Discovering a whole new family of copper-binding proteins

While studying a class of copper-containing enzymes, a team of researchers discovered and characterised a new family of fungal proteins.

Their study has now been published on Nature Chemical Biology, including analysis performed at BioMAX. The article is published together with a parallel study that sheds light on one of the potential biological roles of the proteins in this new family.

In contrast with a certain romanticised idea of research, scientific discoveries seldom come with a shouted “eureka!” as to mark the end of a linear intellectual endeavour. Much more frequently, new scientific findings emerge from observations where a scientist’s first reaction might sound like “that’s odd…”. Perhaps that was how the authors of this study reacted when they realised what they were looking at wasn’t what they were looking for.

In an article published this week on Nature Chemical Biology, a team of scientists from INRA, University of Copenhagen, Marseille Université, and University of York characterised a new family of proteins, named X325, found in various fungal lineages. The article is published together with a parallel study in which one protein of this new family, Bim1, is described as involved in fungal meningitis.

The authors were initially searching for new lytic polysaccharide monooxygenases (LPMOs), copper-dependent enzymes specialised in the degradation of polysaccharides and widely used in the production of biofuels. The proteins of this new family seemed promising candidates since they share many structural features and a probable common ancestor with LPMOs. However, the researchers proved that the members of this LPMO-like protein family are not involved in polysaccharides degradation, but they more likely play a role in the regulation of copper ion content in the organisms where they are expressed.

>Read more on the MAX IV website

Image: Copper binding site of two different proteins. Left: LaX325 protein belonging to the newly identified LPMO-like protein family X325. Right: cellulose cleaving LPMO enzyme TaAA9.
Image developed by Tobias Tandrup, University of Copenhagen.

Stopping yellow spot fungus that attacks wheat crops

Scientists from the Centre for Crop and Disease Management (CCDM) and Curtin University in Western Australia have used an advanced imaging technique at the Australian Synchrotron for an in-depth look at how a fungus found in wheat crops is damaging its leaves.

Prof Mark Gibberd, director of the Centre, said the investigation was thought to be one of the first that utilised high-resolution X-ray imaging to examine biotic stress related to fungal infection in wheat.
Using X-ray fluorescence microscopy (XFM) on leaf samples collected from wheat plants, the team, which included project leader Dr Fatima Naim and ARC Future Fellow Dr Mark Hackett, mapped specific elements in the leaves in and around points of infection.

“Our research project looks at the physiological impact of plant diseases, such as yellow spot, on the function of leaves” said Gibberd.
Yellow spot is a ubiquitous fungal disease caused by Pyrenophora tritici-repentis (Ptr). It can reduce grain yields by up to 20 per cent – a significant amount which could be the difference between a profitable and non-profitable crop for a farmer.
In Australia, it is one of the most costly diseases to the wheat industry, with wheat yield losses due to yellow spot estimated at over $210 million per year. 

>Read more on the Autralisan Synchrotron at ANSTO website

Image: FM image reveals elements present in yellow spot fungs and the wheat leaves.
Credit: Curtin University

Watching complex molecules at work

A new method of infrared spectroscopy developed at BESSY II makes single-measurement observation and analysis of very fast as well as irreversible reaction mechanisms in molecules feasible for the first time.

Previously, thousands of such reactions have had to be run and measured for this purpose. The research team has now used the new device to investigate how rhodopsin molecules change after activation by light – a process that is the basis of how we see.

Time-resolved infrared spectroscopy in the sub-millisecond range is an important method for studying the relationship between function and structure in biological molecules. However, the method only works if the reaction can be repeated many thousands of times. This is not the case for a large number of biological processes, though, because they often are based on very rapid and irreversible reactions, for example in vision. Individual light quanta entering the rods of the retina activate the rhodopsin protein molecules, which then decay after fulfilling their phototransductionfunction.

>Read more on the BESSY II at HZB website

Image: Rhodopsin before (left) and after activation by light (right): The activation causes changes in functional groups inside the molecule (magnifying glass), which affect the entire molecule.
Credit: E. Ritter/HZB

Twisting the helix: salt dependence of conformations of RNA duplexes

Ribonucleic acid (RNA) is a macromolecule essential in various biological roles in coding, decoding, regulation and expression of genes. Its biological functions depend critically on its structure and flexibility. To date, no consistent picture has been obtained that describes the range of conformations assumed by RNA duplexes. Here, Cornell researchers used X-ray scattering at CHESS to quantify these variations. Their results quantify the substantial and solution-dependent deviations of double-stranded (ds) RNA duplexes from the assumed canonical A-form conformation.

>Read more on the CHESS website

Image: Left: Experimental X-ray scattering curves for RNA duplexes in solutions containing dfferent concentrations of KCl and MgCl2. Right: RNA conformations resulting form the experimental data in comparison with the canonical RNA structure.

Scientists observe ultrafast birth of free radicals in water

What they learned could lead to a better understanding of how ionizing radiation can damage material systems, including cells.

Understanding how ionizing radiation interacts with water—like in water-cooled nuclear reactors and other water-containing systems—requires glimpsing some of the fastest chemical reactions ever observed.

In a new study conducted at the Department of Energy’s SLAC National Accelerator Laboratory, researchers have witnessed for the first time the ultrafast proton transfer reaction following ionization of liquid water. The findings, published today in Science, are the result of a world-wide collaboration led by scientists at the DOE’s Argonne National Laboratory, Nanyang Technological University, Singapore (NTU Singapore) and the German research center DESY.

The proton transfer reaction is a process of great significance to a wide range of fields, including nuclear engineering, space travel and environmental remediation. This observation was made possible by the availability of ultrafast X-ray free electron laser pulses, and is basically unobservable by other ultrafast methods. While studying the fastest chemical reactions is interesting in its own right, this observation of water also has important practical implications.

>Read more on the LCLS at SLAC website

Image: X-rays capture the ultrafast proton transfer reaction in ionized liquid water, forming the hydroxyl radical (OH) and the hydronium (H3O+) ion. Credit: Argonne National Laboratory

Milestone in ALS-Upgrade project will bring in a new ring

Construction of innovative accumulator ring as part of ALS-U project will keep Berkeley Lab at the forefront of synchrotron light source science.

An upgrade of the Advanced Light Source (ALS) at the U.S. Department of Energy’s (DOE’s) Lawrence Berkeley National Laboratory (Berkeley Lab) has passed an important milestone that will help to maintain the ALS’ world-leading capabilities.

On Dec. 23 the DOE granted approval for a key funding step that will allow the project to start construction on a new inner electron storage ring. Known as an accumulator ring, this inner ring will feed the upgraded facility’s main light-producing storage ring, and is a part of the upgrade project (ALS-U).

This latest approval, known as CD-3a, authorizes an important release of funds that will be used to purchase equipment and formally approves the start of construction on the accumulator ring.

>Read more on the Advanced Light Source at Berkeley Lab website

Image: This cutaway rendering of the Advanced Light Source dome shows the layout of three electron-accelerating rings. A new approval step in the ALS Upgrade project will allow the installation of the middle ring, known as the accumulator ring.
Credit: Matthaeus Leitner/Berkeley Lab

Sizing up red phosphorus for use in future battery technologies

A step forward in the search for better anodes for sodium-ion batteries

In 2015, the world used around 16 TW of energy, and this is predicted to rise to about 24 TW by 2035. The need for high-performing energy storage is growing, with the increased use of both intermittent, renewable power sources and electric vehicles. The current technology of choice is lithium-ion batteries (LIBs), which have high specific energies, rate capabilities, and cycle lives. However, LIBs rely on lithium and cobalt, two elements with an uneven geographical distribution. Disruptions to supply can cause price spikes, and there are concerns that the world’s total cobalt reserves may not meet future demand. Scientists are therefore investigating the potential of other battery technologies, which use cheap and widely available materials, such as sodium-ion batteries (SIBs). Although operation and manufacturing processes for SIBs are similar to those for LIBs, they cannot use the graphite anodes that are common in LIS. In research recently published in Energy Fuels, a team of researchers from the University of Oxford investigated how the particle-size distribution of red phosphorus affects the performance of composite anodes for SIBs.

Image: a) TEM image of the composite material made by mixing phosphorus (Dv90 = 0.79 μm) with graphite for 48 h in which graphene planes can be seen on the surface of the phosphorus particle. (b) Plotting the ratio between the integrated areas of the peaks fitted on the photoelectron spectra collected from the composite versus the probing depth shows that surficial P–C chemical bonds gradually decrease and P–P bonds increase as we move deeper toward the particle bulk. The areas are calculated from the fit shown in panels c–e, with the photoelectron spectra of the P 2p region acquired using increasing incident radiation energy.

>Read more on the Diamond Light Source website

Educational science project: what trees tell about your community

Grade 6 to 12 classrooms from across Canada can participate for free.

The Canadian Light Source (CLS) at the University of Saskatchewan has launched a unique initiative that creates opportunities for school students across the country to be directly involved in a national research project: children across Canada can participate in a free, nation-wide science project to learn the secrets trees can tell about their communities.

The Trans-Canadian Research and Environmental Education (TREE) program involves the Canadian Light Source (CLS) and the Mistik Askiwin Dendrochronology Laboratory (MAD Lab), both located at the University of Saskatchewan (USask), in a study of how the environment affects trembling aspen trees. By combining CLS techniques for chemical analysis and MAD Lab expertise in the science of tree rings, TREE aims to paint a detailed picture of how trembling aspen are doing in communities throughout Canada.

>Read more on the Canadian Light Source website

Image: Tracy Walker (right) helps students to use the IDEAS beamline at the CLS.

First light for SESAME’s MS beamline

On Monday, 23rd December 2019, at 13:21, scientists at the SESAME light source successfully delivered the first X-ray monochromatic beam to the experimental station of the Materials Science (MS) beamline, that will be used in applications of the X-ray powder diffraction (XRD) technique in materials science, The beamline will provide a powerful tool for studying microcrystalline or disordered/amorphous material on the atomic scale, the evolution of nano-scale structures and materials in various environmental conditions and for developing and characterising new smart materials.  

To have seen the X-ray signal inside the MS experimental station was very exciting said the MS beamline scientist, Mahmoud Abdellatief. It was the realization of four years of hard work, and has given me added stimulus for the new challenges lying ahead before the beamline may host users in some six months. 

Picture: SESAME scientists just after obtaining the first monochromatic X-ray fluorescence signal (from left to right: Mahmoud Abdellatief, MS beamline scientist, Messaoud Harfouche, XAFS/XRF beamline scientist, and Gihan Kamel, IR beamline scientist)
Credit: SESAME

First x-ray microtomography images obtained at Sirius

Two days after storing electrons in Sirius’ storage ring, the CNPEM´s team have performed the first x-ray microtomography analysis at the new Brazilian synchrotron light source. Through a simple proof of concept experiment, using less than ten thousandth of the expected power, it was possible to observe the arrival of synchrotron light for the first time in one of Sirius’ future experimental stations. This is a major milestone for the project, and a victory for Brazil’s science and technology.

“These early rock microtomography demonstrate the functionality of this great machine, designed and built by Brazilians to bring our science to a new level. Sirius is still in the early stages of commissioning, but these early tests that allowed X-ray images to be made ensure that the future will be very bright! We are very excited about the possibility to provide to the Brazilian scientific community a new level of experimental techniques as soon as possible”, said Antonio José Roque da Silva, Director General of CNPEM and the Sirius Project.
The first images were taken at one of the beamlines set up for testing, using X-ray tomography imaging techniques. These analyses mark another important milestone in the Sirius commissioning process. The team is now dedicated to achieving higher and higher currents needed to produce synchrotron light of enough intensity for the first scientific experiments.

>Read more on the LNLS website

Image: (screenshot) Projection of a carbonate rock sample, which has the same composition of the rocks from the Brazilian pre-salt reservoirs.

60 years of DESY – From Hamburg particle accelerator to global research centre

Germany’s largest accelerator centre turns 60 on 18 December 2019

The story of DESY began on 18 December 1959 with the signing of a contract in Hamburg’s town hall. It is a story of success, for global research and for Germany as a science hub! For the past 60 years, fundamental research has been carried out at DESY in Hamburg-Bahrenfeld – which was joined in 1991 by a second DESY site in Zeuthen. In those 60 years, DESY has become a world leader in accelerator technology, structure research, particle physics and astroparticle physics. During these 60 years, DESY has developed pioneering technologies, which have been used by scientists from all over the world to make outstanding advances. Among other things, the gluon was discovered and the structure of ribosomes was determined at DESY.
“It is now a question of the big challenges of our times,” says DESY’s director Professor Helmut Dosch. “We have developed a new generation of research tools in the form of so-called X-ray lasers. These afford fundamental insights in medicine and in materials engineering, for example, which will help shape the world of tomorrow.” DESY offers unique conditions for this: the combination of the radiation sources PETRA III, FLASH and European XFEL means that international scientists can carry out experiments using high-intensity X-rays. In addition to this, DESY offers structure researchers and businesses from all over the world a unique “toolbox” in the form of supplementary methods for manufacturing, processing and examining nano-samples and nanomaterials. DESY’s second site in Zeuthen is also an international magnet as a growing centre of excellence in astroparticle physics. Zeuthen operates the only accelerator in Brandenburg and is one of the largest scientific institutions in the region.

>Read more on the DESY website

Image: Part of the DESY staff in Hamburg holds the DESY-60 logo
Credit: DESY/H. Müller-Elsner

Covalent Organic Framework (COF‐1) under pressure

Covalent Organic Frameworks (COF’s) form a family of polymeric materials composed only by light elements. The absence of metal atoms in their structure makes COF’s distinctly different compared to their relatives, Metal Organic Framework materials (MOF’s). Historically first COF structure (named COF-1) was reported back in 2005 by Cote et al., (Science 310 (2015) 1166).  It consists of benzene rings linked by B3Ointo hexagon-shaped 2D sheets which are stacked into a layered structure, resembling in this respect the structure of graphite composed by graphene layers. By analogy with graphene the single layer of COF material could be named as COFene since it represents a true 2D material composed by carbon, hydrogen, boron and oxygen. Unlike graphite, COF-1 is porous material with relatively high surface area which makes it promising for various applications, e.g. for energy storage devices, as a sorbents for gas storage or for membranes.  However, little was known about mechanical properties of COF’s or single layered COFenes except for few theoretical estimations. Unlike graphite or MOF’s, no high pressure studies were available for COFs. The study by A. Talyzin group from Umeå University (Sweden) performed at Elettra at the Xpress beamline and SOLEIL synchrotrons in collaboration with the Technical University of Dresden (Germany) and the Chalmers University (Sweden) is first to evaluate compressibility and pressure limits for stability of COF-1 structure.

>Read more on the Elettra website

Picture: schematics of the high pressure experiments involving diamond anvil cell

Sirius reaches his first stored electron beam

The new Brazilian synchrotron light source continues its successful commissioning

On Saturday, December 14th, CNPEM’s team stored electrons in Sirius’s storage ring for several hours. This is a prerequisite for producing synchrotron light, and it happens only a few weeks after the first electron loop around the main accelerator was achieved.
In addition, on Monday, December 16th, with the connection of the accelerator to one of the beamlines set up for testing, it was possible to receive the first X-ray pulse, still discrete due to the small number of circulating electrons.
The achievement came after an intense and thorough work of adjusting hundreds of equipment parameters, another very important milestone in the Sirius commissioning process. The team is now dedicated to achieving higher and higher currents needed to produce synchrotron light of enough intensity for the first scientific experiments.
Sirius is the largest and most complex scientific infrastructure ever built in Brazil and one of the first 4th generation synchrotron light source to be built in the world and it was designed to put Brazil at the forefront of this type of technology.

>Read more on the LNLS website

Scientists probe Earth’s deep mantle in the laboratory

Extreme conditions experiments sharpen view of our planet’s interior

Simulating the conditions 2700 kilometres deep underground, scientists have studied an important transformation of the most abundant mineral on Earth, bridgmanite. The results from the Extreme Conditions Beamline at DESY’s X-ray light source PETRA III reveal how bridgmanite turns into a structure known as post-perovskite, a transformation that affects the dynamics of Earth’s lower mantle, including the spreading of seismic waves. The analysis can provide an explanation for a range of peculiar seismic observations, as the team headed by Sébastien Merkel from the Université de Lille in France report in the Journal Nature Communications.
Bridgmanite is a magnesian-iron mineral ((Mg,Fe)SiO3) with a crystal structure that is not stable under ambient conditions. It forms about 660 kilometres below the surface of the Earth, and microcrystalline grains found as inclusions in meteorites are the only samples ever recovered on the surface. “In order to study bridgmanite under the conditions of the lower mantle, we had to produce the mineral first,” explains Merkel. To do so, the scientists compressed tiny amounts of iron-magnesium-silicon-oxide in a diamond anvil cell (DAC), a device that can squeeze samples with high pressure between two small diamond anvils.

Image: The crystal structures of bridgmanite (left) and post-perovskite (right).

Credit: Université de Lille, Sébastien Merkel
>Read more on the PETRA III (DESY) website

Rare dinosaur skin offers insights into evolution

International team of scientists finds rare piece of preserved dinosaur skin and, in a world first, compares it directly to modern animals to gain insight into evolution.

Mauricio Barbi has loved dinosaurs for as long as he can remember and dreamed of one day being a paleontologist. “When I was a kid, I loved space, stars, and dinosaurs,” he said.
Fast-forward a few years, and Barbi is trekking through the Alberta Badlands alongside famous paleontologist Philip Currie, whose professional life became the inspiration for characters in the Jurassic Park movies. During this fieldwork, he also met paleontologist and rising star, Phil Bell, who had recently found a well-preserved hadrosaur. When he joined Bell in the excavations, Barbi was shocked and thrilled by what they discovered.

>Read more on the Canadian Light Source website

Picture of the dig site.