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X-ray fluorescence sheds light on the growth patterns of extinct hyaena

2019/03/152019/03/18

A novel synchrotron technique examines growth patterns in fossil bones

Until recently, it was thought that warm-blooded animals experienced uninterrupted high rates of growth, whilst cold-blooded animals showed zonal growth – alternating periods of fast and slow growth. The identification of zonal growth in a range of mammals and birds disproved that theory, but as yet we don’t know how widespread zonal growth is in vertebrates, or which factors affect the speed of bone growth. Conventional techniques lack the resolution to correlate variations in bone chemistry with histological features, but in work recently published in the Journal of Analytical Atomic Spectrometry, an international team of researchers carried out the first direct comparison between optical histology (bone tissue identification) and synchrotron-based chemical mapping, quantification, and characterisation of trace elements (biochemistry) within cyclic growth tissues, and reported the first case of zonal tissue within the Hyaenidae.

Image: Lead author Jennifer Anné with a spotted hyaena mount.

Signatures of enhanced superconducting phase coherence in cuprates

2019/03/142019/03/21

The capability to control material properties on short timescales is one of the key challenges of modern condensed matter physics. This possibility becomes even more attractive in the case of intriguing material phases, such as superconductivity. As a matter of fact, despite the evolution of non-equilibrium spectroscopies of the last two decades have increased our understanding of the physics of strongly correlated materials, after more than 30 years from its discovery, High Temperature Superconductivity is still discussed and a clear and unanimous explanation of the origin of the phenomenon is still lacking. Moreover, the understanding of the phenomena at the basis of this effects could affect several technological applications, from the need for fast digital circuits and for speeding up computer performances, to the detection of very low magnetic fields, with implication in geology (mineral exploration and earthquake prediction), medical sciences (neuron activity and magnetic resonance), oil prospecting and, of course, research.
We focused our research on cuprates, a class of materials known for displaying unconventional superconductivity at relatively temperatures, and on which various studies have shown the possibility of turning off (and, to some extent, on) superconductivity by ultrashort light pulses. In our work, we reveal that light pulses characterized by long wavelength (and a peculiar polarization) can induce, for a very short time interval (1-2 ps), a state displaying superconductivity even above the critical temperature, i.e. in conditions where superconductivity is not observed at equilibrium.

Figure: Difference between the transient reflectivity due to Cu-Cu and Cu-O polarized pump in time and temperature, induced by excitations with (a) 70 and (b) 170 meV pump photon energies. The dashed lines highlight the critical temperature Tc.

A new molecule could help put the STING on cancer

2019/03/132019/03/18

The protein STING (stimulator of interferon genes) is a component of the innate immune system. It plays a major role in the immune response to cancer, and abnormal STING signaling has been shown to be associated with certain cancers. Immunomodulatory approaches using agonists to target STING signaling are therefore being investigated as anticancer treatments. However, the compounds in clinical trials typically are injected intratumorally in patients with solid cancers. In this study, researchers discovered a novel STING agonist, known as an amidobenzimidazole (ABZI), which can be given by intravenous injection and could therefore potentially open up its evaluation as a treatment for hard-to-reach cancers. Using x-ray diffraction data collected at the U.S. Department of Energy’s Advanced Photon Source (APS), researchers from GlaxoSmithKline (GSK) investigated ABZI compounds and STING. Their results, published in the journal Nature, may have important implications for anticancer immunotherapy.

STING is a protein that mediates innate immunity, and one function of the STING signaling pathway is in mobilizing an immune response against tumors. STING proteins can be activated by cyclic dinucleotides, small molecules that are made by the cytosolic DNA sensor, cGAS, upon sensing of DNA leaking out of the nucleus as a result of DNA damage, including that which might be associated with cancer development.

Figure: X-ray crystal structure of the STING protein bound to one of the new molecules.

A new lens allows researchers to watch shock waves travel through silicon

2019/03/132019/04/03

Researchers used a unique approach to learn more about what happens to silicon under intense pressure.

Elasticity, the ability of an object to bounce back to its original shape, is a universal property in solid materials. But when pushed too far, materials change in unrecoverable ways: Rubber bands snap in half, metal frames bend or melt and phone screens shatter.

For instance, when silicon, an element abundant in the Earth’s crust, is subjected to extreme heat and pressure, an initial “elastic” shock wave travels through the material, leaving it unchanged, followed by an “inelastic” shock wave that irreversibly transforms the structure of the material.

>Read more on the LCLS website

Image: After blasting silicon with intense laser pulses at SLAC’s Linac Coherent Light Source, researchers saw an unexpected shock wave appear in the material before its structure was irreversibly changed.
Credit: Gregory Stewart/SLAC National Accelerator Laboratory

New technique for two-dimensional material analysis

2019/03/112019/03/13

Discovery allows scientists to look at how 2D materials move with ultrafast precision.

Using a never-before-seen technique, scientists have found a new way to use some of the world’s most powerful X-rays to uncover how atoms move in a single atomic sheet at ultrafast speeds.

The study, led by researchers at the U.S. Department of Energy’s (DOE) Argonne National Laboratory and in collaboration with other institutions, including the University of Washington and DOE’s SLAC National Accelerator Laboratory, developed a new technique called ultrafast surface X-ray scattering. This technique revealed the changing structure of an atomically thin two-dimensional crystal after it was excited with an optical laser pulse.
>Read more on the Advanced Photon Source at Argonne website
>Another article is also available on the Linac Coheren Light Source at SLAC website

Image: An experimental station at SLAC’s Linac Coherent Light Source X-ray free-electron laser, where scientists used a new tool they developed to watch atoms move within a single atomic sheet.
Credit: SLAC National Accelerator Laboratory

A deep dive into the imperfect world of 2D materials

2019/03/082019/03/12

Berkeley Lab-led team combines several nanoscale techniques to gain new insights on the effects of defects in a well-studied monolayer material

Nothing is perfect, or so the saying goes, and that’s not always a bad thing. In a study at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), scientists learned how nanoscale defects can enhance the properties of an ultrathin, so-called 2D material. They combined a toolbox of techniques to home in on natural, nanoscale defects formed in the manufacture of tiny flakes of a monolayer material known as tungsten disulfide (WS₂) and measured their electronic effects in detail not possible before. “Usually we say that defects are bad for a material,” said Christoph Kastl, a postdoctoral researcher at Berkeley Lab’s Molecular Foundry and the lead author of the study, published in the journal ACS Nano. “Here they provide functionality.”

Tungsten disulfide is a well-studied 2D material that, like other 2D materials of its kind, exhibits special properties because of its atomic thinness. It is particularly well-known for its efficiency in absorbing and emitting light, and it is a semiconductor.

Image: This image shows an illustration of the atomic structure of a 2D material called tungsten disulfide. Tungsten atoms are shown in blue and sulfur atoms are shown in yellow. The background image, taken by an electron microscope at Berkeley Lab’s Molecular Foundry, shows groupings of flakes of the material (dark gray) grown by a process called chemical vapor deposition on a titanium dioxide layer (light gray).
Credit: Katherine Cochrane/Berkeley Lab

A step closer to early detection of multiple sclerosis

2019/03/082019/03/11

Synchrotron techniques identify the critical conditions that alter myelin structure

Multiple sclerosis (MS) is a chronic inflammatory autoimmune disease resulting in the destruction of myelin, a fatty substance that insulates nerves and increases the speed at which signals travel between nerve cells. MS affects more than 2.3 million people worldwide and has no cure. In work recently published in PNAS, a team of researchers from Tel Aviv University and the Technion-Israel Institute of Technology mapped, for the first time, the delicate and complicated force balance between the myelin sheath constituents, and their effect on the myelin structure. This new information will allow the identification of critical components involved in neurodegenerative diseases such as MS.

First ever images of fuel debris fallout particles from Fukushima

2019/03/072019/03/09

Unique synchrotron visualisation techniques offer new forensic insights into the provenance of radioactive material from the Fukushima nuclear accident to understand the sequence of events related to the accident.

In April 2017, a joint team comprising the University of Bristol, the Japan Atomic Energy Agency (JAEA) and Diamond, the UK’s national synchrotronlight source, undertook the first experiment of its kind to be performed at Diamond. A small radioactive particle (450μm x 280μm x 250 μm) from the Fukushima Daiichi nuclear accident in 2011 underwent a comprehensive and independent analysis of its internal structure and 3D elemental distribution, to establish the source of the material and the potential environmental risks associated with it.

Image: Fukushima Particles research group (L-R): Cristoph Rau (I13), Yukihiko Satou, (researcher from the Collaborative Laboratories for Advanced Decommissioning Science, Japan Atomic Energy Agency), with Tom Scott and Peter Martin (University of Bristol).

Sakura Pascarelli appointed scientific director at European XFEL

2019/03/072019/03/08

Italian physicist will be responsible for scientific development of hard X-ray instruments

The Italian physicist Dr. Sakura Pascarelli will be the new scientific director at European XFEL. Pascarelli will join European XFEL on 1 September from the European Synchrotron Radiation Facility, ESRF in Grenoble, France. She succeeds Andreas Schwarz who retired at the end of 2018. As one of three scientific directors, Pascarelli will be responsible for the four short-waved hard X-ray instruments at European XFEL: FXE for studying extremely fast processes, SPB/SFX for investigating biomolecules and biological samples, HED for studying matter under extreme pressures and temperatures, and MID for investigating nanostructures or irregularly ordered materials such as glass, liquids and biological substances. In addition, Pascarelli will also be responsible for developing the scientific research program for these experiment stations.

>Read more on the European XFEL website

Image: Sakura Pascarelli
Credit: Chantal Argoud (ESRF)

Clear view of “Robo” neuronal receptor opens door for new cancer drugs

2019/03/072019/03/12

During brain development, billions of neuron nerve cells must find accurate pathways in the brain in order to form trillions of neuronal circuits enabling us to enjoy cognitive, sensory and emotional wellbeing.

To achieve this remarkable precision, migrating neurons use special protein receptors that sense the environment around them and guide the way so these neurons stay on the right path. In a new study published in Cell, researchers from Bar-Ilan University and Tel Aviv University in Israel, EMBL Grenoble in France and University of Exeter in the UK report on their discovery of the intricate molecular mechanism that allows a key guidance receptor, “Robo”, to react to signals in its environment.

One of the most important protein signaling systems that guide neurons consists of the cell surface receptor “Robo” and its external guidance cue, “Slit”. “Slit and Robo can be identified in virtually all animals with a nervous system, from a 1 mm-long nematode all the way to humans,” explains researcher Yarden Opatowsky, associate professor and head of the Laboratory of Structural Biology at Bar-Ilan University and who led the research.

Image: A surface representation of the crystal structure of the extracellular portion of human Robo2. The yellow region represents the domain where dimerisation takes place. Here, we see it blocked by the other domains, meaning dimerisation cannot take place and that Robo2 is inactivated.
Credit: Y. Opatowsky.

Unleashing perovskites’ potential for solar cells

2019/03/062019/03/07

Perovskites — a broad category of compounds that share a certain crystal structure — have attracted a great deal of attention as potential new solar-cell materials because of their low cost, flexibility, and relatively easy manufacturing process. But much remains unknown about the details of their structure and the effects of substituting different metals or other elements within the material. Now, researchers using the U.S. Department of Energy’s (DOE’s) Advanced Photon Source (APS) have been able to decipher a key aspect of the behavior of perovskites made with different formulations: With certain additives there is a kind of “sweet spot” where sufficient amounts will enhance performance and beyond which further amounts begin to degrade it. The findings were detailed in the journal Science.
Conventional solar cells made of silicon must be processed at temperatures above 1,400 degrees Celsius, using expensive equipment that limits their potential for production scale-up. In contrast, perovskites can be processed in a liquid solution at temperatures as low as 100 degrees, using inexpensive equipment. What’s more, perovskites can be deposited on a variety of substrates, including flexible plastics, enabling a variety of new uses that would be impossible with thicker, stiffer silicon wafers.

Image: Perovskite-based solar cells are flexible, lightweight, can be produced cheaply, and could someday bring down the cost of solar energy. Shown here is the type of perovskite solar cell measured at the CNM/XSD Hard X-ray Nanoprobe at the APS.
Credit: Rob Felt

Scientists develop printable water sensor

2019/03/042019/03/04

X-ray investigation reveals functioning of highly versatile copper-based compound

A new, versatile plastic-composite sensor can detect tiny amounts of water. The 3d printable material, developed by a Spanish-Israeli team of scientists, is cheap, flexible and non-toxic and changes its colour from purple to blue in wet conditions. The researchers lead by Pilar Amo-Ochoa from the Autonomous University of Madrid (UAM) used DESY’s X-ray light source PETRA III to understand the structural changes within the material that are triggered by water and lead to the observed colour change. The development opens the door to the generation of a family of new 3D printable functional materials, as the scientists write in the journal Advanced Functional Materials (early online view).

Image: When dried, for example in a water-free solvent, the sensor material turns purple.
Credit: UAM, Verónica García Vegas

How to catch a magnetic monopole in the act

2019/03/042019/03/08

Berkeley Lab-led study could lead to smaller memory devices, microelectronics, and spintronics

A research team led by the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has created a nanoscale “playground” on a chip that simulates the formation of exotic magnetic particles called monopoles. The study – published recently in Science Advances – could unlock the secrets to ever-smaller, more powerful memory devices, microelectronics, and next-generation hard drives that employ the power of magnetic spin to store data.

Follow the ‘ice rules’
For years, other researchers have been trying to create a real-world model of a magnetic monopole – a theoretical magnetic, subatomic particle that has a single north or south pole. These elusive particles can be simulated and observed by manufacturing artificial spin ice materials – large arrays of nanomagnets that have structures analogous to water ice – wherein the arrangement of atoms isn’t perfectly symmetrical, leading to residual north or south poles.

Image: Full image here. This nanoscale “playground” on a chip uses nanomagnets to simulate the formation of exotic magnetic particles called “monopoles.” Credit: Farhan/Berkeley Lab

Towards X-ray transient grating spectroscopy at SwissFEL

2019/03/012019/04/16

The high brilliance of new X-ray sources such as X-ray Free Electron Laser opens the way to non-linear spectroscopies.

These techniques can probe ultrafast matter dynamics that would otherwise be inaccessible. One of these techniques, Transient Grating, involves the creation of a transient excitation grating by crossing X-ray beams on the sample. Scientists at PSI have realized a demonstration of such crossing by using an innovative approach well suited for the hard X-ray regime. The results of their work at the Swiss Free Electron Laser have been published in the journal Optics Letters.
Non-linear optics is an important field of physics where the non-linear response of matter in extreme electromagnetic fields is studied and exploited for novel applications. It has been widely used for creating new laser wavelengths (Sum/Difference Frequency Generation – S/DFG) as well as for studying a variety of properties such as charge, spin, magnetic transfer as well as heat diffusion. A broad class of non-linear spectroscopy is Four Wave Mixing (FWM) where three laser beams are overlapped in space and time in a sample and a fourth beam with different wavelength and angle is detected, background free. This allows studying specific transitions and selectively excite the sample tuning the incoming beams’ wavelength while studying their dynamics by controlling the relative time delays between the laser pulses. Transient Grating (TG) spectroscopy is a special case of degenerate FWM where two of the incoming beams have the same wavelength and are crossed at the sample creating an interference pattern, or transient grating, which excites the sample as long as the field is present. When the TG impinges on the material, its index of refraction is locally perturbed and electrons exposed to the radiation are excited. These electrons then transfer their extra energy to the lattice and the heat is then dissipated by the system. A third beam, delayed with respect to the pump TG, probes the dynamics of this excitation.

Image: Layout depicting the experimental conditions at the Alvra experimental station. (Find all the details here)

Mechanism of thiopurine resistance in acute lymphoblastic leukemia

2019/02/282019/03/13

Acute lymphoblastic leukemia (ALL) is an aggressive lymphoid malignancy that is currently the leading cause of cancer in pediatric patients¹. Despite intensified chemotherapy regimens, the cure rates of ALL only approaches 40%². Specific mutations in the cytosolic 5’-nucleotidase II (NT5C2) gene are present in about 20% of relapsed pediatric T-ALL and 3-10% of relapsed B-precursor ALL cases^3,4.

NT5C2 is a cytosolic nucleotidase that maintains intracellular nucleotide pool levels by exporting excess purine nucleotides out of the cell⁵. NT5C2 can also dephosphorylate and inactivate the metabolites of the 6-thioguanine (6-TG) and 6-mercaptopurine (6-MP) commonly used to treat ALL⁶. Thus, relapse associated activating mutations in NT5C2 confer resistance to 6-MP and 6-TG chemotherapy. Upon allosteric activation, a disordered region of NT5C2 adopts a helical configuration (helix A) and facilitates substrate binding and catalysis (Fig. 1a)⁷. Mutations in this regulatory region of NT5C2 have been modeled to strongly activate NT5C2. However, the majority of NT5C2 mutations associated with relapsed ALL do not occur in this region.
To better understand the mechanisms by which these gain-of function NT5C2 mutations lead to increased nucleotidase activity, Dieck, Tzoneva, Forouhar and colleagues investigated additional regulatory elements that may control NT5C2 activation. They collected crystallographic data for several mutant NT5C2 homotetramers at SSRL (NT5C2-537X D52N/D407A in active state (BL9-2), NT5C2-Q523X D52N in basal state and in active state (BL14-1) and full-length NT5C2 R39Q/D52N in basal state (BL12-2)) and used the structural information as a guide in the understanding of the mechanistic details.

Figure (a) A ribbon diagram of the active structure of NT5C2 WT, in which the allosteric helix A (αA) is shown in dark purple. The N and C termini amino acids (S4 and S488), and the termini amino acids (L402 and R421) of the disordered region in the arm segment are also labeled. Panels b and c shows ribbon and surface (for subunit B) depictions of basal (b) and active dimers (c) of WT.

Structural basis of neurosteroid anesthetic action on GABAA receptors

2019/02/282019/03/13

Type A γ-aminobutyric acid receptors (GABA_ARs) control neuronal excitability¹. They are targets for the treatment of neurological diseases and disorders and also for general anesthetics. The underlying mechanisms of these drugs’ action on GABA_ARs remain to be determined.
One of the mechanisms is to potentiate function of GABA_ARs via binding to the transmembrane domain (TMD)². Ample experimental evidence suggests that the TMD of GABA_ARs harbors sites for the primary actions of general anesthetics and neurosteroids. The TMD plays an essential role in functional transitions among the resting, activated, and desensitized states of these Cl^－-conducting channels.
Alphaxalone (5α-pregnan-3α-ol-11,20 dione) is a potent neurosteroid anesthetic. The anxiolytic, anticonvulsant, analgesic, and sedative-hypnotic effects of alphaxalone have been linked to its potentiation of GABA-evoked currents and direct activation of GABA_ARs³. However, the data about the alphaxalone binding site in GABA_ARs and the underlying structural basis of alphaxalone’s action are sparse.

Figure: Alphaxalone-induced structural changes at the bottom of the TMD (a) Bottom view of overlaid TM1-TM2 structures of the apo (orange) and alphaxalone-bound (cyan) α1GABA_AR chimera. (b) Side view of overlaid structures of apo (principal subunit – gold; complementary subunit – orange) and alphaxalone-bound (principal subunit – blue; complementary subunit – cyan) α1GABA_AR chimera. For clarity, only TM2 and TM3 are shown in the principal subunit and only TM1 and TM2 are shown in the complementary subunit. The arrow highlights structural perturbations originating from the alphaxalone binding site near W246 through the TM1-TM2 linker to the pore-lining residues P253 (-2′) and V257 (2′). (c) The 2F_O-F_C electron density maps (blue mesh, contoured at 1 σ) covering TM1-TM2 in the apo (left) and alphaxalone-bound (right) α1GABA_AR chimera. The sidechains are shown only for residues W246 to V257 (2′).