Satoshi Kume

RIKEN | RIKEN AICS · Center for Biosystems Dynamics Research

In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capillary electrophoresis-mass spectrometry (CE-MS). In order to obtain a fatigued animal group, rats were placed in a cage filled with water to...

Chronic fatigue syndrome (CFS) is a persistent and unexplained pathological state characterized by exertional and severely debilitating fatigue, with/without infectious or neuropsychiatric symptoms, lasting at least 6 consecutive months. Its pathogenesis remains incompletely understood. Here, we performed comprehensive metabolomic analyses of 133 p...

It is widely accepted that listening to music improves subjective feelings and reduces fatigue sensations, and different kinds of music lead to different activations of these feelings. Recently, cardiac autonomic nervous modulation has been proposed as a useful objective indicator of fatigue. However, scientific considerations of the relation betwe...

Low water solubility of candidate drug compounds is a major problem in pharmaceutical research and development. We developed a novel drug delivery system (DDS) for poorly water-soluble drugs using lipocalin-type prostaglandin D synthase (L-PGDS), which belongs to the lipocalin superfamily and binds a large variety of hydrophobic molecules. In this...

We introduce the RIKEN Microstructural Imaging Metadatabase, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF) and detailed biological properties observed in the images can be represented as Linked Open Data. The metadata are used to develop a large-scale imaging viewer that p...

X-ray microscopes adopting computed tomography (CT) enable nondestructive 3D visualization of biological specimens at micron-level resolution without conventional 2D serial sectioning that is a destructive/laborious method and is routinely used for analyzing renal biopsy in clinical diagnosis of kidney diseases. Here we applied a compact commercial...

We propose a methodology for extracting concepts for a target domain from large-scale linked open data (LOD) to support the construction of domain ontologies providing field-specific knowledge and definitions. The proposed method defines search entities by linking the LOD vocabulary with technical terms related to the target domain. The search enti...

Imaging data is one of the most important fundamentals in the current life sciences. We aimed to construct an ontology to describe imaging metadata as a data schema of the integrated database for optical and electron microscopy images combined with various bio-entities. To realise this, we applied Resource Description Framework (RDF) to an Open Mic...

We introduce the RIKEN Microstructural Imaging Metadatabase, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF) and detailed biological properties observed in the images can be represented as Linked Open Data. The metadata are used to develop a large-scale imaging viewer that p...

In this study, in order to support the construction of domain ontologies, we propose a methodology for extracting target domain concepts from a large-scale public Linked Open Data (LOD) system. In the proposed method, we obtain the class-related hierarchy of the domain concept by the occurrences of common upper entities and the chain of those path...

Three Dimensional Structure Analysis of Cell Nuclei in Mice Cerebellar Cortex Using Array Tomography - Volume 24 Supplement - M. Suga, H. Nisioka, M. Nakamura, K. Suzuki, K. Konishi, T. Nonaka, S. Kume, M. Maeda, Y. Kataoka, K. Ohta

Recently, the number and heterogeneity of life science datasets published on the Web have increased significantly. However, biomedical scientists face numerous serious difficulties finding, using and publishing useful databases. To address these issues, the authors developed a Resource Description Framework-based database platform, called the RIKEN...

The life sciences are data driven. However, as life science datasets are highly heterogeneous, the comprehensible data publication, published data discovery and data integration are urgent problems for researchers. Our database publication platform called RIKEN Meta- Database was developed to solve the problems in the metadata approach based on the...

We developed the RIKEN Microstructural Imaging Metadatabase for electron microscopy, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF). In this metadatabase, detailed biological properties observed in the images and biosamples, and experimental conditions can be represented as...

細胞等の生体組織の微細構造を撮像した顕微鏡画像は、生命現象を形態 情報から理解するための最も基本的なデータである。網羅的に細胞形態 などからナノスケール微細形態情報が解析可能なモルフォミクス (Morphomics)技術の構築を、日本電子株式会社との連携センターにて 走査型電子顕微鏡(SEM)の技術開発を中心に据えて行ってきた。その成 果として、哺乳類の生体組織から約1平方ミリメートルスケールの広範囲 かつ大量に生体画像データを取得し、微細形態情報のビッグデータ化に 成功した。さらには、画像データにメタデータを付与して既存の生命科 学系データと統合した。より具体的には、「顕微鏡オントロジー」を構 築して、撮像された被写体(バイオリソース)、撮像条件、表現型等との データ統合を実現させ、さらに...

Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical technique and has been widely used in metabolomics. However, the intrinsic low sensitivity of NMR prevents its applications to systems with limited sample availabilities. In this study, a new experimental approach is presented to analyze mass-scarce samples in limited volumes of...

Imaging data is one of the most important fundamentals in the current life sciences. Here, we constructed a microscopy ontology in Resource Description Framework (RDF) / Web Ontology Language (OWL) based on the XML-based Open Microscopy Environment (OME) data model. Our ontology is an extension that can describe not only imaging metadata for optica...

NG2-expressing neural progenitor cells (i.e., NG2 glial cells) maintain their proliferative and migratory activities even in the adult mammalian central nervous system (CNS) and produce myelinating oligodendrocytes and astrocytes. Although NG2 glial cells have been observed in close proximity to neuronal cell bodies in order to receive synaptic inp...

In spite of a number of studies to characterize ferredoxin (Fd):ferredoxin NADP(+) reductase (FNR) interactions at limited conditions, detailed energetic investigation on how these proteins interact under near physiological conditions and its linkage to FNR activity are still lacking. We herein performed systematic Fd:FNR binding thermodynamics usi...

Imaging data is one of the most important fundamentals in the current life sciences. We aimed to construct an ontology to describe imaging metadata as a data schema of the integrated database for optical and electron microscopy images combined with various bio-entities. To realise this, we applied Resource Description Framework (RDF) to an Open Mic...

ALTHOUGH ELECTROSTATIC INTERACTIONS BETWEEN NEGATIVELY-CHARGED FERREDOXIN FD AND POSITIVELY-CHARGED SULFITE REDUCTASE SIR HAVE BEEN PREDOMINANTLY HIGHLIGHTED TO CHARACTERIZE COMPLEX FORMATION, THE DETAILED NATURE OF INTERMOLECULAR FORCES REMAINS TO BE FULLY ELUCIDATED : WE HEREIN INVESTIGATED INTERPROTEIN FORCES FOR FORMATION OF AN ELECTRON-TRANSFE...

Unlabelled: Neural stem cells in two neurogenic regions, the subventricular zone and the subgranular zone (SGZ) of the hippocampal dentate gyrus, can divide and produce new neurons throughout life. Hippocampal neurogenesis is related to emotions, including depression/anxiety, and the therapeutic effects of antidepressants, as well as learning and...

Fatigue is best defined as difficulty in initiating or sustaining voluntary activities and is accompanied by deterioration of performance. In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capil...

Alzheimer disease (AD) is a progressive neurodegenerative disorder characterized by loss of neurons and formation of pathological extracellular deposits induced by amyloid-β peptide (Aβ). Numerous studies have established Aβ amyloidogenesis as a hallmark of AD pathogenesis, particularly with respect to mitochondrial dysfunction. We have previously...

Although acidic residues of ferredoxin (Fd) are known to be essential for activities of various Fd-dependent enzymes, including ferredoxin NADP+ reductase (FNR) and sulfite reductase (SiR), through electrostatic interactions with basic residues of partner enzymes, non-electrostatic contributions such as hydrophobic forces remain largely unknown. We...

During acute viral infections such as influenza, humans often experience not only transient fever, but also prolonged fatigue or depressive feelings with a decrease in social activity for days or weeks. These feelings are thought to be due to neuroinflammation in the brain. Recent studies have suggested that chronic neuroinflammation is a precipita...

The hydrophobic cavity of lipocalin-type prostaglandin D synthase (L-PGDS) has been suggested to accommodate various lipophilic ligands through hydrophobic effects, but its energetic origin remains unknown. We characterized 18 buffer-independent binding systems between human L-PGDS and lipophilic ligands using isothermal titration calorimetry. Alth...

L-PGDS [lipocalin-type PG (prostaglandin) D synthase] is a multi-functional protein, acting as a PGD2-producing enzyme and a lipid-transporter. In the present study, we focus on the function of L-PGDS as an extracellular transporter for small lipophilic molecules. We characterize the binding mechanism of human L-PGDS for the molecules, especially b...

Lipocalin-type prostaglandin D synthase (L-PGDS) is a member of the lipocalin superfamily and a secretory lipid-transporter protein, which binds a wide variety of hydrophobic small molecules. Here we show the feasibility of a novel drug delivery system (DDS), utilizing L-PGDS, for poorly water-soluble compounds such as diazepam (DZP), a major benzo...