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Unusual outbreaks of food poisoning in Japan were reported in which Clostridium perfringens was strongly suspected to be the cause based on epidemiological information and fingerprinting of isolates. The isolated strains lack the typical C. perfringens enterotoxin (CPE) but secrete a new enterotoxin consisting of two components: C. perfringens iota-like enterotoxin-a (CPILE-a), which acts as an enzymatic ADP-ribosyltransferase, and CPILE-b, a membrane binding component. Here we present the crystal structures of apo-CPILE-a, NAD+-CPILE-a and NADH-CPILE-a. Though CPILE-a structure has high similarity with known iota toxin-a (Ia) with NAD+, it possesses two extra-long protruding loops from G262-S269 and E402-K408 that are distinct from Ia. Based on the Ia–actin complex structure, we focused on actin-binding interface regions (I-V) including two protruding loops (PT) and examined how mutations in these regions affect the ADP-ribosylation activity of CPILE-a. Though some site-directed mutagenesis studies have already been conducted on the actin binding site of Ia, in the present study, mutagenesis studies were conducted against both α- and β/γ-actin in CPILE-a and Ia. Interestingly, CPILE-a ADP-ribosylates both α- and β/γ-actin, but its sensitivity towards β/γ-actin is 36% compared with α-actin. Our results contrast to that only C2-I ADP-ribosylates β/γ-actin. We also showed that PT-I and two convex-concave interactions in CPILE-a are important for actin binding. The current study is the first detailed analysis of site-directed mutagenesis in the actin binding region of Ia and CPILE-a against both α- and β/γ-actin. [ABSTRACT FROM AUTHOR]

Abstract: Foliated antigorite serpentinites are contributing to seismic anisotropy in subduction zones. However, uncertainty remains regarding the development of antigorite crystal preferred orientations (CPO). This study analyzes the CPOs of antigorite and olivine in variably serpentinized samples of antigorite serpentinite from three localities in Southwest Japan, using U-stage, EBSD, and synchrotron X-rays. In all samples (010) poles show a maximum parallel to the lineation, and (001) poles concentrate normal to the foliation with a partial girdle about the lineation. (100) poles are less distinct and scatter widely. The three measurement methods give similar results, though orientation distributions from X-ray analysis which averages over larger sample volumes are more regular and weaker than U-stage and EBSD which focuses on local well-crystallized grains. In olivine-bearing serpentinite, the olivine CPO does not appear to control the antigorite CPO, though there are some topotactic relationships. The antigorite CPO formed contemporaneously with serpentinization and shear deformation. Based on our analyses, in a subduction zone mantle wedge, the (010) pole of antigorite is parallel to the direction of the subduction, and (001) lattice planes are parallel to the interface of the subducting oceanic plate. By averaging single crystal elastic properties over orientation distributions wave velocities have been calculated. Fast P velocities are parallel to the subduction direction and slow velocities are perpendicular to the subducting plate with an anisotropy of 10–15%. [Copyright &y& Elsevier]

Abstract: Neutron imaging using a pulsed neutron source is one of useful method to investigate microstructure of materials depending on position in the material. Recently an analysis code to obtain quantitative information on crystallite size, preferred orientation, and strain has been developed, which can treat extinction, anisotropy, shift of the Bragg edge. Furthermore, various experiments to see the position dependent change of the crystallographic characteristics. Here, the function of the analysis code is explained and some experimental results indicating the crystallographic information are presented. [Copyright &y& Elsevier]

The crystal chemistry of Ti-rich ferriallanite-(Ce) in syenites from Cape Ashizuri, Shikoku Island, Japan, was studied using electron microprobe analysis (EMPA) and single-crystal X-ray diffraction methods. Our specimens (AS001 and AS304) are characterized by high-Ti (~3.6 wt% TiO2) and Fe contents (~21.3 wt% FeO*; Fe2+/total Fe = 0.6-0.7). Structure refinements of two ferriallanite-(Ce) crystals converged to R1 = 1.50-1.57%. In both specimens, the dominant cations at A1, A2, and M3 are Ca, Ce, and Fe2+, respectively. However, depending on Ti assignment, two different schemes of the cation distributions at M1 and M2 can be considered: (1) (Fe0.72Ti0.23Al0.05)M1(Al0.82 Due to image rights restrictions, multiple line equation(s) cannot be graphically displayed.)M2 and (2) (Fe0.90Al0.10)M1(Al0.77Ti0.23)M2 for AS001, and (1) (Fe0.65Ti0.29Al0.06)M1 (Al0.89Due to image rights restrictions, multiple line equation(s) cannot be graphically displayed.)M2 and (2) (Fe0.76Ti0.13Al0.11)M1(Al0.84Ti0.16) for AS304. The Si2O7 group is compressed along Si1-O9-Si2 direction because of the expansions of the M1O6 and M3O6 octahedra due to substitution of large octahedral cations for Al. This compression is monitored by the atom position of O9 that shifts away from the cation at A1 decreasing the Si1-O9-Si2 angle. In allanite-subgroup minerals, the A1-O9 distance is longer and the bridging angle is smaller than those of clinozoisite-subgroup minerals. Although the A1 polyhedron is generally described as a ninefold-coordinated site, it is appropriately described as sevenfold-coordinated in Ti-rich allanite-(Ce) because of the lengthened A1-O9 (x2) distance. The cation substitutions at M1 and M3 indirectly affect the topology of the A1 polyhedron. [ABSTRACT FROM AUTHOR]

Abstract: Antigorite (Atg) is stable throughout large parts of the wedge mantle of most subduction zones. Atg shows strong acoustic anisotropy and crystallographic preferred orientation (CPO) patterns of this mineral may contribute significantly to seismic anisotropy in convergent margins. Atg CPO patterns from the Higashi-Akaishi (HA) forearc mantle body of southwest Japan adds to the data set suggesting the most common Atg CPO pattern has a c-axis perpendicular to the foliation and a b-axis parallel to the stretching lineation. Statistical analysis using the eigenvector method of Atg CPO from two mutually perpendicular directions in the same sample (YZ-section and XZ-section) shows no significant differences implying sample preparation has no significant affect on the resulting Atg CPO. Reuss (uniform stress) averages of anisotropy for the Higashi-Akaishi samples are approximately treble the values for Voigt (uniform strain) averages. When comparing calculated anisotropy of hydrated mantle peridotite samples—such as the Higashi-Akaishi unit—with observed S-wave delay times in convergent margins, the appropriate averaging method needs to be considered. [Copyright &y& Elsevier]

Abstract: We have a plan to build an imaging beam line, Energy-Resolved Neutron Imaging System (ERNIS), at Materials and Life Science Experimental Facility (MLF) at Japan Proton Accelerator Research Complex (J-PARC). In pulsed neutron imaging, we use characteristic features of the neutron total cross section, depending on the neutron wavelength, to get sample information such as crystallographic structure and nuclide composition. One of the most important items to be determined for a beam line at J-PARC is the choice of moderator among coupled, decoupled, and poisoned moderators. From the wavelength resolution point of view, we decided to use the decoupled moderator, which could cover major experiments performed at a pulsed neutron source. Here, we discuss the structure of the imaging beam line at beam line 22 of the J-PARC neutron source as well as the arrangement of insertion devices and the experimental area. [Copyright &y& Elsevier]

We determined P- and S-wave tomography and P-wave anisotropic structure under the Honshu arc from the Japan Trench to the backarc area under the Japan Sea using 310 749 P- and 150 563 S-wave arrivals from 4655 local earthquakes recorded by 982 seismograph stations. Arrival times from 1451 suboceanic earthquakes relocated with sP depth phases enable us to determine the structures under the Pacific Ocean and Japan Sea, which expand the study region from the land area to the whole arc from the Japan Trench to the Japan Sea with a width of more than 500 km. The results show strong heterogeneities above the subducting Pacific slab under the Pacific Ocean and most large thrust-type earthquakes occurred in the high-velocity areas where the Pacific slab and the overriding continental plate may be strongly coupled. Low-velocity (low- V) zones are imaged in the mantle wedge with significant along-arc variations under the volcanic front. The mantle-wedge low- V zone extends westwards under the Japan Sea and it is connected with the subducting Pacific slab at depths of 150-200 km under the backarc. The results indicate that the HO and fluids brought downwards by the subducting Pacific slab are released into the mantle wedge by dehydration and are subsequently transported to the surface by the upwelling flow in the mantle wedge. Significant P-wave anisotropic anomalies are revealed under the Honshu arc. The predominant fast velocity direction (FVD) is E-W in the mantle wedge while it is N-S in the subducting Pacific slab. The anisotropy in the mantle wedge is the result of deformation caused by the subduction of the Pacific plate and the induced mantle-wedge convection, while the FVD pattern in the middle of the mantle wedge argues for the 3-D mantle flow or the specific alignment of the olivine in the partial-melting mantle. The N-S (trench-parallel) FVD in the subducting Pacific slab represents either the original fossil anisotropy when the Pacific plate formed or the trench-parallel crystallographic and shaped preferred orientation in the subducting slab due to the slab bending. The present results shed new light on the structural heterogeneities and seismic anisotropy under the Honshu arc, which may improve our understanding of the dynamic processes of subduction zones. [ABSTRACT FROM AUTHOR]

The article reports on the Ibaraki biological crystal diffractometer (IBIX) for protein crystallography, a next-generation neutron source that is installed at the Japan Proton Accelerator Research Complex in December 2008. The IBIX performed according to expectation when it is used to analyze a sampling of organic crystals at an accelerator power of 120 kilowatts. The facility plans to operate the IBIX at one megawatt to improve its efficiency.

The article discusses the highlights of the Twenty-First General Assembly and International Congress of Crystallography, held at the Osaka International Convention Centre in Osaka, Japan from August 23-31, 2008. The event was attended by 2,477 scientists, 140 accompanying members and 58 exhibitors from 66 countries. It comprised of 38 keynote lectures, 98 microsymposia and open commission meetings.

A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7 Å resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high-resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A. Numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines were also determined at 1.7 Å resolution. The protonation and deprotonation states of all of the charged amino-acid residues allowed us to provide a definitive description of the hydrogen-bonding network around the active site and the H atoms of the key His48 residue. Differences in hydrogen-bond strengths for the α-helices and β-sheets were inferred from determination of the hydrogen-bond lengths and the H/D-exchange ratios of the backbone amide H atoms. The correlation between the B factors and hydrogen-bond lengths of the hydration water molecules was also determined. [ABSTRACT FROM AUTHOR]

The article discusses the highlights of the International Union of Crystallography Twenty-First General Assembly and International Congress of Crystallography which was held in Osaka, Japan from August 23 to 31, 2008. Sessions at the conference focused on music, the future of female crystallographers and art and crystallography. Among those present at the event include Professor T. Tsukihara and Professor Y. Ohashi.

The distribution of seismic anisotropy in the mantle wedge beneath northeast Japan is inferred from deformation mechanisms: a lattice-preferred orientation and seismic anisotropy are generated by deformation via dislocation creep in the upper mantle, but not by diffusion creep or frictional sliding. Based on the thermal structure and stress field of the upper mantle beneath northeast Japan, deformation throughout most of the mantle wedge is inferred to be controlled by diffusion creep, and the region of dislocation creep is limited to a thin layer of 10-20 km thickness within a region of relatively high stress and low temperature located above the subducting slab and beneath the island arc crust. The relatively short delay time recorded in northeast Japan is consistent with the occurrence of a thin anisotropic layer within the mantle wedge. [ABSTRACT FROM AUTHOR]

Abstract: Analysis of seismic anisotropy in the crust and mantle wedge above subduction zones gives much information about the dynamic processes inside the Earth. For this reason, we measure shear wave polarization anisotropy in the crust and upper mantle beneath central and southwestern Japan from local shallow, intermediate, and deep earthquakes occurring in the subducting Pacific slab. We analyze S phases from 198 earthquakes recorded at 42 Japanese F-net broadband seismic stations. This data set yields a total of 980 splitting parameter pairs for central and southwestern Japan. Dominant fast polarization directions of shear waves obtained at most stations in the Kanto–Izu–Tokai areas are oriented WNW–ESE, which are sub-parallel to the subduction direction of the Pacific plate. However, minor fast polarization directions are oriented in NNE–SSW directions being parallel to the strike of the Japan Trench, especially in the north of Izu Peninsula and the northern Tokai district. Generally, fast directions obtained at stations located in Kii Peninsula and the Chubu district are oriented ENE–WSW, almost parallel to the Nankai Trough, although some fast directions have NW–SE trends. The fast directions obtained at stations in northern central Honshu are oriented N–S. Delay times vary considerably and range from 0.1 to 1.25s depending on the source depth and the degree of anisotropy along the ray path. These lateral variations in splitting character suggest that the nature of anisotropy is quite different between the studied areas. Beneath Kanto–Tokai, the observed WNW–ESE fast directions are probably caused by the olivine A-fabric induced by the corner flow. However, the slab morphology in this region is relatively complicated as the Philippine Sea slab is overriding the Pacific slab. This complex tectonic setting may induce lateral heterogeneity in the flow and stress state of the mantle wedge, and may have produced NNE–SSW orientations of fast directions. The ENE–WSW fast directions in Kii Peninsula and the Chubu district are more coherent and may be partly induced by the subduction of the Philippine Sea plate. The N–S fast directions in northern central Honshu might be produced by the trench-parallel stretching of the wedge due to the curved slab at the arc–arc junction. [Copyright &y& Elsevier]

BL-17A is a new structural biology beamline at the Photon Factory, Japan. The high-brilliance beam, derived from the new short-gap undulator (SGU#17), allows for unique protein crystallographic experiments such as data collection from microcrystals and structural determination using softer X-rays. However, microcrystal experiments require robust beam stability during data collection and minor fluctuations could not be ignored. Initially, significant beam instability was observed at BL-17A. The causes of the beam instability were investigated and its various sources identified. Subsequently, several effective counter-measures have been implemented, and the fluctuation of the beam intensity successfully suppressed to within 1%. Here the instability reduction techniques used at BL-17A are presented. [ABSTRACT FROM AUTHOR]

Processes of crystal separation in a magma heavily laden with crystals without phase change are investigated from observations on frozen magma systems: Nosappumisaki and other shoshonite intrusions in the Nemuro peninsula, Japan, for which the origin of the crystals and the initial conditions are well constrained. The Nosappumisaki intrusion is 120 m in thickness and extends for more than 1·5 km. It exhibits a wide range of lithological variation, principally as a result of crystal redistribution after intrusion. Crystals in each lithology can be clearly divided into two kinds according to their composition and texture: those present before the intrusion of the magma (‘phenocrysts’) and those that crystallized in situ after intrusion. From the vertical change in mode and size of ‘phenocrysts’, it is shown that (1) augite ‘phenocrysts’ were rapidly deposited, with little overgrowth after intrusion, by significant coagulation or clustering on a time-scale of more than a few years, and (2) plagioclase ‘phenocrysts’, definitely denser than the melt but concentrated in the upper level, floated by counter flow of massive deposition of augite ‘phenocrysts’. These results indicate that in a magma heavily laden with crystals of a few millimeters in size (>20 vol. %), crystal–crystal and crystal–melt interaction play an important role in the separation of crystals from the host melt. [ABSTRACT FROM AUTHOR]

Abstract: In this study, we utilize data from 64 broadband seismic stations of the Japanese F-net network to investigate the three-dimensional pattern of anisotropy in the subduction system beneath Japan. We have compiled a database of approximately 1900 high-quality splitting measurements, selected by visual inspection of over 25,000 records of S, SKS, and SKKS phases at F-net stations, covering a wide range of incidence angles, incoming polarization angles, and backazimuths. Analysis of the variations of measured splitting parameters with these parameters allows us to consider complexities in structure such as multiple anisotropic layers, dipping symmetry axes, and small-scale lateral variations in anisotropic properties. Here we focus on the presentation of the splitting measurements themselves; a detailed interpretation in terms of tectonics and mantle flow is beyond the scope of this paper. In the southern part of the F-net array, along the Ryukyu arc, we find that fast directions are consistently trench-parallel, with splitting times of 1s or more. Moving northward along the array, the measured splitting patterns become more complicated, with significant variations in apparent splitting parameters that indicate complex anisotropic structure. Additionally, measured fast directions vary significantly over short length scales, and stations separated by less than 100km often exhibit very different splitting behavior. This increase in complexity of anisotropic structure coincides geographically with the complicated slab morphology of the subducting Pacific plate. At stations on Hokkaido, to the north, and Kyushu, to the south, we see some evidence that the fast direction of anisotropy may rotate from trench-parallel close to the trench to subduction-parallel further away from the trench, which may correspond either to a change in stress conditions and/or volatile content, or to a change in flow regime. [Copyright &y& Elsevier]

Introduces the high-performance neutron diffractometer for biological crystallography (BIX-3) at JRR-3M in Japan Atomic Energy Research Institute in Tokaimura, Japan. Determination of hydrogen-atom positions in biological macromolecules; Features of the device; Performance of the device for neutron protein crystallography.

In the present paper, a new method of selective image amplification using two photorefractive BaTiO3 crystals is proposed and the amplification characteristics of this method are investigated. The gain of beam amplification obtained using the proposed method is almost equal to the product of the gain obtained from each crystal. The rise time of the amplification output also changes when the signal beam power changes with time. The blurring of images caused by the amplification reveals a very small region. The images obtained using this method are more distinct than those obtained using single BaTiO3 crystals, and amplified images obtained by the selective image amplification are of high quality. © 2000 Scripta Technica, Electron Comm Jpn Pt 2, 83(7): 14–21, 2000 [ABSTRACT FROM AUTHOR]

Protein Data Bank (PDB), jointly founded in 1971 by Brookhaven National Laboratory, USA, and the Cambridge Crystallographic Data Centre, UK, is the single global archive of experimentally determined biological macromolecular structures. PDB deposition is mandatory for publication in most scientific journals, which means 'no PDB deposition, no structural publication'. The current PDB archive contains more than 180,000 entries and includes many structures from Asian institutions. The first protein structure from Japan was that of cytochrome c determined by Prof Masao Kakudo's group at the Institute for Protein Research, Osaka University, in 1971 at a resolution of 4 Å, and a subsequent atomic structure at 2.3 Å resolution was deposited to PDB in 1976 as the 1st Asian and 21st entry of the entire PDB archive. Since then, 317 protein structures whose primary citation was the Journal of Biochemistry (J. Biochem.) have been deposited to PDB. Based on this long history between PDB and J. Biochem., a statistical analysis of all structural reports in J. Biochem. has been carried out using the relational database system at PDBj (https://pdbj.org) and reviewed the yearly distribution, resolution, quality of structure, type of target protein, number of citations and comparison against other major journals., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.)

A calendar of events of interest to crystallographers from February 2009 to October 2009 is presented including the nanotech2009 International Nanotechnology Exhibition and Conference in Japan, XXI Conference on Applied Crystallography in Poland, and Clays, Clay Minerals and Layered materials 2009 in Russia.

The Gram-negative aerobic eubacterium Thermus thermophilus is an extremely important thermophilic microorganism that was originally isolated from a thermal vent environment in Japan. The molybdenum cofactor in this organism is considered to be an essential component required by enzymes that catalyze diverse key reactions in the global metabolism of carbon, nitrogen and sulfur. The molybdenum-cofactor biosynthesis protein C derived from T. thermophilus was crystallized in two different space groups. Crystals obtained using the first crystallization condition belong to the monoclinic space group P21, with unit-cell parameters a = 64.81, b = 109.84, c = 115.19 Å, β = 104.9°; the crystal diffracted to a resolution of 1.9 Å. The other crystal form belonged to space group R32, with unit-cell parameters a = b = 106.57, c = 59.25 Å, and diffracted to 1.75 Å resolution. Preliminary calculations reveal that the asymmetric unit contains 12 monomers and one monomer for the crystals belonging to space group P21 and R32, respectively. [ABSTRACT FROM AUTHOR]

Highlights events about the synchrotron radiation community. Discussion of techniques in crystallographic studies at the 8th International Conference on Biology and Synchrotron Radiation in Himeji, Japan; Impact of the typhoon on September 7, 2004 in the Kansai Region in Japan on the Shinkansen network and on the roof of SPring-8.