Bacterial communities of some brown and red algae from Peter the Great Bay, the Sea of Japan

The structure of microbial communities of brown algae, red algae, and of the red alga Gracilaria verrucosa, healthy and affected with thallus rot, were comparatively investigated; 61 strains of heterotrophic bacteria were isolated and characterized. Most of them were identified to the genus level, some Vibrio spp., to the species level according to their phenotypic properties and the fatty acid composition of cellular lipids. The composition of the microflora of two species of brown algae was different. In Chordaria flagelliphormis, Pseudomonas spp. prevailed, and in Desmarestia viridis, Bacillus spp. The composition of the microflora of two red algae, G. verrucosa and Camphylaephora hyphaeoides, differed mainly in the ratio of prevailing groups of bacteria. The most abundant were bacteria of the CFB cluster and pseudoalteromonads. In addition, the following bacteria were found on the surface of the algae: Sulfitobacter spp., Halomonas spp., Acinetobacter sp., Planococcus sp., Arthrobacter sp., and Agromyces sp. From tissues of the affected G. verrucosa, only vibrios were isolated, both agarolytic and nonagarolytic. The existence of specific bacterial communities characteristic of different species of algae is suggested and the relation of Vibrio sp. to the pathological process in the tissues of G. verrucosa is supposed.     

Ni3+‐Induced Formation of Active NiOOH on the Spinel Ni–Co Oxide Surface for Efficient Oxygen Evolution Reaction

Efficient and earth abundant electrocatalysts for high‐performance oxygen evolution reaction (OER) are essential for the development of sustainable energy conversion technologies. Here, a new hierarchical Ni–Co oxide nanostructure, composed of small secondary nanosheets grown on primary nanosheet arrays, is synthesized via a topotactic transformation of Ni–Co layered double hydroxide. The Ni³⁺‐rich surface benefits the formation of NiOOH, which is the main redox site as revealed via in situ X‐ray absorption near edge structure and extended X‐ray absorption fine structure spectroscopy. The Ni–Co oxide hierarchical nanosheets (NCO–HNSs) deliver a stable current density of 10 mA cm^?2 at an overpotential of ≈0.34 V for OER with a Tafel slope of as low as 51 mV dec^?1 in alkaline media. The improvement in the OER activity can be ascribed to the synergy of large surface area offered by the 3D hierarchical nanostructure and the facile formation of NiOOH as the main active sites on the surface of NCO–HNSs to decrease the overpotential and facilitate the catalytic reaction.     

X‐ray crystal structure of anhydrous chitosan at atomic resolution

We determined the crystal structure of anhydrous chitosan at atomic resolution, using X‐ray fiber diffraction data extending to 1.17 Å resolution. The unit cell [a = 8.129(7) Å, b = 8.347(6) Å, c = 10.311(7) Å, space group P2₁2₁2₁] of anhydrous chitosan contains two chains having one glucosamine residue in the asymmetric unit with the primary hydroxyl group in the gt conformation, that could be directly located in the Fourier omit map. The molecular arrangement of chitosan is very similar to the corner chains of cellulose II implying similar intermolecular hydrogen bonding between O6 and the amine nitrogen atom, and an intramolecular bifurcated hydrogen bond from O3 to O5 and O6. In addition to the classical hydrogen bonds, all the aliphatic hydrogens were involved in one or two weak hydrogen bonds, mostly helping to stabilize cohesion between antiparallel chains. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 361–368, 2016.     

Determination of protein oligomeric structure from small‐angle X‐ray scattering

Small‐angle X‐ray scattering (SAXS) is useful for determining the oligomeric states and quaternary structures of proteins in solution. The average molecular mass in solution can be calculated directly from a single SAXS curve collected on an arbitrary scale from a sample of unknown protein concentration without the need for beamline calibration or protein standards. The quaternary structure in solution can be deduced by comparing the experimental SAXS curve to theoretical curves calculated from proposed models of the oligomer. This approach is especially robust when the crystal structure of the target protein is known, and the candidate oligomer models are derived from the crystal lattice. When SAXS data are obtained at multiple protein concentrations, this analysis can provide insight into dynamic self‐association equilibria. Herein, we summarize the computational methods that are used to determine protein molecular mass and quaternary structure from SAXS data. These methods are organized into a workflow and demonstrated with four case studies using experimental SAXS data from the published literature.     

X‐ray structure of Danio rerio secretagogin: A hexa‐EF‐hand calcium sensor

Many essential physiological processes are regulated by the modulation of calcium concentration in the cell. The EF‐hand proteins represent a superfamily of calcium‐binding proteins involved in calcium signaling and homeostasis. Secretagogin is a hexa‐EF‐hand protein that is highly expressed in pancreatic islet of Langerhans and neuroendocrine cells and may play a role in the trafficking of secretory granules. We present the X‐ray structure of Danio rerio secretagogin, which is 73% identical to human secretagogin, in calcium‐free form at 2.1‐Å resolution. Secretagogin consists of the three globular domains each of which contains a pair of EF‐hand motifs. The domains are arranged into a V‐shaped molecule with a distinct groove formed at the interface of the domains. Comparison of the secretagogin structure with the solution structure of calcium‐loaded calbindin D_28K revealed a striking difference in the spatial arrangement of their domains, which involves ～180° rotation of the first globular domain with respect to the module formed by the remaining domains. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

The non‐hierarchical,non‐uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X‐ray microtomography

Hammel, J.U., Filatov, M.V., Herzen, J, Beckmann, F., Kaandorp, J.A. and Nickel M. 2011. The non‐hierarchical, non‐uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X‐ray microtomography. —Acta Zoologica (Stockholm) 00 :1–12. As sessile filter feeders, sponges rely on a highly efficient fluid transport system. Their physiology depends on efficient water exchange, which is performed by the aquiferous system. This prominent poriferan anatomical character represents a dense network of incurrent and excurrent canals on which we lack detailed 3D models. To overcome this, we investigated the complex leucon‐type architecture in the demosponge Tethya wilhelma using corrosion casting, microtomography, and 3D reconstructions. Our integrative qualitative and quantitative approach allowed us to create, for the first time, high‐resolution 3D representations of entire canal systems which were used for detailed geometric and morphometric measurements. Canal diameters lack distinct size classes, and bifurcations are non‐uniformly ramified. A relatively high number of bifurcations show previously unknown and atypical cross‐sectional area ratios. Scaling properties and topological patterns of the canals indicate a more complex overall architecture than previously assumed. As a consequence, it might be more convenient to group canals into functional units rather than hierarchical clusters. Our data qualify the leucon canal system architecture of T. wilhelma as a highly efficient fluid transport system adapted toward minimal flow resistance. Our results and approach are relevant for a better understanding of sponge biology and cultivation techniques.     

Characterizing the S‐layer structure and anti‐S‐layer antibody recognition on intact Tannerella forsythia cells by scanning probe microscopy and small angle X‐ray scattering

Tannerella forsythia is among the most potent triggers of periodontal diseases, and approaches to understand underlying mechanisms are currently intensively pursued. A ~22‐nm‐thick, 2D crystalline surface (S‐) layer that completely covers Tannerella forsythia cells is crucially involved in the bacterium–host cross‐talk. The S‐layer is composed of two intercalating glycoproteins (TfsA‐GP, TfsB‐GP) that are aligned into a periodic lattice. To characterize this unique S‐layer structure at the nanometer scale directly on intact T. forsythia cells, three complementary methods, i.e., small‐angle X‐ray scattering (SAXS), atomic force microscopy (AFM), and single‐molecular force spectroscopy (SMFS), were applied. SAXS served as a difference method using signals from wild‐type and S‐layer‐deficient cells for data evaluation, revealing two possible models for the assembly of the glycoproteins. Direct high‐resolution imaging of the outer surface of T. forsythia wild‐type cells by AFM revealed a p4 structure with a lattice constant of ~9.0 nm. In contrast, on mutant cells, no periodic lattice could be visualized. Additionally, SMFS was used to probe specific interaction forces between an anti‐TfsA antibody coupled to the AFM tip and the S‐layer as present on T. forsythia wild‐type and mutant cells, displaying TfsA‐GP alone. Unbinding forces between the antibody and wild‐type cells were greater than with mutant cells. This indicated that the TfsA‐GP is not so strongly attached to the mutant cell surface when the co‐assembling TfsB‐GP is missing. Altogether, the data gained from SAXS, AFM, and SMFS confirm the current model of the S‐layer architecture with two intercalating S‐layer glycoproteins and TfsA‐GP being mainly outwardly oriented. Copyright © 2013 John Wiley & Sons, Ltd.     

X‐ray crystallographic structure of BshB,the zinc‐dependent deacetylase involved in bacillithiol biosynthesis

Many gram‐positive bacteria produce bacillithiol to aid in the maintenance of redox homeostasis and degradation of toxic compounds, including the antibiotic fosfomycin. Bacillithiol is produced via a three‐enzyme pathway that includes the action of the zinc‐dependent deacetylase BshB. Previous studies identified conserved aspartate and histidine residues within the active site that are involved in metal binding and catalysis, but the enzymatic mechanism is not fully understood. Here we report two X‐ray crystallographic structures of BshB from Bacillus subtilis that provide insight into the BshB catalytic mechanism.     

X‐Ray Microscopy of Halide Perovskites: Techniques,Applications, and Prospects

X‐ray microscopy can provide unique chemical, electronic, and structural insights into perovskite materials and devices leveraging bright, tunable synchrotron X‐ray sources. Over the last decade, fundamental understanding of halide perovskites and their impressive performance in optoelectronic devices has been furthered by rigorous research regarding their structural and chemical properties. Herein, studies of perovskites are reviewed that have used X‐ray imaging, spectroscopy, and scattering microscopies that have proven valuable tools toward understanding the role of defects, impurities, and processing on perovskite material properties and device performance. Together these microscopic investigations have augmented the understanding of the internal workings of perovskites and have helped to steer the perovskite community toward promising directions. In many ways, X‐ray microscopy of perovskites is still in its infancy, which leaves many exciting paths unexplored including new ptychographic, multimodal, in situ, and operando experiments. To explore possibilities, pioneering X‐ray microscopy along these lines is briefly highlighted from other semiconductor systems including silicon, CdTe, GaAs, CuIn_xGa_1?xSe₂, and organic photovoltaics. An overview is provided on the progress made in utilizing X‐ray microscopy for perovskites and present opportunities and challenges for future work.     

Measurement of protein size in concentrated solutions by small angle X‐ray scattering

By simulations on the distance distribution function (DDF) derived from small angle X‐ray scattering (SAXS) theoretical data of a dense monodisperse system, we found a quantitative mathematical correlation between the apparent size of a spherically symmetric (or nearly spherically symmetric) homogenous particle and the concentration of the solution. SAXS experiments on protein solutions of human hemoglobin and horse myoglobin validated the correlation. This gives a new method to determine, from the SAXS DDF, the size of spherically symmetric (or nearly spherically symmetric) particles of a dense monodisperse system, specifically for protein solutions with interference effects.     

On interpretation of protein X‐ray structures: Planarity of the peptide unit

Pauling's mastery of peptide stereochemistry—based on small molecule crystal structures and the theory of chemical bonding—led to his realization that the peptide unit is planar and then to the Pauling–Corey–Branson model of the α‐helix. Similarly, contemporary protein structure refinement is based on experimentally determined diffraction data together with stereochemical restraints. However, even an X‐ray structure at ultra‐high resolution is still an under‐determined model in which the linkage among refinement parameters is complex. Consequently, restrictions imposed on any given parameter can affect the entire structure. Here, we examine recent studies of high resolution protein X‐ray structures, where substantial distortions of the peptide plane are found to be commonplace. Planarity is assessed by the ω‐angle, a dihedral angle determined by the peptide bond (C? N) and its flanking covalent neighbors; for an ideally planar trans peptide, ω = 180°. By using a freely available refinement package, Phenix [Afonine et al. (2012) Acta Cryst. D, 68:352–367], we demonstrate that tightening default restrictions on the ω‐angle can significantly reduce apparent deviations from peptide unit planarity without consequent reduction in reported evaluation metrics (e.g., R‐factors). To be clear, our result does not show that substantial non‐planarity is absent, only that an equivalent alternative model is possible. Resolving this disparity will ultimately require improved understanding of the deformation energy. Meanwhile, we urge inclusion of ω‐angle statistics in new structure reports in order to focus critical attention on the usual practice of assigning default values to ω‐angle constraints during structure refinement. Proteins 2015; 83:1687–1692. © 2015 Wiley Periodicals, Inc.     

Structure of full‐length class I chitinase from rice revealed by X‐ray crystallography and small‐angle X‐ray scattering

The rice class I chitinase OsChia1b, also referred to as RCC2 or Cht‐2, is composed of an N‐terminal chitin‐binding domain (ChBD) and a C‐terminal catalytic domain (CatD), which are connected by a proline‐ and threonine‐rich linker peptide. Because of the ability to inhibit fungal growth, the OsChia1b gene has been used to produce transgenic plants with enhanced disease resistance. As an initial step toward elucidating the mechanism of hydrolytic action and antifungal activity, the full‐length structure of OsChia1b was analyzed by X‐ray crystallography and small‐angle X‐ray scattering (SAXS). We determined the crystal structure of full‐length OsChia1b at 2.00‐Å resolution, but there are two possibilities for a biological molecule with and without interdomain contacts. The SAXS data showed an extended structure of OsChia1b in solution compared to that in the crystal form. This extension could be caused by the conformational flexibility of the linker. A docking simulation of ChBD with tri‐N‐acetylchitotriose exhibited a similar binding mode to the one observed in the crystal structure of a two‐domain plant lectin complexed with a chitooligosaccharide. A hypothetical model based on the binding mode suggested that ChBD is unsuitable for binding to crystalline α‐chitin, which is a major component of fungal cell walls because of its collisions with the chitin chains on the flat surface of α‐chitin. This model also indicates the difference in the binding specificity of plant and bacterial ChBDs of GH19 chitinases, which contribute to antifungal activity. Proteins 2010. © 2010 Wiley‐Liss,Inc.     

Blastogeny in tabulate corals: case studies using X‐ray microtomography

X‐ray microtomography (XMT) is a non‐invasive and non‐destructive method that has often been used to study fossils. It allows serial sections to be made as little as few micrometers apart; such a resolution is unachievable for classical serial sectioning; moreover, in contrast to the latter, the specimen is not destroyed. Microtomography can, however, be applied only in cases where differences in X‐ray absorption between the skeleton and its infilling are great. We show that this method may be also applied to tabulate corals. Case studies of blastogeny are based on Silurian (Aulopora, Favosites) and Devonian (Thamnopora) specimens from Poland. We show that the sequence of events in the blastogeny of Aulopora sp. is different from that of ‘Aulopora serpens minor’ from the Devonian of the Holy Cross Mountains and similar to auloporids from the Devonian of England. Blastogeny in Favosites is very similar to that known from the related genera Squameofavosites and Thamnopora. This suggests that members of the genus Aulopora may be more diversified within the genus (as presently understood) than genera within the Favositidae.     

qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps

New X‐ray crystallography and cryo‐electron microscopy (cryo‐EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open‐source under the MIT license, and is available at https://github.com/ExcitedStates/qfit-3.0 .     

Unraveling the Morphology of High Efficiency Polymer Solar Cells Based on the Donor Polymer PBDTTT‐EFT

The microstructure of the polymer PBDTTT‐EFT and blends with the fullerene derivative PC₇₁BM that achieve solar conversion efficiencies of over 9% is comprehensively investigated. A combination of synchrotron techniques are employed including surface‐sensitive near‐edge X‐ray absorption fine structure (NEXAFS) spectroscopy and bulk‐sensitive grazing‐incidence wide angle X‐ray scattering (GIWAXS). A preferential “face‐on” orientation of PBDTTT‐EFT is observed in the bulk of both pristine and blend thin films, with π–π stacking largely normal to the substrate, which is thought to be beneficial for charge transport. At the surface of the blend, a slight “edge‐on” structure of the polymer is observed with side‐chains aligned normal to the substrate. The effect of the solvent additive 1,8‐diiodooctane (DIO) on solar cell efficiency and film microstructure is also investigated, where the addition of 3 vol% DIO results in an efficiency increase from ≈6.4% to ≈9.5%. GIWAXS studies indicate that the addition of DIO improves the crystallization of the polymer. Furthermore, atomic force microscopy and transmission electron microscopy are employed to image surface and bulk morphology revealing that DIO suppresses the formation of large PC₇₁BM aggregates.     

Conformational analysis of an acyclic tetrapeptide: ab‐initio structure determination from X‐ray powder diffraction,Hirshfeld surface analysis and electronic structure

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc‐Tyr‐Aib‐Tyr‐Ile‐OMe·2H₂O ( 1 ), has been determined directly from powder X‐ray diffraction data. The backbone conformation of tetrapeptide ( 1 ) exhibiting two consecutive β‐turns is stabilized by two 4 → 1 intramolecular N―H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water‐mediated O―H · · · O hydrogen bonds to form two‐dimensional molecular sheets, which are further linked by intermolecular C―H · · · O hydrogen bonds into a three‐dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of ( 1 ) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in ( 1 ) has been analyzed quantitatively through the Hirshfeld surface and two‐dimensional fingerprint plot. The DFT optimized molecular geometry of ( 1 ) agrees closely with that obtained from the X‐ray structure analysis. The present structure analysis of Boc‐Tyr‐Aib‐Tyr‐Ile‐OMe·2H₂O ( 1 ) represents a case where ab‐initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X‐ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Application of Synchrotron Radiation Technologies to Electrode Materials for Li‐ and Na‐Ion Batteries

The search for superior‐energy‐density electrode materials for rechargeable batteries is prompted by the continuously growing demand for new electric vehicles and large energy‐storage grids. The structural properties of electrode materials affect their electrochemical performance because their functionality is correlated to their structure at the atomic scale. Although challenging, a deeper and comprehensive understanding of the basic structural operating units of electrode materials may contribute to the advancement of new energy‐storage technologies and many other technologies. Therefore, we must strategically control both the structure and kinetics of electrode materials to achieve optimal electrochemical performance. In this contribution, advancements in synchrotron radiation techniques, specifically in situ/operando experiments on electrode materials for rechargeable batteries, are presented and discussed. Indeed, the latest synchrotron radiation methods offer deeper insights into pristine and chemically modified electrode materials, opening new opportunities to optimize these materials and exploit new technologies. In particular, the most recent results from in situ/operando synchrotron radiation measurements, which play a critical role in the fundamental understanding of the kinetics processes that occur in rechargeable batteries, are discussed.