Chiral selection in supercoiling and wrapping of DNA

This paper gives an account of our recent studies on the mechanisms for chiral selection in super-coiling and wrapping of DNA. We first present a compact model of double-stranded DNA (Model 1), which consists of two elastic chains that mutually intertwine in a right-handed manner to form a double-stranded helix. Numerical analysis of this model suggests an intrinsic propensity of DNA to writhe in the left direction upon bending. Based on this asymmetric elasticity of DNA, we present a further simplified model of DNA (Model 2), which is a single-chained homopolymer with the propensity to writhe in the left direction upon bending. This simplified model is incorporated into a Langevin dynamics study to explore the origin of the uniform left-handed wrapping of DNA around a nucleosome core particle in nature. We finally show that the propensity of DNA to writhe in the left direction upon bending gives rise to the selective left-handed wrapping, provided that the size of the core particle is appropriate. This result suggests the fundamental significance of the asymmetric elasticity of helical biopolymers in their structural dynamics and functions.     

Preparation of bismuth nanowire encased in quartz template for Hall measurements using focused ion beam processing

ABSTRACT: Forming electrodes on opposite sides of an individual bismuth nanowire was attempted to prepare for Hall measurements. Although a 1-mm-long bismuth nanowire which is completely covered with a quartz template has been successfully fabricated to prevent oxidation, it is very difficult to attach Hall electrodes on the opposite sides of the nanowire due to the quartz covering. One side of the cylindrical quartz template was removed by polishing without exposure of the nanowire to the atmosphere; the thickness between the polished template surface and the nanowire was estimated to be several micrometers. Focused ion beam processing was successfully employed to expose both surfaces of the nanowire under high vacuum by removing part of the quartz template. A carbon thin film was then deposited in situ on the wire surface to fabricate an electrical contact on the bismuth nanowire sample. Furthermore, the energy dispersive X-ray analysis was performed to the area processed by focused ion beam, and the bismuth component of the nanowire was successfully detected. It was confirmed that the focused ion beam processing was applicable to attach electrodes to bismuth nanowire for Hall measurement.     

High‐temperature latent heat storage technology to utilize exergy of solar heat and industrial exhaust heat

Latent heat storage (LHS) using phase change materials is quite attractive for utilization of the exergy of solar energy and industrial exhaust heat because of its high‐heat storage capacity, heat storage and supply at constant temperature, and repeatable utilization without degradation. In this article, general LHS technology is outlined, and then recent advances in the uses of LHS for high‐temperature applications (over 100 °C) are discussed, with respect to each type of phase change material (e.g., sugar alcohol, molten salt, and alloy). The prospects of future LHS systems are discussed from a principle of exergy recuperation. In addition, the technologies to minimize exergy loss in the future LHS system are discussed on the basis of the thermodynamic analysis by ‘thermodynamic compass’. Copyright © 2016 John Wiley & Sons, Ltd.     

Correlations of Hepatic Hemodynamics,Liver Function,and Fibrosis Markers in Nonalcoholic Fatty Liver Disease: Comparison with Chronic Hepatitis Related to Hepatitis C Virus

The progression of chronic liver disease differs by etiology. The aim of this study was to elucidate the difference in disease progression between chronic hepatitis C (CHC) and nonalcoholic fatty liver disease (NAFLD) by means of fibrosis markers, liver function, and hepatic tissue blood flow (TBF). Xenon computed tomography (Xe-CT) was performed in 139 patients with NAFLD and 152 patients with CHC (including liver cirrhosis (LC)). The cutoff values for fibrosis markers were compared between NAFLD and CHC, and correlations between hepatic TBF and liver function tests were examined at each fibrosis stage. The cutoff values for detection of the advanced fibrosis stage were lower in NAFLD than in CHC. Although portal venous TBF (PVTBF) correlated with liver function tests, PVTBF in initial LC caused by nonalcoholic steatohepatitis (NASH-LC) was significantly lower than that in hepatitis C virus (C-LC) (p = 0.014). Conversely, the liver function tests in NASH-LC were higher than those in C-LC (p < 0.05). It is important to recognize the difference between NAFLD and CHC. We concluded that changes in hepatic blood flow occurred during the earliest stage of hepatic fibrosis in patients with NAFLD; therefore, patients with NAFLD need to be followed carefully.     

Multilayered reasoning by means of conceptual fuzzy sets

The real world consists of instances of events and continuous numeric values, while people represent and process their knowledge in terms of symbols. Fuzzy sets provide a strong notation connecting the symbolic representation to the real world. In previously proposed Conceptual Fuzzy Sets (CFS), the meaning of a concept is represented by the distribution of activations of labels in a bidirectional associative memory. In particular, a multilayered structured CFS represents the meaning of the same concept as it is used in various expressions in each layer. The propagation of activations corresponds to reasoning. Therefore, we propose a multilayered reasoning method associated to a multilayered structured CFS, which has the following features: (1) capable of simultaneous symbolic and quantitative processing, (2) capable of simultaneous top-down and bottom-up processing. The effectiveness of the proposed method is illustrated by practical examples of decision regarding the amount of steering in the task of parking a car, and recognition of facial expressions for an image understanding system. © 1996 John Wiley & Sons, Inc.     

Accumulation and elimination profiles of paralytic shellfish poison in the short-necked clam Tapes japonica fed with the toxic dinoflagellate Gymnodinium catenatum

The paralytic shellfish poison (PSP)-producing dinoflagellate Gymnodinium catenatum (Gc) was fed to the short-necked clam Tapes japonica, and the accumulation, transformation and elimination profiles of PSP were investigated by means of high-performance liquid chromatography with postcolumn fluorescence derivatization (HPLC-FLD). The short-necked clams ingested most of the Gc cells (4 x 10(6) cells) supplied as a bolus at the beginning of the experiment, and accumulated a maximal amount of toxin (181 nmol/10 clams) after 12 hr. The rate of toxin accumulation at that time was 16%, which rapidly decreased thereafter. During the rearing period, a variation in toxin composition, derived presumably from the transformation of toxin analogues in the clams, was observed, including a reversal of the ratio of C2 to C1, and the appearance of carbamate (gonyautoxin (GTX) 2, 3) and decarbamoyl (dc) derivatives (decarbamoylsaxitoxin (dcSTX) and dcGTX2, 3), which were undetectable in Gc cells. The total amount of toxin contained in clams and residue (remaining Gc cells and/or excrement in the rearing tank) gradually declined, and only about 1% of the supplied toxin was detected at the end of the experiment.     

Evaluation of drug toxicity with hepatocytes cultured in a micro-space cell culture system

A micro-space cell culture system was recently developed in which cells such as hepatocytes can be cultured and formed into a multicellular three-dimensional (3D) architecture. In this study, we assessed the performance of HepG2 cells cultured in this micro-space cell culture system in a drug toxicity test, and evaluated the effects of micro-space culture on their hepatocyte-specific functions. The micro-space cell culture facilitated the formation of 3D HepG2 cell architecture. HepG2 cells cultured in a micro-space culture plate exhibited increased albumin secretion and enhanced mRNA expression levels of cytochrome P450 (CYP) enzyme compared to those cultured in a monolayer culture. When the cells were exposed to acetaminophen, a hepatotoxic drug, the damage to the HepG2 cells grown in micro-space culture was greater than the damage to the HepG2 cells grown in monolayer culture. In addition, human primary hepatocytes grown in micro-space culture also exhibited increased albumin secretion, enhanced CYP mRNA expression levels and increased sensitivity to acetaminophen compared to those grown in monolayer culture. These results suggest that this micro-space culture method enhances the hepatocyte-specific functions of hepatocytes, including drug-metabolizing enzyme activities, making hepatocytes grown in the micro-space culture system a useful tool for evaluating drug toxicity in vitro.     

Metastatic Voyage of Ovarian Cancer Cells in Ascites with the Assistance of Various Cellular Components

Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy and has a unique metastatic route using ascites, known as the transcoelomic root. However, studies on ascites and contained cellular components have not yet been sufficiently clarified. In this review, we focus on the significance of accumulating ascites, contained EOC cells in the form of spheroids, and interaction with non-malignant host cells. To become resistant against anoikis, EOC cells form spheroids in ascites, where epithelial-to-mesenchymal transition stimulated by transforming growth factor-β can be a key pathway. As spheroids form, EOC cells are also gaining the ability to attach and invade the peritoneum to induce intraperitoneal metastasis, as well as resistance to conventional chemotherapy. Recently, accumulating evidence suggests that EOC spheroids in ascites are composed of not only cancer cells, but also non-malignant cells existing with higher abundance than EOC cells in ascites, including macrophages, mesothelial cells, and lymphocytes. Moreover, hetero-cellular spheroids are demonstrated to form more aggregated spheroids and have higher adhesion ability for the mesothelial layer. To improve the poor prognosis, we need to elucidate the mechanisms of spheroid formation and interactions with non-malignant cells in ascites that are a unique tumor microenvironment for EOC.     

Synthetic Molecular Gear Based on Double-Decker Porphyrin Complexes

New rotary molecular machines (1 and 2) were synthetically constructed from two distinct porphyrin-based rotors, a cerium(IV) bis(porphyrinate)s double-decker (CeDD) and a porphyrinatorhodium(III)-based rotor. These rotors are adjacently mounted on rotational axes aligned to near vertical as resembling the bevel-gear-shaped structure. Structural study using NMR analysis reveals that these distinct rotors are connected through a coordination bond between rhodium(III) and a pyridyl group. At temperature from 193 to 393 K, each rotor represents rotational motion driven by heat fluctuation without decomposition into the corresponding precursors in dichloromethane-d ₂ and tetrachloroethane-d ₄. Importantly, the mechanical interaction between the teeth of these rotors is strongly dependent on the central metal atom in a DD rotor and the teeth structure in a porphyrinatorhodium(III)-based rotor. Understanding such relationship between the chemical structures and mechanical interaction is of importance for generating cooperative motion in the hybrid machinery system.