Dimethylsulfoxide-quenched hydrogen/deuterium exchange method to study amyloid fibril structure

AbstractA general method to analyze the structure of a supramolecular complex of amyloid fibrils at amino acid residue resolution has been developed. This method combines the NMR-detected hydrogen/deuterium (H/D) exchange technique to detect hydrogen-bonded amide groups and the ability of the aprotic organic solvent dimethylsulfoxide (DMSO) to dissolve amyloid fibrils into NMR-observable, monomeric components while suppressing the undesired H/D exchange reaction. Moreover, this method can be generally applied to amyloid fibrils to elucidate the distribution of hydrogen-bonded amino acid residues in the three-dimensional molecular organization in the amyloid fibrils. In this study, we describe theoretical considerations in the H/D exchange method to obtain the structural information of proteins, and the DMSO-quenched H/D exchange method to study a supramolecular complex of amyloid fibrils. A possible application of this method to study the interaction of a protein/peptide with phospholipid membrane is also discussed

Local Atomic Structures around Implanted Phosphorus Atoms in Diamond Analyzed by X-ray Absorption Near Edge Structure

Formation of highly controlled p-type and n-type conductive layers in diamond by ion implantation technique has been strongly desired for realizing diamond-based electronic devices for decades; however practically available doping condition has not been found especially in n-type doping. In this study, we comprehensively determined the local structures and depth profiles of implanted P atoms as n-type dopant to find out the origin of inactivation of implanted P atoms. The local structure around the implanted P atoms was analyzed by X-ray absorption fine structure using synchrotron-radiation-light and the first-principle calculation based on density functional theory. We found at least four components for all prepared samples in the near edge X-ray absorption structure, suggesting that implanted P atoms locate in four different chemical environments. We eventually assigned all the components by comparing the simulated X-ray absorption with the first-principle theoretical calculation: one of the components corresponds to active phosphorus atom in the substitutional site, and others are the elemental P-P bonds and some defect complexes probably acting as inactive species for n-type dopant. These facts suggest that the knowledge of local structure of implanted P atoms and control of them are substantially important to reduce the inactivation factors of the implanted dopants.Full-Length Paper　By a grant from Research Institute for Integrated Science, Kanagawa Universitydepartmental bulletin pape

Separation and Estimation of the Effects of Household Inventory Variables and Brand Switching Behaviors on Brand No-purchases

本研究の目的は商品の非購買に対する家庭内在庫の効果と，ブランドスイッチングの効果を分離し推定する手法を提案することである。商品の非購買行動の主な原因として家庭内在庫と他ブランドへのスイッチングが考えられるが，両者には消費者行動の点においても，また経営上の示唆を考える上においても大きな違いがある。従って両者の商品非購買への影響度を分離し推定することは重要な課題となる。本研究ではブランドの効用間に時系列関係を仮定することでブランドスイッチングを探索可能にし，加えて家庭内在庫変数が強く影響すると考えられているカテゴリー購買行動を同時にモデル化する。これにより，通常の動的ブランド選択モデルでは不可能であった家庭内在庫変数の効果の分離を行い，正確にブランドスイッチングの効果を推定できるようにする

RVS for small lesion in hepatectomy

Background : Systemic chemotherapy can drastically downsize metastatic liver tumors and these small liver lesions could sometimes be difficult for surgeons to detect during hepatectomy. We assessed the usefulness of intraoperative real-time virtual sonography (RVS) with contrast-enhanced ultrasonography (CEUS) using ‘Sonazoid’ contrast agent (RVS-CEUS). Methods : We performed the intraoperative RVS-CEUS technique on 10 tumor lesions in six cases, which were scheduled for hepatic resection of < 10 mm in diameter in our liver metastases series. These lesions were preoperatively diagnosed by contrast enhanced-computed tomography (CE-CT) or Gadolinium-ethoxybenzyl-diethylenetriamine pentaacetic acid (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (EOB-MRI). We assessed the detectability of a tumor with RVS-CEUS during surgery and compared it with that of preoperative CE-CT or EOB-MRI. Results : Detectability of RVS-CEUS for 10 small lesions was 90% (n = 9/10) and that of other preoperative modalities were 50% (n = 5/10, CE-CT) and 100% (n = 10/10, EOB-MRI). Minimum tumor size detected was 3.0 mm in diameter, and maximum depth of detection with RVS-CEUS was 43.5 mm ; these results could be an advantage when compared with other intraoperative diagnostic modalities. Conclusion : Intraoperative RVS-CEUS was useful for detecting small metastatic liver lesions after chemotherapy and could be an effective intraoperative diagnostic technique for hepatic resection of a size < 10 mm

Dynamical Breakdown of Chirality and Parity in (2+1)-dimensional QED

In the (2+1)-dimensional QED with and without the Chern-Simons term, we find the non-local gauge in which there is no wavefunction renormalization for the fermion in the framework of the Schwinger-Dyson equation. By solving the Schwinger-Dyson equation in the non-local gauge, we find a finite critical value $N_f^c$ for the number of flavors $N_f$ of four-component Dirac fermions, above which the chiral symmetry restores irrespective of presence or absence of the Chern-Simons term. In the same framework, we study the possibility of dynamical breakdown of the parity. It is shown that the parity is not dynamically broken. We discuss this reason from the viewpoint of the Schwinger-Dyson equation.Comment: 22 pages, LaTeX, to be published in Nucl. Phys.

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes

Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into the overlying seawater. Although SMVs act as a natural pipeline connecting the Earth’s surface and subsurface biospheres, the dispersal of deep-biosphere microorganisms and their ecological roles remain largely unknown. In this study, we investigated the microbial communities in sediment and overlying seawater at two SMVs located on the Ryukyu Trench off Tanegashima Island, southern Japan. The microbial communities in mud volcano sediments were generally distinct from those in the overlying seawaters and in the well-stratified Pacific margin sediments collected at the Peru Margin, the Juan de Fuca Ridge flank off Oregon, and offshore of Shimokita Peninsula, northeastern Japan. Nevertheless, in-depth analysis of different taxonomic groups at the sub-species level revealed that the taxon affiliated with Atribacteria, heterotrophic anaerobic bacteria that typically occur in organic-rich anoxic subseafloor sediments, were commonly found not only in SMV sediments but also in the overlying seawater. We designed a new oligonucleotide probe for detecting Atribacteria using the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). CARD-FISH, digital PCR and sequencing analysis of 16S rRNA genes consistently showed that Atribacteria are abundant in the methane plumes of the two SMVs (0.58 and 1.5 × 104 cells/mL, respectively) but not in surrounding waters, suggesting that microbial cells in subseafloor sediments are dispersed as “deep-biosphere seeds” into the ocean. These findings may have important implications for the microbial transmigration between the deep subseafloor biosphere and the hydrosphere

Brain Dp140 alters glutamatergic transmission and social behaviour in the mdx52 mouse model of Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is a muscle disorder caused by DMD mutations and is characterized by neurobehavioural comorbidities due to dystrophin deficiency in the brain. The lack of Dp140, a dystrophin short isoform, is clinically associated with intellectual disability and autism spectrum disorders (ASDs), but its postnatal functional role is not well understood. To investigate synaptic function in the presence or absence of brain Dp140, we utilized two DMD mouse models, mdx23 and mdx52 mice, in which Dp140 is preserved or lacking, respectively. ASD-like behaviours were observed in pups and 8-week-old mdx52 mice lacking Dp140. Paired-pulse ratio of excitatory postsynaptic currents, glutamatergic vesicle number in basolateral amygdala neurons, and glutamatergic transmission in medial prefrontal cortex-basolateral amygdala projections were significantly reduced in mdx52 mice compared to those in wild-type and mdx23 mice. ASD-like behaviour and electrophysiological findings in mdx52 mice were ameliorated by restoration of Dp140 following intra-cerebroventricular injection of antisense oligonucleotide drug-induced exon 53 skipping or intra-basolateral amygdala administration of Dp140 mRNA-based drug. Our results implicate Dp140 in ASD-like behaviour via altered glutamatergic transmission in the basolateral amygdala of mdx52 mice

Blockade of constitutively activated ERK signaling enhances cytotoxicity of microtubule-destabilizing agents in tumor cells.

The extracellular signal-regulated kinase (ERK) signaling pathway is constitutively activated in many human tumor cell types. Given the cytoprotective role of this pathway, we examined whether its specific blockade might sensitize human tumor cells to the induction of apoptosis by various anticancer drugs. Although blockade of ERK signaling alone did not induce substantial cell death, it resulted in marked and selective enhancement of the induction of apoptosis by microtubule-destabilizing agents in tumor cells in which the ERK pathway is constitutively activated. The synergistic activation of c-Jun NH(2)-terminal kinase by the combination of an ERK pathway inhibitor and a microtubule-destabilizing agent appeared to be responsible, at least in part, for this effect. These results suggest that administration of the combination of an ERK pathway inhibitor and a microtubule-destabilizing agent is a potential chemotherapeutic strategy for the treatment of tumor cells with constitutive activation of the ERK pathway