Tokyo University of Agriculture and Technology

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

Plastics debris in the marine environment, including resin pellets, fragments and microscopic plastic fragments, contain organic contaminants, including polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons, petroleum hydrocarbons, organochlorine pesticides (2,2'-bis(p-chlorophenyl)-1,1,1-trichloroethane, hexachlorinated hexanes), polybrominated diphenylethers, alkylphenols and bisphenol A, at concentrations from sub ng g(-1) to microg g(-1). Some of these compounds are added during plastics manufacture, while others adsorb from the surrounding seawater. Concentrations of hydrophobic contaminants adsorbed on plastics showed distinct spatial variations reflecting global pollution patterns. Model calculations and experimental observations consistently show that polyethylene accumulates more organic contaminants than other plastics such as polypropylene and polyvinyl chloride. Both a mathematical model using equilibrium partitioning and experimental data have demonstrated the transfer of contaminants from plastic to organisms. A feeding experiment indicated that PCBs could transfer from contaminated plastics to streaked shearwater chicks. Plasticizers, other plastics additives and constitutional monomers also present potential threats in terrestrial environments because they can leach from waste disposal sites into groundwater and/or surface waters. Leaching and degradation of plasticizers and polymers are complex phenomena dependent on environmental conditions in the landfill and the chemical properties of each additive. Bisphenol A concentrations in leachates from municipal waste disposal sites in tropical Asia ranged from sub microg l(-1) to mg l(-1) and were correlated with the level of economic development.

Plant compounds that are perceived by humans to have color are generally referred to as 'pigments'. Their varied structures and colors have long fascinated chemists and biologists, who have examined their chemical and physical properties, their mode of synthesis, and their physiological and ecological roles. Plant pigments also have a long history of use by humans. The major classes of plant pigments, with the exception of the chlorophylls, are reviewed here. Anthocyanins, a class of flavonoids derived ultimately from phenylalanine, are water-soluble, synthesized in the cytosol, and localized in vacuoles. They provide a wide range of colors ranging from orange/red to violet/blue. In addition to various modifications to their structures, their specific color also depends on co-pigments, metal ions and pH. They are widely distributed in the plant kingdom. The lipid-soluble, yellow-to-red carotenoids, a subclass of terpenoids, are also distributed ubiquitously in plants. They are synthesized in chloroplasts and are essential to the integrity of the photosynthetic apparatus. Betalains, also conferring yellow-to-red colors, are nitrogen-containing water-soluble compounds derived from tyrosine that are found only in a limited number of plant lineages. In contrast to anthocyanins and carotenoids, the biosynthetic pathway of betalains is only partially understood. All three classes of pigments act as visible signals to attract insects, birds and animals for pollination and seed dispersal. They also protect plants from damage caused by UV and visible light.

We report the observation of a narrow charmoniumlike state produced in the exclusive decay process ${B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}{K}^{\ifmmode\pm\else\textpm\fi{}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$. This state, which decays into ${\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$, has a mass of $3872.0\ifmmode\pm\else\textpm\fi{}0.6\mathrm{(}\mathrm{s}\mathrm{t}\mathrm{a}\mathrm{t}\mathrm{)}\ifmmode\pm\else\textpm\fi{}0.5\mathrm{(}\mathrm{s}\mathrm{y}\mathrm{s}\mathrm{t}\mathrm{)}\text{ }\text{ }\mathrm{M}\mathrm{e}\mathrm{V}$, a value that is very near the ${M}_{{D}^{0}}+{M}_{{D}^{*0}}$ mass threshold. The results are based on an analysis of 152M $B$-$\overline{B}$ events collected at the $\ensuremath{\Upsilon}(4S)$ resonance in the Belle detector at the KEKB collider. The signal has a statistical significance that is in excess of $10\ensuremath{\sigma}$.

UNLABELLED: The system SOSUI for the discrimination of membrane proteins and soluble ones together with the prediction of transmembrane helices was developed, in which the accuracy of the classification of proteins was 99% and the corresponding value for the transmembrane helix prediction was 97%. AVAILABILITY: The system SOSUI is available through internet access: http://www.tuat.ac.jp/mitaku/sosui/. CONTACT: sosui@biophys.bio.tuat. ac.jp.

Plastic resin pellets (small granules 0.1-0.5 centimeters in diameter) are widely distributed in the ocean all over the world. They are an industrial raw material for the plastic industry and are unintentionally released to the environment both during manufacturing and transport. They are sometimes ingested by seabirds and other marine organisms, and their adverse effects on organisms are a concern. In the present study, PCBs, DDE, and nonylphenols (NP) were detected in polypropylene (PP) resin pellets collected from four Japanese coasts. Concentrations of PCBs (4-117 ng/g), DDE (0.16-3.1 ng/g), and NP (0.13-16 microg/g) varied among the sampling sites. These concentrations were comparable to those for suspended particles and bottom sediments collected from the same area as the pellets. Field adsorption experiments using PP virgin pellets demonstrated significant and steady increase in PCBs and DDE concentrations throughout the six-day experiment, indicating that the source of PCBs and DDE is ambient seawater and that adsorption to pellet surfaces is the mechanism of enrichment. The major source of NP in the marine PP resin pellets was thought to be plastic additives and/or their degradation products. Comparison of PCBs and DDE concentrations in mari

A key challenge of future mobile communication research is to strike an attractive compromise between wireless network's area spectral efficiency and energy efficiency. This necessitates a clean-slate approach to wireless system design, embracing the rich body of existing knowledge, especially on multiple-input-multiple-ouput (MIMO) technologies. This motivates the proposal of an emerging wireless communications concept conceived for single-radio-frequency (RF) large-scale MIMO communications, which is termed as SM. The concept of SM has established itself as a beneficial transmission paradigm, subsuming numerous members of the MIMO system family. The research of SM has reached sufficient maturity to motivate its comparison to state-of-the-art MIMO communications, as well as to inspire its application to other emerging wireless systems such as relay-aided, cooperative, small-cell, optical wireless, and power-efficient communications. Furthermore, it has received sufficient research attention to be implemented in testbeds, and it holds the promise of stimulating further vigorous interdisciplinary research in the years to come. This tutorial paper is intended to offer a comprehensive state-of-the-art survey on SM-MIMO research, to provide a critical appraisal of its potential advantages, and to promote the discussion of its beneficial application areas and their research challenges leading to the analysis of the technological issues associated with the implementation of SM-MIMO. The paper is concluded with the description of the world's first experimental activities in this vibrant research field.

We report the novel concept of photochemical sterilization. Microbial cells were killed photoelectrochemically with semiconductor powder (platinum-loaded titanium oxide, TiO2/Pt). Coenzyme A, (CoA) in the whole cells was photo-electrochemically oxidized and, as a result, the respiration of cells was inhibited. Inhibition of respiratory activity caused death of the cells. Lactobacillus acidophilus, Saccharomyces cerevisiae and Escherichia coli (103 cells/ml respectively) were completely sterilized when they were incubated with TiO2/Pt particles under metal halide lamp irradiation for 60–120 min.

Soil contamination by potentially toxic elements (PTEs) has led to adverse environmental impacts. In this review, we discussed remediation of PTEs contaminated soils through immobilization techniques using different soil amendments with respect to type of element, soil, and amendment, immobilization efficiency, underlying mechanisms, and field applicability. Soil amendments such as manure, compost, biochar, clay minerals, phosphate compounds, coal fly ash, and liming materials are widely used as immobilizing agents for PTEs. Among these soil amendments, biochar has attracted increased interest over the past few years because of its promising surface properties. Integrated application of appropriate amendments is also recommended to maximize their use efficiency. These amendments can reduce PTE bioavailability in soils through diverse mechanisms such as precipitation, complexation, redox reactions, ion exchange, and electrostatic interaction. However, soil properties such as soil pH, and clay, sesquioxides and organic matter content, and processes, such as sorption/desorption and redox processes, are the key factors governing the amendments' efficacy for PTEs immobilization in soils. Selecting proper immobilizing agents can yield cost-effective remediation techniques and fulfill green and sustainable remediation principles. Furthermore, long-term stability of immobilized PTE compounds and the environmental impacts and cost effectiveness of the amendments should be considered before application.

We first succeeded in synthesizing ionic liquids from 20 natural amino acids. Amino acid ionic liquids dissolved native amino acids, despite water-free conditions. Furthermore, these ionic liquids are soluble in various organic solvents, such as chloroform. Effects of acidity, hydrogen bonding ability, and steric factors on the properties of these ionic liquids were analyzed as the function of side groups.

This is a review article on the current status and future prospects of the research and development on gallium oxide (Ga2O3) power devices. Ga2O3 possesses excellent material properties, in particular for power device applications. It is also attractive from an industrial viewpoint since large-size, high-quality wafers can be manufactured from a single-crystal bulk synthesized by melt–growth methods. These two features have drawn much attention to Ga2O3 as a new wide bandgap semiconductor following SiC and GaN. In this review, we describe the recent progress in the research and development on fundamental technologies of Ga2O3 devices, covering single-crystal bulk and wafer production, homoepitaxial thin film growth by molecular beam epitaxy and halide vapor phase epitaxy, as well as device processing and characterization of metal–semiconductor field-effect transistors, metal–oxide–semiconductor field-effect transistors and Schottky barrier diodes.

Loop-mediated isothermal amplification (LAMP), a novel gene amplification method, enables the synthesis of larger amounts of both DNA and a visible byproduct--namely, magnesium pyrophosphate--without thermal cycling. A positive reaction is indicated by the turbidity of the reaction solution or the color change after adding an intercalating dye to the reaction solution, but the use of such dyes has certain limitations. Hydroxy naphthol blue (HNB), a metal indicator for calcium and a colorimetric reagent for alkaline earth metal ions, was used for a new colorimetric assay of the LAMP reaction. Preaddition of 120 microM HNB to the LAMP reaction solution did not inhibit amplification efficiency. A positive reaction is indicated by a color change from violet to sky blue. The LAMP reaction with HNB could also be carried out in a 96-well microplate, and the reaction could be measured at 650 nm with a microplate reader. The colorimetric LAMP method using HNB would be helpful for high-throughput DNA and RNA detection.

Fatty acids are metabolized and synthesized as energy substrates during biological responses. Long- and medium-chain fatty acids derived mainly from dietary triglycerides, and short-chain fatty acids (SCFAs) produced by gut microbial fermentation of the otherwise indigestible dietary fiber, constitute the major sources of free fatty acids (FFAs) in the metabolic network. Recently, increasing evidence indicates that FFAs serve not only as energy sources but also as natural ligands for a group of orphan G protein-coupled receptors (GPCRs) termed free fatty acid receptors (FFARs), essentially intertwining metabolism and immunity in multiple ways, such as via inflammation regulation and secretion of peptide hormones. To date, several FFARs that are activated by the FFAs of various chain lengths have been identified and characterized. In particular, FFAR1 (GPR40) and FFAR4 (GPR120) are activated by long-chain saturated and unsaturated fatty acids, while FFAR3 (GPR41) and FFAR2 (GPR43) are activated by SCFAs, mainly acetate, butyrate, and propionate. In this review, we discuss the recent reports on the key physiological functions of the FFAR-mediated signaling transduction pathways in the regulation of metabolism and immune responses. We also attempt to reveal future research opportunities for developing therapeutics for metabolic and immune disorders.

The phytohormone auxin plays critical roles in the regulation of plant growth and development. Indole-3-acetic acid (IAA) has been recognized as the major auxin for more than 70 y. Although several pathways have been proposed, how auxin is synthesized in plants is still unclear. Previous genetic and enzymatic studies demonstrated that both TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) flavin monooxygenase-like proteins are required for biosynthesis of IAA during plant development, but these enzymes were placed in two independent pathways. In this article, we demonstrate that the TAA family produces indole-3-pyruvic acid (IPA) and the YUC family functions in the conversion of IPA to IAA in Arabidopsis ( Arabidopsis thaliana ) by a quantification method of IPA using liquid chromatography–electrospray ionization–tandem MS. We further show that YUC protein expressed in Escherichia coli directly converts IPA to IAA. Indole-3-acetaldehyde is probably not a precursor of IAA in the IPA pathway. Our results indicate that YUC proteins catalyze a rate-limiting step of the IPA pathway, which is the main IAA biosynthesis pathway in Arabidopsis .

The oxidation of model sulfur compounds (thiophene derivatives, benzothiophene derivatives, and dibenzothiophene derivatives), straight run-light gas oil (SR-LGO, S: 1.35 wt %), and vacuum gas oil (VGO, S: 2.17 wt %) were conducted with a mixture of hydrogen peroxide and formic acid. The thiophene derivatives with 5.696 to 5.716 electron densities on the sulfur atoms could not be oxidized at 50 °C. Benzo[b]thiophene with 5.739 electron density and other benzothiophene and dibenzothiophenes with higher electron densities could be oxidized. The sulfur compounds in SR-LGO and VGO appeared to be oxidized to a detectable levels (c.a., 0.01 wt % S) by GC-FPD analysis. The IR spectra of oxidized SR-LGO and VGO showed that sulfones were formed by oxidation. The removal of sulfur compounds by extraction became more effective for the oxidized samples than for the original samples. Lighter sulfur compounds were preferentially extracted. The extraction efficiencies of solvents, i.e., N,N‘-dimethylformamide (DMF), acetonitrile (ACN), methanol, varied greatly. The most effective solvent for the removal of sulfur compounds was DMF. The recovery of oil was, however, lowest with DMF.

BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is caused by SFTS virus (SFTSV), a novel bunyavirus reported to be endemic in central and northeastern China. This article describes the first identified patient with SFTS and a retrospective study on SFTS in Japan. METHODS: Virologic and pathologic examinations were performed on the patient's samples. Laboratory diagnosis of SFTS was made by isolation/genome amplification and/or the detection of anti-SFTSV immunoglobulin G antibody in sera. Physicians were alerted to the initial diagnosis and asked whether they had previously treated patients with symptoms similar to those of SFTS. RESULTS: A female patient who died in 2012 received a diagnosis of SFTS. Ten additional patients with SFTS were then retrospectively identified. All patients were aged ≥50 years and lived in western Japan. Six cases were fatal. The ratio of males to females was 8:3. SFTSV was isolated from 8 patients. Phylogenetic analyses indicated that all of the Japanese SFTSV isolates formed a genotype independent to those from China. Most patients showed symptoms due to hemorrhage, possibly because of disseminated intravascular coagulation and/or hemophagocytosis. CONCLUSIONS: SFTS has been endemic to Japan, and SFTSV has been circulating naturally within the country.

We describe the behavior of the conductivity, viscosity, and vapor pressure of various binary liquid systems in which proton transfer occurs between neat Brönsted acids and bases to form salts with melting points below ambient. Such liquids form an important subgroup of the ionic liquid (IL) class of reaction media and electrolytes on which so much attention is currently being focused. Such "protic ionic liquids" exhibit a wide range of thermal stabilities. We find a simple relation between the limit set by boiling, when the total vapor pressure reaches one atm, and the difference in pK(a) value for the acid and base determined in dilute aqueous solutions. For DeltapK(a) values above 10, the boiling point elevation becomes so high (>300 degrees C) that preemptive decomposition prevents its measurement. The completeness of proton transfer in such cases is suggested by the molten salt-like values of the Walden product, which is used to distinguish good from poor ionic liquids. For the good ionic liquids, the hydrogen bonding of acid molecules to the proton-transfer anion is strong enough that boiling points, but not melting points, may maximize at the hydrogen-bonded dianion composition. High boiling liquids of this type constitute an interesting class of high-temperature protonic acid that may have high-temperature fuel cell applications.

Two broad categories of extracellular vesicles (EVs), exosomes and shed microvesicles (sMVs), which differ in size distribution as well as protein and RNA profiles, have been described. EVs are known to play key roles in cell-cell communication, acting proximally as well as systemically. This Review discusses the nature of EV subtypes, strategies for isolating EVs from both cell-culture media and body fluids, and procedures for quantifying EVs. We also discuss proteins selectively enriched in exosomes and sMVs that have the potential for use as markers to discriminate between EV subtypes, as well as various applications of EVs in clinical diagnosis.

During feeding, the gut microbiota contributes to the host energy acquisition and metabolic regulation thereby influencing the development of metabolic disorders such as obesity and diabetes. Short-chain fatty acids (SCFAs) such as acetate, butyrate, and propionate, which are produced by gut microbial fermentation of dietary fiber, are recognized as essential host energy sources and act as signal transduction molecules via G-protein coupled receptors (FFAR2, FFAR3, OLFR78, GPR109A) and as epigenetic regulators of gene expression by the inhibition of histone deacetylase (HDAC). Recent evidence suggests that dietary fiber and the gut microbial-derived SCFAs exert multiple beneficial effects on the host energy metabolism not only by improving the intestinal environment, but also by directly affecting various host peripheral tissues. In this review, we summarize the roles of gut microbial SCFAs in the host energy regulation and present an overview of the current understanding of its physiological functions.

A global assessment of precipitation chemistry and deposition has been carried out under the direction of the World Meteorological Organization (WMO) Global Atmosphere Watch (GAW) Scientific Advisory Group for Precipitation Chemistry (SAG-PC). The assessment addressed three questions: (1) what do measurements and model estimates of precipitation chemistry and wet, dry and total deposition of sulfur, nitrogen, sea salt, base cations, organic acids, acidity, and phosphorus show globally and regionally? (2) has the wet deposition of major ions changed since 2000 (and, where information and data are available, since 1990) and (3) what are the major gaps and uncertainties in our knowledge? To that end, regionally-representative measurements for two 3-year-averaging periods, 2000–2002 and 2005–2007, were compiled worldwide. Data from the 2000–2002 averaging period were combined with 2001 ensemble-mean modeling results from 21 global chemical transport models produced in Phase 1 of the Coordinated Model Studies Activities of the Task Force on Hemispheric Transport of Air Pollution (TF HTAP). The measurement data and modeling results were used to generate global and regional maps of major ion concentrations in precipitation and deposition. A major product of the assessment is a database of quality assured ion concentration and wet deposition data gathered from regional and national monitoring networks. The database is available for download from the World Data Centre for Precipitation Chemistry (http://wdcpc.org/). The assessment concludes that global concentrations and deposition of sulfur and nitrogen are reasonably well characterized with levels generally highest near emission sources and more than an order of magnitude lower in areas largely free of anthropogenic influences. In many parts of the world, wet deposition of reduced nitrogen exceeds that of oxidized nitrogen and is increasing. Sulfur and nitrogen concentrations and deposition in North America and Europe have declined significantly in line with emission reduction policies. Major regions of the world, including South America, the more remote areas of North America, much of Asia, Africa, Oceania, polar regions, and all of the oceans, are inadequately sampled for all of the major ions in wet and dry deposition, and particularly so for phosphorus, organic forms of nitrogen, and weak acids including carbonates and organic acids. Measurement-based inferential estimates of dry deposition are limited to sulfur and some nitrogen in only a few regions of the world and methods are highly uncertain. The assessment concludes with recommendations to address major gaps and uncertainties in global ion concentration and deposition measurements.