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.     

New approaches to liquid interfaces through changes in the refractive index and nonlinear susceptibility utilizing ultrashort laser pulses.

Molecules in inhomogeneous liquid environments, such as air/liquid, liquid/liquid, solid/liquid interfaces interact with each other specifically, and sometimes form characteristic structures and emerge unique properties. Here, we introduce two newly developed spectroscopic techniques, the total-internal-reflection ultrafast transient lens method (TIR-UTL) and second harmonic generation-coherent vibrational spectroscopy (SHG-CVS), to investigate the characteristic behaviors of molecules in such inhomogeneous environments. TIR-UTL probes the refractive-index change with sub-picosecond resolution and provides information on ultrafast changes in the population, density, and thermal properties, such as temperature increase and energy transfer from the solute molecules to the surrounding solvent molecules. On the other hand, SHG-CVS probes nonlinear susceptibility changes at the interfacial areas, and is expected to provide spectroscopic information on the low-frequency vibrational modes that reflect the corrective motion of the molecules in such an inhomogeneous environment. These new approaches are based on pump-probe techniques utilizing (ultra) short laser pulses. They are expected to provide further information on inhomogeneous environments from the viewpoints of solute-solvent interactions, changes in the molecular orientation, and the corrective motion of molecules at liquid interfaces.     

A simple and sensitive method for the determination of hydroxylamine in fresh-water samples using hypochlorite followed by gas chromatography.

A new and simple method for the determination of hydroxylamine in environmental water, such as fresh rivers and lakes using hypochlorite, followed by its gas choromatographic detection, has been developed. A glass vial filled with sample water was sealed by a butyl-rubber stopper and aluminum cap without head-space, and then sodium hypochlorite solution was injected into the vial through a syringe to convert hydroxylamine to nitrous oxide. The head-space in the glass vial was prepared with 99.9% grade N2 using a gas-tight syringe. After the glass vial was shaken for a few minutes, nitrous oxide in the gas-phase was measured by a gas chromatograph with an electron-capture detector. The dissolved nitrous oxide in the liquid-phase was calculated according to the solubility formula. The proposed method was applied to the analysis of fresh-water samples taken from Iu river and Hii river, flowing into brackish Lakes Nakaumi and Shinji, respectively.     

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.     

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.