The developmental process of flood shoals based on observations in Toufutsu lake, Japan

Recently, the flood tidal sand bars have been developed at the entrance channel of Toufutsu Lake located along Okhotsk Sea in Hokkaido, and they affect flood control, inland water fisheries in lake, and so forth. In this study, we aimed to reveal the developmental process of sand bars by observations, which are velocity observation, water level observation, bed material investigation and video monitoring. Followings were major accomplishments of this study. (1) The maximum magnitude of reverse velocity at St.400 in the entrance channel during the periods of flood-tide was faster than that of normal velocity during the periods of ebb-tide. (2) The relationship between velocity at SP400 and friction velocity at SP400 during the periods of flood-tide is different from that during the periods of ebb-tide. (3) The\ud flood tidal sand bars at the entrance channel of Toufutsu Lake were developed by not only sea waves, but also adverse tidal current in the spring-tide

Phase boundary exchange coupling in the mixed magnetic phase regime of a Pd-doped FeRh epilayer

Spin-wave resonance measurements were performe in the mixed magnetic phase regime of a Pd-doped FeRh epilayer that appears as the first-order ferromagnetic-antiferromagnetic phase transition takes place. It is seen that the measured value of the exchange stiffness is suppressed throughout the measurement range when compared to the expected value of the fully ferromagnetic regime, extracted via the independent means of a measurement of the Curie point, for only slight changes in the ferromagnetic volume fraction. This behavior is attributed to the influence of the antiferromagnetic phase: inspired by previous experiments that show ferromagnetism to be most persistent at the surfaces and interfaces of FeRh thin films, we modelled the antiferromagnetic phase as forming a thin layer in the middle of the epilayer through which the two ferromagnetic layers are coupled up to a certain critical thickness. The development of this exchange stiffness is then consistent with that expected from the development of an exchange coupling across the magnetic phase boundary, as a consequence of a thickness dependent phase transition taking place in the antiferromagnetic regions and is supported by complimentary computer simulations of atomistic spin-dynamics. The development of the Gilbert damping parameter extracted from the ferromagnetic resonance investigations is consistent with this picture

Emergent Phenomena Induced by Spin-Orbit Coupling at Surfaces and Interfaces

Spin-orbit coupling (SOC) describes the relativistic interaction between the spin and momentum degrees of freedom of electrons, and is central to the rich phenomena observed in condensed matter systems. In recent years, new phases of matter have emerged from the interplay between SOC and low dimensionality, such as chiral spin textures and spin-polarized surface and interface states. These low-dimensional SOC-based realizations are typically robust and can be exploited at room temperature. Here we discuss SOC as a means of producing such fundamentally new physical phenomena in thin films and heterostructures. We put into context the technological promise of these material classes for developing spin-based device applications at room temperature

Planar Hall effect from the surface of topological insulators

A prominent feature of topological insulators (TIs) is the surface states comprising of spin-nondegenerate massless Dirac fermions. Recent technical advances have made it possible to address the surface transport properties of TI thin films by tuning the Fermi levels of both top and bottom surfaces. Here we report our discovery of a novel planar Hall effect (PHE) from the TI surface, which results from a hitherto-unknown resistivity anisotropy induced by an in-plane magnetic field. This effect is observed in dual-gated devices of bulk-insulating Bi2−x Sb x Te3 thin films, where the field-induced anisotropy presents a strong dependence on the gate voltage with a characteristic two-peak structure near the Dirac point. The origin of PHE is the peculiar time-reversal-breaking effect of an in-plane magnetic field, which anisotropically lifts the protection of surface Dirac fermions from backscattering. The observed PHE provides a useful tool to analyze and manipulate the topological protection of the TI surface

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

<div><h3>Background</h3><p>The development of rice (<em>Oryza sativa</em>) seed is closely associated with assimilates storage and plant yield, and is fine controlled by complex regulatory networks. Exhaustive transcriptome analysis of developing rice embryo and endosperm will help to characterize the genes possibly involved in the regulation of seed development and provide clues of yield and quality improvement.</p> <h3>Principal Findings</h3><p>Our analysis showed that genes involved in metabolism regulation, hormone response and cellular organization processes are predominantly expressed during rice development. Interestingly, 191 transcription factor (TF)-encoding genes are predominantly expressed in seed and 59 TFs are regulated during seed development, some of which are homologs of seed-specific TFs or regulators of <em>Arabidopsis</em> seed development. Gene co-expression network analysis showed these TFs associated with multiple cellular and metabolism pathways, indicating a complex regulation of rice seed development. Further, by employing a cold-resistant <em>cultivar</em> Hanfeng (HF), genome-wide analyses of seed transcriptome at normal and low temperature reveal that rice seed is sensitive to low temperature at early stage and many genes associated with seed development are down-regulated by low temperature, indicating that the delayed development of rice seed by low temperature is mainly caused by the inhibition of the development-related genes. The transcriptional response of seed and seedling to low temperature is different, and the differential expressions of genes in signaling and metabolism pathways may contribute to the chilling tolerance of HF during seed development.</p> <h3>Conclusions</h3><p>These results provide informative clues and will significantly improve the understanding of rice seed development regulation and the mechanism of cold response in rice seed.</p> </div

Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds

Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily occurs in the endosperm, a seed tissue that supports the embryo during its growth and development. Previously, we demonstrated that widespread DNA demethylation at remnants of transposable elements accompanies endosperm development and that a subset of these methylation changes are associated with gene imprinting. Here we assay imprinted gene expression genome-wide by performing high-throughput sequencing of RNA derived from seeds of reciprocal intraspecific crosses. We identify more than 200 loci that exhibit parent-of-origin effects on gene expression in the endosperm, including a large number of transcription factors, hormone biosynthesis and response genes, and genes that encode regulators of epigenetic information, such as methylcytosine binding proteins, histone methyltransferases, and chromatin remodelers. The majority of these genes are partially, rather than completely, imprinted, suggesting that gene dosage regulation is an important aspect of imprinted gene expression

Morphogenesis of the T4 tail and tail fibers

Remarkable progress has been made during the past ten years in elucidating the structure of the bacteriophage T4 tail by a combination of three-dimensional image reconstruction from electron micrographs and X-ray crystallography of the components. Partial and complete structures of nine out of twenty tail structural proteins have been determined by X-ray crystallography and have been fitted into the 3D-reconstituted structure of the "extended" tail. The 3D structure of the "contracted" tail was also determined and interpreted in terms of component proteins. Given the pseudo-atomic tail structures both before and after contraction, it is now possible to understand the gross conformational change of the baseplate in terms of the change in the relative positions of the subunit proteins. These studies have explained how the conformational change of the baseplate and contraction of the tail are related to the tail's host cell recognition and membrane penetration function. On the other hand, the baseplate assembly process has been recently reexamined in detail in a precise system involving recombinant proteins (unlike the earlier studies with phage mutants). These experiments showed that the sequential association of the subunits of the baseplate wedge is based on the induced-fit upon association of each subunit. It was also found that, upon association of gp53 (gene product 53), the penultimate subunit of the wedge, six of the wedge intermediates spontaneously associate to form a baseplate-like structure in the absence of the central hub. Structure determination of the rest of the subunits and intermediate complexes and the assembly of the hub still require further study

An essential role for the baseplate protein Gp45 in phage adsorption to Staphylococcus aureus

Despite the importance of phages in driving horizontal gene transfer (HGT) among pathogenic bacteria, the underlying molecular mechanisms mediating phage adsorption to S. aureus are still unclear. Phage φ11 is a siphovirus with a high transducing efficiency. Here, we show that the tail protein Gp45 localized within the φ11 baseplate. Phage φ11 was efficiently neutralized by anti-Gp45 serum, and its adsorption to host cells was inhibited by recombinant Gp45 in a dose-dependent manner. Flow cytometry analysis demonstrated that biotin-labelled Gp45 efficiently stained the wild-type S. aureus cell but not the double knockout mutant ΔtarM/S, which lacks both α- and β-O-GlcNAc residues on its wall teichoic acids (WTAs). Additionally, adsorption assays indicate that GlcNAc residues on WTAs and O-acetyl groups at the 6-position of muramic acid residues in peptidoglycan are essential components of the φ11 receptor. The elucidation of Gp45-involved molecular interactions not only broadens our understanding of siphovirus-mediated HGT, but also lays the groundwork for the development of sensitive affinity-based diagnostics and therapeutics for S. aureus infection