Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus

Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the n-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown, partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables the formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable the determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.     

Experimental study for adsorption and photocatalytic reaction of ethyl methylphosphonate molecule as organophosphorus compound adsorbed at surface of titanium dioxide under UV irradiation in ambient condition

The adsorption and photocatalytic degradation of Ethyl methylphosphonate (EMPA) on powdery TiO₂ film has experimentally investigated using attenuated total reflection-infrared Fourier transform spectroscopy (ATR-FTIR) in ambient condition. Characteristic IR frequency as P-O-C vibration mode as EtO was observed by EMPA adsorbed at the surface of TiO₂. By TiO₂ photocatalysis, the adsorbed EMPA was decomposed to methyl phosphonic acid and phosphoric acid. The increment of IR intensity of which is assigned to Ti–O-P-O-Ti of EMPA was accompanied with increasing the IR peak intensity assigned to MPA. About that, we suggest that the appearance of the Ti–O-P-O-Ti of EMPA by the TiO₂ photocatalysis is regarded as acceleration of the hydrolysis of EMPA by the surface OH groups of TiO₂. The plausible adsorption structure and the photocatalytic reaction mechanism of EMPA at the surface of TiO₂ photocatalyst were elucidated.

     

The kinetics of the light-induced defect creation in hydrogenated amorphous silicon – Stretched exponential relaxation

Our model for light-induced defect creation in hydrogenated amorphous silicon is applied to its kinetics, i.e., the growing curve of light-induced dangling bond density as a function of illumination time, which is fitted to a stretched exponential function. Two parameters β and τ involved in the function are estimated as functions of saturated dangling bond density in terms of our model. These are compared with two experimental results, i.e., our results obtained from ESR measurements and Shimakawa et al.’s results obtained from photoconductivity measurements. The saturated dangling bond density is also measured as a function of the generation rate of free carriers. The experimental results are compared with calculated results and discussed.     

Classical in-plane negative magnetoresistance and quantum positive magnetoresistance in undoped InSb thin films on GaAs (1 0 0) substrates

Magnetoresistance (MR) effects have been investigated in perpendicular and parallel magnetic fields at 300, 80 K and liquid He temperatures for undoped InSb thin films 0.1–2.3 μm thick grown on GaAs(1 0 0) substrates by MBE. At high temperatures, the intrinsic carriers show the parabolic negative MR observable only in magnetic fields parallel to the film. The skipping-orbit effect due to surface boundary scattering in the classical orbits in the plane vertical to the film has been argued to be responsible for the negative MR. At low temperatures (T=80 K), the transport is dominated by the two-dimensional (2D) electrons in the accumulation layers at the InSb/GaAs(1 0 0) hetero interface; MR is positive and shows a logarithmic increase with anisotropy between parallel and perpendicular field orientation, arising from the 2D weak anti-localization (WAL) that reflects the interplay between the spin-Zeeman effect and strong spin–orbit interaction caused by the asymmetric potential at the interface (Rashba term). The zero-field spin splitting energy of Δ₀13 meV, the electron effective mass of m^*0.10m₀ seven times of the band edge mass in bulk InSb and the effective g-factor of |g^*|15 in the accumulation layer have been inferred from fits of MR for the 0.1 μm thick film to the 2D WL theory.     

Compact directed acyclic word graphs for a sliding window

Suffix trees are a well-known and widely-studied data structure highly useful for string matching. The suffix tree of a string w can be constructed in O(n) time and space, where n denotes the length of w. Larsson achieved an efficient algorithm to maintain suffix trees for a sliding window. It contributes to prediction by partial matching (PPM) style statistical data compression scheme. Compact directed acyclic word graphs (CDAWGs) are a more space-economical data structure for indexing strings. In this paper we propose a linear-time algorithm to maintain CDAWGs for a sliding window.     

Charge density study under high pressure

The experimental and analytical method of the high-pressure powder experiment at BL10XU, SPring-8, is described. There is no doubt that BL10XU must be one of the most appropriate beam lines for high pressure X-ray diffraction experiment taking advantage of third generation synchrotron source. As an example of the advanced charge density study under high pressure, the structural change of Cs₂Au₂Br₆ by applying pressure is studied by Rietveld/MEM analysis. It reveals that the structural change of Cs₂Au₂Br₆ by applying pressure occurs basically at electron level, such as valence state change and chemical bonding, which may be called the electronic phase transition.     

Mechanistic aspects regarding the formation of metal vinylidenes from alkynes and related reactions

This review focuses on the tautomerization mechanism between alkynes and vinylidene units taking place in the coordination sphere of transition metal fragments. Reactions of vinylidene complexes as well as catalytic reactions involving a metal-vinylidene intermediate are also reviewed from the mechanistic point of view.     

Endoscopic Observation of Tissue by Narrowband Illumination

We propose a new illumination method for a medical endoscope: narrow band imaging (NBI), in which the spectral bandwidth of the filtered light is narrowed. To confirm how the spectral specifications of the filtered light influence a reproduced image, an experiment was conducted observing the endoscopic images of the back mucosa of a human tongue. In addition, the effect of NBI on endoscopic images was investigated through preliminary clinical tests in colonoscopy and upper gastrointestinal endoscopy. It has been shown that NBI can enhance the capillary pattern and the crypt pattern on the mucosa. These patterns are useful features for diagnosing an early cancer.     

5-Aza-2′-deoxycytidine reactivates the CDH1 gene without influencing methylation of the entire CpG island or histone modification in a human cancer cell line

It is well-recognized that DNA methylation and histone modifications play critical roles in epigenetic regulation of gene activity through the alteration of chromatin structure. Recent studies have shown that in a subset of cancer cells, the silencing of the human E-cadherin (CDH1) gene is associated with hypermethylation of the CpG island. However, the associated molecular mechanism remains unclear. To understand the mechanism, we have investigated the alteration of CpG island methylation and histone modifications during the reactivation of the CDH1 gene by treatment with 5-aza-2′-deoxycytidine (5-aza-dC). Although the CDH1 gene expression was recovered by treatment with 5-aza-dC in a liver cancer cell line Li21, the methylation status of the entire CpG island and acetylation and methylation status of associated histones were not significantly altered. These results demonstrate that the silenced CDH1 gene can be reactivated without apparent alteration of histone modification or CpG island methylation.