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.     

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.     

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.     

Dietary eritadenine-induced alteration of molecular species composition of phospholipids in rats

The effect of dietary eritadenine, a hypocholesterolemic compound found in the mushroomLentinus edodes, on the fatty acid and molecular species profiles of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) in the plasma and liver microsomes was investigated in relation to the hypocholesterolemic action of the compound in rats. Animals were fed the control or eritadenine-supplemented (50 mg/kg diet) diet for 14 d. Eritadenine supplementation significantly decreased the plasma concentrations of cholesterol and phospholipids, but not triglycerides. The PC/PE ratio of liver microsomes, but not plasma, was also markedly decreased by eritadenine. Eritadenine supplementation was found to increase the proportion of 18:2n-6 and, inversely, to decrease the proportion of 20:4n-6 and 22:5n-6 in plasma PC and liver microsomal PC and PE, indicating that eritadenine depressed the metabolism of linoleic acid. The effect of eritadenine on the profile of n-3 fatty acids was dissimilar in PC and PE. These changes in fatty acid composition were selectively reflected in the molecular species composition of both PC and PE; the extent of increase in 16:0–18:2 molecular species or decrease in 18:0–20:4 molecular species was apparently greater than that of other molecular species containing 18:2 or 20:4 in the sn-2 position. These results suggest that, in addition to the decrease in liver microsomal PC/PE ratio, the alteration of plasma PC molecular species composition might also participate in the hypocholesterolemic action of eritadenine.     

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.     

Cytoskeletal Protein 4.1G Is Essential for the Primary Ciliogenesis and Osteoblast Differentiation in Bone Formation

The primary cilium is a hair-like immotile organelle with specific membrane receptors, including the receptor of Hedgehog signaling, smoothened. The cilium organized in preosteoblasts promotes differentiation of the cells into osteoblasts (osteoblast differentiation) by mediating Hedgehog signaling to achieve bone formation. Notably, 4.1G is a plasma membrane-associated cytoskeletal protein that plays essential roles in various tissues, including the peripheral nervous system, testis, and retina. However, its function in the bone remains unexplored. In this study, we identified 4.1G expression in the bone. We found that, in the 4.1G-knockout mice, calcium deposits and primary cilium formation were suppressed in the trabecular bone, which is preosteoblast-rich region of the newborn tibia, indicating that 4.1G is a prerequisite for osteoblast differentiation by organizing the primary cilia in preosteoblasts. Next, we found that the primary cilium was elongated in the differentiating mouse preosteoblast cell line MC3T3-E1, whereas the knockdown of 4.1G suppressed its elongation. Moreover, 4.1G-knockdown suppressed the induction of the cilia-mediated Hedgehog signaling and subsequent osteoblast differentiation. These results demonstrate a new regulatory mechanism of 4.1G in bone formation that promotes the primary ciliogenesis in the differentiating preosteoblasts and induction of cilia-mediated osteoblast differentiation, resulting in bone formation at the newborn stage.     

Heat transfer and flow characteristics of flow boiling of CO2‐oil mixtures in horizontal smooth and micro‐fin tubes

Experiments were carried out on the flow pattern, heat transfer, and pressure drop of flow boiling of pure CO₂ and CO₂‐oil mixtures in horizontal smooth and micro‐fin tubes. The smooth tube is a stainless steel tube with an inner diameter of 3.76 mm. The micro‐fin tube is a copper tube with a mean inner diameter of 3.75 mm. The experiments were carried out at mass velocities from 100 to 500 kg/(m²·s), saturation temperature of 10 °C, and the circulation ratio of lubricating oil (PAG) was from 0 to 1.0 mass%. Flow pattern observations mainly showed slug and wavy flow for the smooth tube, but annular flow for the micro‐fin tube. Compared with the flow patterns in the case of pure CO₂, an increase in frequency of slug occurrence in the slug flow region, and a decrease in the quantity of liquid at the top of the tube in the annular flow region were observed in the case of CO₂‐oil mixtures. With pure CO₂, the flow boiling heat transfer was dominated by nucleate boiling in the low vapor quality region, and the heat transfer coefficients for the micro‐fin tube were higher than those of the smooth tube. With CO₂‐oil mixtures, the flow boiling heat transfer was dominated by convective evaporation, especially in the high vapor quality region. In addition, the heat transfer coefficient decreased significantly when the oil circulation ratio was larger than 0.1 mass%. For the pressure drop characteristics, in the case of pure CO₂, the homogeneous flow model agreed with the experimental results within ±30% for the smooth tube. The pressure drops of the micro‐fin tube were 0–70% higher than those predicted with the homogeneous flow model, and the pressure drops increased for the high oil circulation ratio and high vapor quality conditions. The increases in the pressure drops were considered to be due to the increase in the thickness of the oil film and the decrease in the effective flow cross‐sectional area. © 2010 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/htj.20287     

Motion control of underactuated linkage robot based on gymnastic skill

In this paper, a reproduction of a swing‐up and a giant swing motion of underactuated robots based on technique of the horizontal bar gymnast is discussed with focusing on an equivalent center of mass (ECM) of underactuated robots and the gymnast. At first, the behaviors of the ECM of the gymnast (ECMG) are analyzed by using a motion capturing technique and an efficient motion of the ECMG for the swing‐up and for the giant swing motion are identified from analysis results, respectively. Next, a partial linearization method, which can realize that the ECM of the Acrobot (ECMA) replicates this efficient motion, is designed and reproduces the underactuated robots the swing‐up and giant swing motion like the gymnast. Finally, an effectiveness of the proposed controller is shown by numerical simulations.