The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin.

In this paper, we provide evidence that Zn 2 + ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments [1].

A compact-rigid multi-analyser for energy and angle filtering of high-resolution X-ray experiments. Part 2. Efficiency of a single-crystal-comb.

Diffraction instruments using filtering by one or several analyser crystals exist since the 1980s and 1990s at synchrotron radiation sources, but, due to its low efficiency, this filtering is little used on laboratory sources. In order to overcome this limitation, the efficiency of a small diffraction filtering multi-analyzer block (MAD block) realized with a `single-crystal-comb' curved on a rigid support is demonstrated here. The geometry of this curved surface is logarithmic spiral and is optimized to allow multi-filtering over a relatively important diffraction angular range and to be also applicable over an X-ray spectral range. The efficiency of such a small rigid-compact MAD block consisting of this single-crystal-comb generating 20-50 Si(111) single-crystal blades, associated with a block of Soller collimators, is demonstrated. The angle between each crystal is 0.1°, so the measurement range of the comb is 2-5°. The geometry of this system has been optimized for operation with a synchrotron X-ray source over an energy range of 22 keV to 46 keV and could be used with laboratory X-ray sources (Ag Kα1, 22.1 keV). This MAD block complements and exploits the qualities of the `photon-counting' detectors which have very low intrinsic noise. Their joint efficacy is supported by powder pattern measurements of a LaB6 reference sample and of several heterogeneous samples of cultural heritage materials, carried out at 22 keV on the D2AM beamline at the ESRF. Their signal-to-noise ratio is excellent (1000/1) and allows the detection thresholds of the measurements (from 3-1% to 0.1%) to detect minor phases in the studies of `real' heterogeneous materials to be drastically improved.

Metal Ion Binding in Wild-Type and Mutated Frataxin: A Stability Study.

This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal.

Sub-ppm level high energy resolution fluorescence detected X-ray absorption spectroscopy of selenium in articular cartilage.

The speciation of highly-diluted elements by X-ray absorption spectroscopy in a diverse range of materials is extremely challenging, especially in biological matrices such as articular cartilage. Here we show that using a high energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD-XAS) technique coupled to an array of crystal analyzers, selenium speciation down to 400 ppb (µg kg-1) within articular cartilage can be demonstrated. This is a major advance in the speciation of highly-diluted elements through X-ray absorption spectroscopy and opens new possibilities to study the metabolic role of selenium and other elements in biological samples.

Pools of cadmium in Chlamydomonas reinhardtii revealed by chemical imaging and XAS spectroscopy.

The green micro-alga Chlamydomonas reinhardtii is commonly used as a model to investigate metallic stress in photosynthetic organisms. The aim of this study was to explore processes implemented by three C. reinhardtii strains to cope with cadmium (Cd), and particularly to evidence Cd sequestration in the cell. For that, we used a combination of subcellular fractionation and chemical imaging (micro X-ray fluorescence (µXRF) and transmission electron microscopy (TEM/X-EDS)) to identify subcellular compartments of Cd accumulation, and X-ray absorption spectroscopy (XAS) to determine chemical Cd speciation. C. reinhardtii wild type strain 11/32b (wt), a newly design strain (pcs1) expressing a modified phytochelatin synthase in the chloroplast and a cell wall less strain CC400 (cw15) were exposed to 70 µM Cd. At this Cd concentration, cell vitality was not affected, however, the strains showed various strategies to cope with Cd stress. In wt, most of Cd was diffused in the whole cell, and complexed by thiol ligands, while the other part was associated with phosphate in vacuolar Ca polyphosphate granules. Thiol ligands increased with exposure time, confirming their important role in Cd stress. In pcs1, Cd was also present as vacuolar Ca polyphosphate granules, and diffused in the cell as Cd-thiol complexes. In addition, while it should be regarded with caution, a minor proportion of Cd complexed by carboxyl groups, was potentially provided by starch produced around the pyrenoid and in the chloroplast. Results suggested that pcs1 uses thiol compounds such as PC to a lesser extent for Cd sequestration than wt. In cw15, an excretion of Cd, Ca polyphosphate granules has to be considered. Finally, Cd was detected in the pyrenoid of all strains.

Low temperature ferromagnetism in chemically ordered FeRh nanocrystals.

In sharp contrast to previous studies on FeRh bulk, thin films, and nanoparticles, we report the persistence of ferromagnetic order down to 3 K for size-selected 3.3 nm diameter nanocrystals embedded into an amorphous carbon matrix. The annealed nanoparticles have a B2 structure with alternating atomic Fe and Rh layers. X-ray magnetic dichroism and superconducting quantum interference device measurements demonstrate ferromagnetic alignment of the Fe and Rh magnetic moments of 3 and 1µ(B), respectively. The ferromagnetic order is ascribed to the finite-size induced structural relaxation observed in extended x-ray absorption spectroscopy.

Random alloy-like local structure of Fe(Se, S)(1-x)Te(x) superconductors revealed by extended x-ray absorption fine structure.

The local structure of Fe(Se, S)(1-x)Te(x) ternary (11-type) chalcogenides has been studied by temperature dependent Fe K-edge extended x-ray absorption fine structure measurements. We find that the Fe-Se and Fe-Te distances in ternary FeSe(1-x)Te(x) are closer to the respective distances in the binary systems, revealing significant divergence of the local structure from the average one. The mean square relative displacements show a systematic change with Te content, consistent with bond relaxation in the inhomogeneous ternary phases. Also, the Fe-Te and Fe-S distances in the FeS(0.2)Te(0.8) ternary system are found to be different in the crystallographically homogeneous structure. The observed features are characteristic of ternary random alloys, suggesting that a proper consideration should be given to the atomic distribution for describing the complex electronic structure of these multi-band Fe-based chalcogenides.

Combining size fractionation, scanning electron microscopy, and X-ray absorption spectroscopy to probe zinc speciation in pig slurry.

Zinc occurs in high quantity in pig slurry since it is used as an essential micronutrient at high concentrations in animal feeds despite the low Zn assimilation by pigs. Zinc accumulation was measured in soil surface layers that had been amended with pig slurry, while also determining the phytotoxicity as well as the extent of groundwater quality degradation. To accurately predict the mobility and bioavailability of Zn derived from pig slurry spreading, the speciation of this element has to be assessed since the total concentration is not sufficient. This study involved a combination of techniques to investigate Zn speciation in pig slurry. Size fractionation was first performed to account for the complexity of pig slurry, and 75% of total Zn was detected in the 0.45- to 20-mum particle-size range. Then X-ray diffraction, scanning electron microscopy, coupled with energy dispersive spectrometer, and extended X-ray absorption fine structure analyses were combined to assess Zn speciation. The findings highlighted the presence of 49% Zn bound to organic matter, 37% amorphous Zn hydroxides [Zn(OH)(2)], and 14% sphalerite (ZnS).

Speciation of Cd and Pb in dust emitted from sinter plant.

Many studies have provided evidence of the impact of heavy metals in atmospheric emission. Sinter plants represent the first step in steel production, and are important emitters of Cd and Pb. The toxicity of these two metals depends above all on their speciation. Particles collected before and after the filtration system were analysed to determine the Cd- and Pb-bearing phases, using analytical tools such as XRF, EXAFS or ICP-AES and chemical leaching (sequential extractions adapted to steel dusts). Results show that Pb is associated with carbonate and Cd with chloride. These two types of speciation lead to high solubility under common environmental conditions, which may produce impacts on the environment and health.

Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding.

In Bacillus subtilis, the transcription factor PerR is an iron dependant sensor of H(2)O(2). The sensing mechanism relies on a selective metal catalysed oxidation of two histidine residues of the regulatory site. Here we present the first crystal structure of the active PerR protein in complex with a Mn(2+) ion. In addition, X-ray absorption spectroscopy experiments were performed to characterize the corresponding iron form of the protein. Both studies reveal a penta-coordinate arrangement of the regulatory site that involves three histidines and two aspartates. One of the histidine ligand belongs to the N-terminal domain. Binding of this residue to the regulatory metal allows the protein to adopt a caliper-like conformation suited to DNA binding. Since this histidine is conserved in all PerR and a vast majority of Fur proteins, it is likely that the allosteric switch induced by the regulatory metal is general for this family of metalloregulators.

Changes in arsenic speciation through a contaminated soil profile: a XAS based study.

An impacted soil located near an industrial waste site in the Massif Central near Auzon, France, where arsenical pesticides were manufactured, has been studied in order to determine the speciation (chemical forms) of arsenic as a function of soil depth. Bulk As concentrations range from 8780 mg kg(-1) in the topsoil horizon to 150 mg kg(-1) at 60 cm depth. As ores (orpiment As2S3, realgar AsS, arsenopyrite FeAsS) and former Pb- and Al-arsenate pesticides have been identified by XRD at the site and are suspected to be the sources of As contamination for this soil. As speciation was found to vary with depth, based on XRD, SEM-EDS, EPMA measurements and selective chemical extractions. Based on oxalate extraction, As is mainly associated with amorphous Fe oxides through the soil profile, except in the topsoil horizons where As is hosted by another phase. SEM-EDS and EPMA analyses led to the identification of arseniosiderite (Ca2Fe3+3(AsVO4)3O2.3H2O), a secondary mineral that forms upon oxidation of primary As-bearing minerals like arsenopyrite, in these topsoil horizons. These mineralogical and chemical results were confirmed by synchrotron-based X-ray absorption spectroscopy. XANES spectra of soil samples indicate that As occurs exclusively as As(V), and EXAFS results yield direct evidence of changes in As speciation with depth. Linear combination fits of EXAFS spectra of soil samples with those of various model compounds indicate that As occurs mainly As-bearing Fe(III)-(hydr)oxides (65%) and arseniosiderite (35%) in the topsoil horizon (0-5 cm depth). Similar analyses also revealed that there is very little arseniosiderite below 15 cm depth and that As(V) is associated primarily with amorphous Fe oxides below this depth. This vertical change of As speciation likely reflects a series of chemical reactions downward in the soil profile. Arseniosiderite, formed most likely by oxidation of arsenopyrite, is progressively dissolved and replaced by less soluble As-bearing poorly ordered Fe oxides, which are the main hosts for As in well aerated soils.

Determination of zinc speciation in basic oxygen furnace flying dust by chemical extractions and X-ray spectroscopy.

There is a growing concern regarding the environmental and public health risks associated with airborne particulate matter (PM). The basic oxygen furnace is one of the most important atmospheric dust sources of the steel manufacturing process. It emits dust enriched in heavy metal such as Zn, which is assumed to contribute to the toxic potential of atmospheric PM. Dust collected before and after the filtration system was analyzed to determine Zn speciation. To this end, a variety of analytical tools were used and a sequential extraction protocol has been specifically developed for iron and steel dust. The Zn speciation results obtained by EXAFS and sequential extraction were in excellent agreement. Before filtration, the speciation of Zn in BOF was 43% ZnFe(2)O(4), 23% ZnCO(3) and 16% ZnO. The same species were detected after filtration with different proportions. BOF dust after filtration contains more soluble Zn phases which may play a role in the toxic effects of the emissions.

XAS evidence of As(V) association with iron oxyhydroxides in a contaminated soil at a former arsenical pesticide processing plant.

The molecular-level speciation of arsenic has been determined in a soil profile in the Massif Central near Auzon, France that was impacted by As-based pesticides by combining conventional techniques (XRD, selective chemical extractions) with X-ray absorption spectroscopy (XAS). The arsenic concentration is very high at the top (>7000 mg kg(-1)) and decreases rapidly downward to a few hundreds of milligrams per kilogram. A thin layer of schultenite (PbHAsO4), a lead arsenate commonly used as an insecticide until the middle of the 20th century, was found at 10 cm depth. Despite the occurrence of this As-bearing mineral, oxalate extraction indicated that more than 65% of the arsenic was released upon dissolution of amorphous iron oxides, suggesting a major association of arsenic with these phases within the soil profile. Since oxalate extraction cannot unambiguously distinguish among the various chemical forms of arsenic, these results were confirmed by a direct in situ determination of arsenic speciation using XAS analysis. XANES data indicate that arsenic occurs mainly as As(V) along the soil profile except for the topsoil sample where a minor amount (7%) of As(III) was detected. EXAFS spectra of soil samples were fit by linear combinations of model compounds spectra and by a shell-by-shell method. These procedures clearly confirmed that As(V) is mainly (at least 80 wt %) associated with amorphous Fe(III) oxides as coprecipitates within the soil profile. If any, the proportion of schultenite, which was evidenced by XRD in a separate thin white layer, does not account for more than 10 wt % of arsenic in soil samples. This study emphasizes the importance of iron oxides in restricting arsenic dispersal within soils following dissolution of primary As-bearing solids manufactured for use as pesticides and released into the soils.