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.     

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.     

Large-volume injection electrothermal AAS combined with tungsten-treated pyrolytic graphite furnace: determination of cadmium in tap, snow and river water samples with phosphate modifier.

A large-volume (100 microl) injection-ETAAS with W-treated PG furnace combined with a phosphate modifier was applied to the determination of unpolluted levels of Cd in tap, snow and river-water samples. The limit of detection of 1.1 ng l(-1) was observed for a 4 w/v% NH4H2PO4 modifer. Matrix interference studies were tested for major ion species well found in fresh water. The direct determination of Cd in certified river water (12 +/- 2 ng l(-1)) was carried out and the observed value was in agreement with the certified one. The good recoveries of Cd added to real environmental water samples were also observed. This method was applied to the determination of Cd in unpolluted environmental water samples.     

Reconstruction of the Point-Spread Function of the Human Eye Using a New Phase-Retrieval Algorithm

The double-pass method is thought to obtain the point spread function (PSF) in human eyes based on two techniques: the symmetric double-pass method using the same pupil size and the asymmetric double-pass method using a different pupil size. The symmetric double-pass method provides autocorrelation of the retinal PSF and, thus, the modulation transfer function. The asymmetric double-pass method provides low-frequency partial-phase information and the partial phase-retrieval algorithm is applied to obtain the complete-phase information, and to estimate the PSF. The partial phase-retrieval algorithm is based on the iteration method proposed by Fineup and Kowalczyk and requires a lengthy computation. In this study, we propose a new high-speed phase-retrieval algorithm based on the property that the real and imaginary parts of optical transfer functions (OTFs) continuously change in value.     

Measuring Light Field of Light Source with High Directional Resolution Using Mirrored Ball and Pinhole Camera

This paper presents a method of measuring a light field of a light source with high directional resolution using a mirrored ball and a pinhole camera. The light field describes a spatial and directional distribution of radiances from the light source. The directional distribution is expanded by a reflection on the mirrored ball, and the radiances are measured by a charge-coupled device (CCD) camera with a pinhole lens. The light source is laterally moved by a robot arm to measure the directionally expanded light field, and each pixel on a CCD can obtain the radiances from the light source through the pinhole lens with high directional resolution. The light field is estimated from the pixel value and the position of each pixel using a ray tracing technique. The light field of a krypton lamp was experimentally measured by the proposed method, and the accuracy of the measurement was evaluated against the irradiances measured by a spectro-radiometer at sample points.     

Direct determination of benzamides in serum by column-switching high-performance liquid chromatography.

A column-switching high-performance liquid chromatographic method with fluorescence detection was developed for the simultaneous determination of four benzamide-type anti-psychotic drugs: sulpiride, tiapride, sultopride and metoclopramide in human serum. In this method, a TSKgel Super-ODS column was used as an analytical column, and a TSKgel G 2000SW was prepared as a pretreatment column. Under the optimized analytical conditions, four benzamide-type anti-psychotic drugs were eluted within 18 min. The detection limits (S/N = 3) for sulpiride, tiapride, sultopride and metoclopramide are 1 ng/ml, 4 ng/ml, 2 ng/ml and 0.5 ng/ml, respectively. Finally, the method was applied to the determination of sulpiride in human serum samples obtained after a single oral dose of sulpiride.     

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.     

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.