have been funded by the European Commission to build and develop the EOSC, which includes a comprehensive catalogue of services for the storage, management, analysis and re-use of research data.

>Read more on the ESRF website
>To know more about PaNOSC ( Photon and Neutron Open Science Cloud ) please read here

Injecting relativity into Engineering

When you think about the theory of relativity, physics might be the first thing you think about.

But here at Diamond Light Source, our unique facility and state of the art instrument means that even our engineering teams must keep relativity in mind. In our last Year of Engineering spotlight piece, learn more about the unique engineering opportunities that present themselves when working at a synchrotron.
There are many areas where science and engineering work together, but relativity rarely makes an appearance. Most of our daily challenges can be solved by using simpler classical mechanics, where we (correctly) assume that objects travel at speeds which are a minute fraction of the speed of light, and weigh many times less than planets or stars. However, two engineering applications used every day at Diamond involve conditions which breach those assumptions, and so they must enter the strange world of relativity.
If you mention Einstein’s theory of relativity to a physicist, they will tell you how it provides a more accurate solution to any classical mechanics problem – but often with a lot more work involved! Inside Diamond’s linac and booster accelerators, the presence of relativistic effects instead allows for some clever engineering solutions which simplify the difficult task of controlling the movement of five billion electrons.

>Read more on the Diamond Light Source website

Image: The linac, with the gun at the far end and the accelerating structures coming towards us. The electrons are already more than 0.95 times the speed of light by the time they emerge from the copper rings at the back.

Bulgarian President visits SESAME

On 15 December, the President of the Republic of Bulgaria, Rumen Radev, paid an official visit to SESAME. Among the 7 delegates accompanying him were the Deputy Prime Minister and Minister of Foreign Affairs of Bulgaria, Ekaterina Zakharieva, and Bulgaria’s Ambassador to Jordan, Venelin Lazarov. The visit was prompted by the President’s wish to see at first hand SESAME at work.

Bulgaria is one of the 9 countries forming part of SEEIIST (South East European International Institute for Sustainable Technologies), an intergovernmental project designed to promote science for peace in South East Europe following the CERN model. The other countries are Albania, Bosnia and Herzegovina, Kosovo, FYR of Macedonia, Montenegro, Serbia and Slovenia, and in the Declaration of Intent signed by the 9 countries in 2017 SESAME is cited as an example of a similar initiative that came to fruition.

>Read more on the SESAME website

Image: The Director of SESAME, Khaled Toukan, welcoming the President of Bulgaria, Rumen Radev, and the Bulgarian delegation.
Credit: SESAME

Construction starts on new Cryo-EM center

Called the Laboratory of BioMolecular Structure, the new cryo-electron microscope center will offer world-leading imaging capabilities for life sciences research.

Today, the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory broke ground on the Laboratory of BioMolecular Structure (LBMS), a state-of-the-art research center for life science imaging. At the heart of the center will be two new NY-State-funded cryo-electron microscopes (cryo-EM) specialized for studying biomaterials, such as complex protein structures.

“Cryo-electron microscopy is a rapidly-advancing imaging technique that is posting impressive results on a weekly basis,” said LBMS Director Sean McSweeney. “The mission of LBMS is to advance the scientific understanding of key biological processes and fundamental molecular structures.”

“Throughout my career, I have worked hard to make our region of the State a high-tech hub, bringing together the talents and expertise of scientists and facilities across Long Island.  I am pleased to have played a part in the creation of the new cryo-EM center, which will add to the incredible facilities at Brookhaven National Lab and enable our scientific community to lead the way in world-class imaging research and discovery,” said NY State Senator Ken LaValle.

>Read more on the NSLS-II at BNL website

Image: New York State Senator Ken LaValle joined leaders of Empire State Development and Brookhaven Lab for the LBMS groundbreaking ceremony. Pictured from left to right are Jim Misewich (Associate Laboratory Director for Energy and Photon Sciences, Brookhaven Lab), Erik Johnson (NSLS-II Deputy for Construction), Sean McSweeney (LBMS Director and NSLS-II Structural Biology Program Manager), Robert Gordon (DOE-Brookhaven Site Office Manager), Ken LaValle, Cara Longworth (Regional Director, Empire State Development), Danah Alexander (Senior Project Manager, Empire State Development), and John Hill (NSLS-II Director).

Secrets of the deadly white-tail virus revealed

The inner workings of a lethal giant freshwater prawn virus have been revealed by an international team of researchers using data gathered at Diamond Light Source. The results reveal a possible new class of virus and presents the prospect of tackling a disease that can devastate prawn farms around the world.

The detailed structure of a virus that can devastate valuable freshwater prawn fisheries has been revealed by an international team using image data collected in the Electron Bio-Imaging Centre (eBIC) based at Diamond Light Source. The researchers produced high-resolution images of virus like particles, VLP’s, composed of virus shell proteins which they compared with lower resolution images of the complete virus purified from prawn larvae. They found strong similarities between the two suggesting that the more detailed VLP images are a good representation of the intact virus. This research, exposing the inner workings of the MrNV, could make it easier to develop ways of combating the economically important disease, but also suggests that it belongs in a new, separate, group of nodaviruses.
The researchers used the rapidly developing technique of cryo-electron microscopy, cryoEM, which has the ability to produce very high-resolution images of frozen virus particles. Images so detailed that the positions of individual atoms could be inferred. Recent breakthroughs in this technique have transformed the study of relatively large biological complexes like viruses allowing researchers to determine their structures comparatively quickly. The data to produce the MrNV structure described here was captured in two days at the eBIC facility.

>Read more on the Diamond Light Source website

Image: 3D model of the MrNV
Credit: Dr David Bhella

Progress on low energy electronics

Soft X-ray experiments used to characterise new thin film topological Dirac Semimetal

A large international collaboration including scientists from Monash University, the ARC Centre for Future Low Energy Electronics (FLEET), the Monash Centre for Anatomically Thin Materials and the Australian Synchrotron reported today in Nature on the development of an advanced material that is able to switch between an electrically conductive state to an insulating state, simply by applying an electric field.
The work represents a step towards the development of a new generation of ultra-low energy electronics at room temperature. 
Co-author Dr Anton Tadich, a beamline scientist at the Soft X-ray beamline and Partner Investigator with FLEET, collaborated with investigators from Monash University, Singapore and Lawrence Berkeley National Lab on the use of photoemission techniques at the Australian Synchrotron X-ray Photoelectron Spectroscopy (XPS) and the Advanced Light Source in the US Angle Resolved Photoelectron Spectroscopy, (ARPES).
The chemical composition and growth mechanisms of thin films of the topological Dirac semi-metal sodium bismuthide Na3Bi on a silicon substrate was investigated using XPS at the Australian Synchrotron’s Soft X-ray beamline.

>Read more on the Australian Synchrotron at ANSTO website

Topological matters: toward a new kind of transistor

X-ray experiments at Berkeley Lab provide first demonstration of room temperature switching in ultrathin material that could serve as a ‘topological transistor’

Billions of tiny transistors supply the processing power in modern smartphones, controlling the flow of electrons with rapid on-and-off switching. But continual progress in packing more transistors into smaller devices is pushing toward the physical limits of conventional materials. Common inefficiencies in transistor materials cause energy loss that results in heat buildup and shorter battery life, so researchers are in hot pursuit of alternative materials that allow devices to operate more efficiently at lower power.
Now, an experiment conducted at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has demonstrated, for the first time, electronic switching in an exotic, ultrathin material that can carry a charge with nearly zero loss at room temperature. Researchers demonstrated this switching when subjecting the material to a low-current electric field.

>Read more on Advanced Light Source (ALS) at LBNL website

Image: James Collins, a researcher at Monash University in Australia, works on an experiment at Beamline 10.0.1, part of Berkeley Lab’s Advanced Light Source.
Credit: Marilyn Chung/Berkeley Lab

No beam for a while. #SeeUin2020

The 10th December 2018, marks a key date in the history of the ESRF.

Thirty years after the signature of the ESRF Convention, the beam has been stopped for the last time in the original storage ring. Now begins a 20-month shutdown to dismantle the storage ring that has served the international scientific community with bright and reliable X-rays for the last 30 years, to make way for a new and revolutionary X-ray source, the Extremely Brilliant Source (EBS) which will open to users in 2020.

Today, the EBS project is officially entering a new stage, which is the fruit of our hard work of the last four years. Our imagination, engineering design, quality control and assembly, guided by strict project management, has made it possible to start the swap in our tunnel between the old and the new storage ring. This is possible thanks to the great capability of ESRF staff”, said Francesco Sette, ESRF Director General.

>Read more on the ESRF website

In-situ single-shot diffractive fluence mapping for x-ray FEL pulses

Free-electron lasers (FEL) for the extreme-ultraviolet (XUV) and x-ray regime opened up the possibility to investigate and exploit non-linear processes in the interaction of x-rays with matter. Such processes are of considerable interest in numerous research fields, owing to the huge impact of non-linear techniques on optics and spectroscopy in the visible and near-visible spectral range. Generating and understanding non-linear effects requires sophisticated control of the sample illumination. This is especially challenging at FEL sources, where variations of the spatial fluence distribution on a single-shot basis are common. Moreover, the focused spot often exhibits a complex internal structure due to diffraction artefacts from the focusing optics. These factors cause considerable uncertainties with respect to the effective fluence on a solid sample for scattering experiments in the forward direction.
We demonstrate a flexible solution for true in-situfluence monitoring on solid samples in transmission-type diffraction experiments. Our concept measures the detailed beam footprint on the actual sample under study. The image of the illumination is recorded simultaneously with the specimen’s primary scattering signal on a two-dimensional detector. This is facilitated by a shallow grating structure of only a few nanometer depth that is lithographically fabricated into the sample carrier membrane. Such membranes are routinely used in transmission-type diffraction experiments as a transmissive structural support for thin-film or sparsely dispersed samples. The grating structure forms a diffractive optical element that maps the spatial fluence distribution on the sample to a configurable position on the detector.

>Read more on the Elettra Sincrotrone Trieste website

Image: Figure 1.  a) Single-shot diffraction image of a sample with grating-based fluence monitor and ferromagnetic domains on a logarithmic false-color scale. The ring-shaped structure is due to the magnetic domains, while the fluence monitor grating gives rise to the brighter patterns on the image diagonals. Both grating patterns are equivalent images of the beam footprint on the sample. b) Enlarged detail of the diffracted fluence map on the sample on a linear false-color scale. c) AFM image of a single-shot damage crater in the sample’s silicon substrate. The pattern observed matches the in-situ measured beam footprint very well, but belongs to a different FEL shot. Scale bars are 10µm. Adapted from M. Schneider et al., Nature Communications 9, 214 (2018)