Glycoproteomics-based cancer marker discovery adopting dual enrichment with Wisteria floribunda agglutinin for high specific glyco-diagnosis of cholangiocarcinoma.

Unlabelled: Cholangiocarcinoma (CC) is a lethal malignancy because it exhibits asymptomatic growth infiltrating the surrounding structures and therefore is usually detected at an advanced stage. The mainstay of treatment for CC is complete resection with negative surgical margins. Therefore, its diagnosis at a relatively early stage is demanded for performing relevant surgical resection.

Perfluoroalkyl substances in the blood of wild rats and mice from 47 prefectures in Japan: use of samples from nationwide specimen bank.

Numerous studies have reported on the global distribution, persistence, fate, and toxicity of perfluoroalkyl and polyfluoroalkyl substances (PFASs). However, studies on PFASs in terrestrial mammals are scarce. Rats can be good sentinels of human exposure to toxicants because of their habitat, which is in close proximity to humans.

Polymer analysis by supercritical fluid chromatography.

Synthetic polymers always have distributions of the degrees of polymerization. Supercritical fluid chromatography (SFC) is almost only one technique to be able to separate pure polymer that has exactly unique degree of polymerization. For typical examples of SFC separation of polymers, four kinds of polymers: polystyrene, poly(ethylene glycol), some nonionic surfactants, and polyprenol are described about the conditions of SFC.

Discovery of glycoside hydrolase enzymes in an avicel-adapted forest soil fungal community by a metatranscriptomic approach.

To discover the structural and functional novel glycoside hydrolase enzymes from soil fungal communities that decompose cellulosic biomass, transcripts of functional genes in a forest soil were analyzed. Pyrosequencing of the Avicel and wheat-amended soil cDNAs produced 56,084 putative protein-coding sequence (CDS) fragments, and the most dominant group of putative CDSs based on the taxonomic analysis was assigned to the domain Eukarya, which accounted for 99% of the total number of the putative CDSs. Of 9,449 eukaryotic CDSs whose functions could be categorized, approximately 40% of the putative CDSs corresponded to metabolism-related genes, including genes involved in carbohydrate, amino acid, and energy metabolism.

Continuous exposure to a novel stressor based on water aversion induces abnormal circadian locomotor rhythms and sleep-wake cycles in mice.

Psychological stressors prominently affect diurnal rhythms, including locomotor activity, sleep, blood pressure, and body temperature, in humans. Here, we found that a novel continuous stress imposed by the perpetual avoidance of water on a wheel (PAWW) affected several physiological diurnal rhythms in mice. One week of PAWW stress decayed robust circadian locomotor rhythmicity, while locomotor activity was evident even during the light period when the mice are normally asleep.

Simultaneous immunoassay analysis of plasma IL-6 and TNF-α on a microchip.

Sandwich enzyme-linked immunosorbant assay (ELISA) using a 96-well plate is frequently employed for clinical diagnosis, but is time-and sample-consuming. To overcome these drawbacks, we performed a sandwich ELISA on a microchip. The microchip was made of cyclic olefin copolymer with 4 straight microchannels.

Characterization of a recombinant flocculent Saccharomyces cerevisiae strain that co-ferments glucose and xylose: I. Influence of the ratio of glucose/xylose on ethanol production.

Glucose/xylose mixtures (90 g/L total sugar) were evaluated for their effect on ethanol fermentation by a recombinant flocculent Saccharomyces cerevisiae, MA-R4. Glucose was utilized faster than xylose at any ratio of glucose/xylose, although MA-R4 can simultaneously co-ferment both sugars. A high percentage of glucose can increase cell biomass production and therefore increase the rate of glucose utilization (1.

Low molecular weight gelators based on biosurfactants, cellobiose lipids by Cryptococcus humicola.

Cellobiose lipids (CLs) are bolaform glycolipid biosurfactants, which are produced from natural resources by a yeast strain and show fungicidal activity. In this study, the gelation properties of CL in solvents were investigated by several techniques including rheology and atomic force microscopy (AFM). The yeast CL was found to gelate 6 out of 26 solvents.

Sulfated glycosaminoglycan-assisted receptor specificity of human fibroblast growth factor (FGF) 19 signaling in a mouse system is different from that in a human system.

The endocrine action of human (h) intestine-derived fibroblast growth factor 19 (hFGF19) toward liver cells necessitates a highly specific recognition system. We previously reported that at physiological concentrations (~30 pM), hFGF19 requires sulfated glycosaminoglycans (sGAGs) for its signaling via human FGF receptor 4 (hFGFR4) in the presence of a co-receptor, human βKlotho (hKLB), thus establishing specific targeting. Here we report that the specificity of hFGF19 signaling is greatly altered in a mouse model system.

DNA-binding domains of plant-specific transcription factors: structure, function, and evolution.

The families of the plant-specific transcription factors (TFs) are defined by their characteristic DNA-binding domains (DBDs), such as AP2/ERF, B3, NAC, SBP, and WRKY. Recently, three-dimensional structures of the DBDs, including those in complexes with DNA, were determined by NMR spectroscopy and X-ray crystallography. In this review we summarize the functional and evolutionary implications arising from structure analyses.

Neu5Acα2,6Gal and Neu5Acα2,3Gal receptor specificities on influenza viruses determined by a waveguide-mode sensor.

To characterize the differences in the receptor-binding specificities of human and avian influenza viruses with glycan chains, the authors performed binding analyses using an evanescent field-coupled waveguide-mode biosensor. The experiments were performed on intact viruses and hemagglutinin proteins, using gold-nanoparticle-conjugated Neu5Acα2,6Gal and Neu5Acα2,3Gal glycan chains. Several influenza viruses belonging to subtypes H3N2 (A/Udorn/307/1972, A/Shandong/9/1993, A/Kiev/301/1994, A/Panama/2007/1999, A/Wisconsin/67/2005 and A/Brisbane/10/2007), H1N1 (A/Brisbane/59/2007 and A/California/07/2009) and H5N1 (A/chicken/India/NIV33487/2006) were used.

Evaluation of pressurized liquid extraction for determination of organophosphorus and pyrethroid pesticides in soybean.

The purpose of this study was to develop an analytical method for the determination of organophosphorus and pyrethroid pesticides in soybean by pressurized liquid extraction (PLE). Two organic solvents, acetone and acetonitrile, were evaluated as extraction solvents. In both cases, the amount of extract was enhanced with increasing extraction temperature.

Characterization of non-oxidative transaldolase and transketolase enzymes in the pentose phosphate pathway with regard to xylose utilization by recombinant Saccharomyces cerevisiae.

The activity of transaldolase and transketolase, key enzymes in the non-oxidative pentose phosphate pathway, is rate-limiting for xylose utilization in recombinant Saccharomyces cerevisiae. Overexpression of TAL1 and TKL1, the major transaldolase and transketolase genes, increases the flux from the pentose phosphate pathway into the glycolytic pathway. However, the functional roles of NQM1 and TKL2, the secondary transaldolase and transketolase genes, especially in xylose utilization, remain unclear.

Position-controlled marker formation by helium ion microscope for aligning a TEM tomographic tilt series.

We formed nano-dots using a helium ion microscope (HIM) equipped with a gas injection system. Because of position controllability, the nano-dot markers could be placed efficiently on a specimen using the HIM. The sizes of the dots were controlled by changing the beam radiation time.

Reverse vesicle formation from the yeast glycolipid biosurfactant mannosylerythritol lipid-D.

Mannosylerythritol lipids (MELs) are secreted by yeasts and are promising glycolipid biosurfactants. In our study on the non-aqueous phase behaviors of MEL homologues, we found that MEL-D (4-O-[2',3'-di-O-alka(e)noyl-β-D-mannopyranosyl]-(2R,3S)-erythritol) forms aggregates in decane. The microscopic observation and the X-ray scattering measurement of these aggregates revealed that they are reverse vesicles that consist of bilayers whose hydrophilic domains are located in the interior of the bilayers.

Evaluation of genotoxicity of multi-walled carbon nanotubes in a battery of in vitro and in vivo assays.

The genotoxic potential of two products of multi-walled carbon nanotubes (coded as N-MWCNTs, diameter of 44 nm/BET surface area of 69 m²/g and MWNT-7, diameter of 70 nm/BET surface area of 23 m²/g) was evaluated using a battery of genotoxicity assays, comprising a bacterial reverse mutation test, an in vitro mammalian chromosomal aberration test, and a mammalian erythrocytes micronucleus test. Neither type exerted mutagenicity in Salmonella typhimurium TA98, TA100, TA1535, and TA1537, or in Escherichia coli WP2uvrA, in the absence or presence of metabolic activation. The products of MWCNTs did not increase the number of structural chromosomal aberrations either, regardless of metabolic activation, though they increased the number of numerical chromosomal aberrations, one slightly and the other distinctly, in the absence of metabolic activation.

Multiple-gene silencing using antisense RNAs in Escherichia coli.

We have developed four expression vectors to express antisense RNAs (asRNAs) by which genes of interest are silenced in Escherichia coli. The vectors are all IPTG-inducible and co-transformable in any combination and target genes are silenced conditionally and concurrently. Furthermore, in order to improve silencing efficacy, the vectors are designed to express uniquely shaped antisense RNAs, named paired termini antisense RNAs (PTasRNAs).

Diffusion coefficient of an inclusion in a liquid membrane supported by a solvent of arbitrary thickness.

The diffusion coefficient of an inclusion in a liquid membrane is investigated by taking into account the interaction between membranes and bulk solvents of arbitrary thickness. As illustrative examples, the diffusion coefficients of two types of inclusions, a circular domain composed of fluid with the same viscosity as the host membrane and that of a polymer chain embedded in the membrane, are studied. The diffusion coefficients are expressed in terms of the hydrodynamic screening lengths, which vary according to the solvent thickness.

Quantum yields and kinetics of the firefly bioluminescence reaction of beetle luciferases.

Quantum yields of firefly bioluminescence reactions were determined for beetle luciferases from the three main families of luminous beetles emitting different bioluminescence colors. Quantum yield (QY) was significantly correlated with luminescence spectrum. The green light-emitting luciferase of the Brazilian click beetle, Pyrearinus termitilluminans, whose luminescence spectrum had the shortest peak wavelength of all the luciferases investigated, had the highest QY (0.

An efficient carbon precursor for gas phase growth of SWCNTs.

The sp(2) C(2) species, C(2)H(3)/C(2)H(4), has been found as a key precursor for the efficient growth of single-wall carbon nanotubes (SWCNTs) by chemical vapor deposition (CVD) from hydrocarbons.

The making of symbiont capsule in the plataspid stinkbug Megacopta punctatissima.

In stinkbugs of the family Plataspidae, adult females deposit small brownish particles, containing specific symbiotic bacteria inside, on the underside of their egg mass. Newborn nymphs ingest the content of the unique structure, called "symbiont capsule", whereby vertical transmission of the symbiont occurs. We investigated the fine structure and the formation process of the symbiont capsule in the Japanese common plataspid stinkbug, Megacopta punctatissima, by using light and electron microscopy.

A density functional study to choose the best fluorophore for photon-induced electron-transfer (PET) sensors.

Anthracenes bearing aliphatic or aromatic amino substituents, which behave as molecular sensors, have shown their potential to act as photon-induced electron-transfer (PET) systems. In this PET, the fluorophore moieties are responsible for electron release during protonation and deprotonation. The principle of hard and soft acids and bases (HSAB) deals with both intra- and intermolecular electron migration.

Correlation of the structures of agricultural fungicides to gene expression in Saccharomyces cerevisiae upon exposure to toxic doses.

Correlations between the chemical structures of agricultural fungicides and mRNA expression levels following exposure of Saccharomyces cerevisiae to toxic doses of thiuram, zineb, maneb, TPN, and PCP were examined. Structurally, thiuram, zineb, and maneb are dithiocarbamate fungicides, whereas TPN and PCP are not. To characterize chemical toxicity, genes expression was classified according to the functional groups used by the MIPS database.

Transplantation of cultured bone cells using combinations of scaffolds and culture techniques.

The transplantation of cultured bone cells is expected to become a candidate for bone regeneration therapy. For the clinical application of this therapy, there remain several problems to be overcome, for example, the improvements of scaffolds and culture techniques. In this review article, two kinds of porous ceramics, a novel sintered porous hydroxyapatite and a porous beta-tricalcium phosphate (TCP), as well as a collagen-phosphosphoryn sponge are introduced as new scaffolds for bone regeneration.