A5090831758- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Genetic Syndromes and Imprinting
- Epigenetics and DNA Methylation
- Prenatal Screening and Diagnostics
- Microbial Community Ecology and Physiology
- Bacterial biofilms and quorum sensing
- Antibiotic Resistance in Bacteria
- Legume Nitrogen Fixing Symbiosis
- Bacteriophages and microbial interactions
- Genomics and Rare Diseases
- Agricultural pest management studies
- Plant Disease Resistance and Genetics
- Genetics and Neurodevelopmental Disorders
- Helicobacter pylori-related gastroenterology studies
- Chromosomal and Genetic Variations
- Computational Drug Discovery Methods
- Neurogenesis and neuroplasticity mechanisms
- Axon Guidance and Neuronal Signaling
- RNA Research and Splicing
- Galectins and Cancer Biology
- Microbial Metabolism and Applications
- Microbial Metabolites in Food Biotechnology
- Antimicrobial Resistance in Staphylococcus
- Soybean genetics and cultivation
National Center For Child Health and Development
2018-2024
Okinawa Institute of Science and Technology Graduate University
2014-2022
Niigata Agricultural Research Institute
2010
RIKEN Center for Integrative Medical Sciences
2005-2007
Kanagawa University
2000
Aichi Prefectural Government
1999
Structure-based virtual screening is carried out using molecular docking programs. A number of such programs are currently available, and the selection program difficult without knowing characteristics or performance each program. In this study, performances three programs, DOCK, AutoDock, GOLD, were evaluated with 116 target proteins. The validated two novel standards, along a traditional enrichment rate measurement. For evaluations, run was repeated 1000 times initial conformations ligand....
Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (Vigna angularis) using single molecule real-time (SMRT) technology and achieved best contiguity coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with smaller amount gaps compared to SGS-based assemblies....
Abstract Chemosynthetic symbiosis is one of the successful systems for adapting to a wide range habitats including extreme environments, and metabolic capabilities symbionts enable host organisms expand their habitat ranges. However, our understanding adaptive strategies that symbiotic still fragmentary. Here, we report single-ribotype endosymbiont population in an individual vent mussel, Bathymodiolus septemdierum has heterogeneous genomes with regard composition key gene clusters hydrogen...
Loss of pod shattering is one the most important domestication-related traits in legume crops. The non-shattering phenotypes have been achieved either by disturbed formation abscission layer between valves, or loss helical tension sclerenchyma endocarp, that split open pods to disperse seeds. During domestication, azuki bean (Vigna angularis) and yard-long unguiculata cv-gr. Sesquipedalis) reduced lost thus behavior seed pods. Here we performed fine-mapping with back-crossed populations...
In the postgenomic era, many researchers and organizations have been engaged in structural functional analyses of proteins. As a part these efforts, searching for small organic compounds that bind specifically to target proteins is quite important. this study, we developed rational strategy ligand discovery based on three-dimensional structures proteins, which were elucidated by X-ray crystallography nuclear magnetic resonance spectroscopy. The has three features: (i) rapid selection...
ABSTRACT Here, we report the complete genome sequences of low-passage virulent and high-passage avirulent variants pathogenic Leptospira interrogans serovar Manilae strain UP-MMC-NIID, a major causative agent leptospirosis. While there were no differences between sequences, levels base modifications higher in variant.
ABSTRACT A total of 11 multidrug-resistant Pseudomonas aeruginosa clinical isolates were obtained in Nepal. Four these harbored genes encoding one or more carbapenemases (DIM-1, NDM-1, and/or VIM-2), and five a 16S rRNA methyltransferase (RmtB4 RmtF2). novel RmtF variant, RmtF2, had substitution (K65E) compared with the same gene RmtF. To our knowledge, this is first report describing carbapenemase- methyltransferase-coproducing P.
We report the complete genome sequences of eight Helicobacter pylori strains isolated from patients with gastrointestinal diseases in Okinawa, Japan. Whole-genome sequencing and DNA methylation detection were performed using PacBio platform. De novo assembly determined a single, contig for each strain. Furthermore, analysis identified virulence factor genotype-dependent motifs.
Abstract Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna , family Fabaceae, consists many species such kind, as they are often adapted harsh environments marine beach, arid sandy soil, acidic limestone karst and marshes. Here we report long-read assemblies 12 species, achieving 95% or higher BUSCO scores. comparative analyses discovered a new class WUSCHEL -related homeobox ( WOX )...
Introduction: RRAS2, a member of the R-Ras subfamily Ras-like low-molecular-weight GTPases, is considered to regulate cell proliferation and differentiation via RAS/MAPK signaling pathway. Seven RRAS2 pathogenic variants have been reported in patients with Noonan syndrome; however, few functional analyses conducted. Herein, we report two who presented Noonan-like phenotype recurrent novel (p.Gly23Val p.Gly24Glu, respectively) results their analysis. Materials methods: Wild-type (WT) mutant...
A carbapenem-resistant strain of Pseudomonas aeruginosa, NCGM1984, was isolated in 2012 from a hospitalized patient Japan. Immunochromatographic assay showed that the isolate positive for IMP-type metallo-β-lactamase. Complete genome sequencing revealed NCGM1984 harbored two copies blaIMP-34, located at different sites on chromosome. Each blaIMP-34 present same structures class 1 integrons, tnpA(ISPa7)-intI1-qacG-blaIMP-34-aac(6')-Ib-qacEdelta1-sul1-orf5-tniBdelta-tniA. The belonged to...
When brown rice is preserved for a long period of time, stale flavor (komai-shu) develops as result lipid oxidation by enzymes. In order to inactivate the enzymes, was treated with superheated steam. Superheated steam treatment about 1 min, at all temperatures, caused decrease in enzymatic activity related oxidation. On other hand, degree starch damage did not increase during below 150°C. These results show that low temperature and short time enough enzyme rice, does influence quality. It...
The first complete genome sequence of Lactobacillus curvatus was determined by PacBio RS II. single circular chromosome (1,848,756 bp, G+C content 42.1%) L. FBA2, isolated from fermented vegetables, contained low regions (26.9% minimum) and 43 sets >1,000-bp identical pairs. No plasmids were detected.
We report the first complete genomic sequence of Salmonella enterica subsp. serovar Typhimurium strain ATCC 13311, leading food-borne pathogen and a reference used in drug resistance studies. De novo assembly with PacBio sequencing completed its chromosome one plasmid. They will accelerate investigation into multidrug Typhimurium.
Abstract The role of oligodendrocyte lineage cells, the largest glial population in adult central nervous system (CNS), pathogenesis Alzheimer’s disease (AD) remains elusive. Here, we developed a culture method for progenitor cells (aOPCs). Fibroblast growth factor 2 (FGF2) promotes survival and proliferation NG2 + aOPCs serum-free defined medium; subpopulation (~5%) plexin-B3 was also found. FGF2 withdrawal decreased , but increased Aβ1-42 secretion. Plexin-B3 were distributed throughout...
The cystic fibrosis transmembrane conductance regulator (CFTR) gene has been reported as one of the pancreatitis susceptibility genes. Although many variants CFTR have in Caucasian patients, there are few data Japanese patients. We aimed to survey children with idiopathic pancreatitis. Twenty-eight paediatric patients were enroled, who not previously diagnosed by genetic analysis PRSS1 and SPINK1. entire was sequenced combining LA-PCR next-generation sequencing analysis. To determine a...
Abstract Background Imprinting disorders (IDs) show overlapping phenotypes, particularly in Silver–Russell syndrome (SRS), Temple (TS14), and Prader–Willi (PWS). These three IDs include fetal postnatal growth failure, feeding difficulty, muscular hypotonia as major clinical features. However, the mechanism that causes phenotypes has not been clarified. To investigate presence or absence of methylation signatures associated with we performed genome-wide analysis (GWMA). Results GWMA was...
We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA reductive dehalogenase genes showed is highly enriched with Dehalococcoides spp. two vinyl chloride genes, bvcA vcrA, gene, tceA. The metagenome of by next generation sequencer SOLiD 3 Plus suggests sp. homologous D. mccartyi 195 equipped vcrA tceA exists in consortium. isolated this designated it as UCH-ATV1. As growth UCH-ATV1 too...
The mcr-1 gene encodes a phosphoethanolamine transferase that confers resistance to colistin by transferring lipid A. A 33-kb IncX4 plasmid harboring was detected in Klebsiella pneumoniae isolate and two Escherichia coli isolates, 66-kb IncI2 three E. isolates hospitals Okinawa, Japan.
The first complete genome sequences of Staphylococcus aureus subsp. Rosenbach 1884 strain DSM 20231(T), the type bacterium causing staphylococcal disease, were determined using PacBio RS II. represent chromosome (2,755,072 bp long; G+C content, 32.86%) and a plasmid (27,490 30.69%).
Isoprene is the most abundant type of nonmethane, biogenic volatile organic compound in atmosphere, and it produced mainly by terrestrial plants. The tropical tree species Ficus septica Burm. F. (Rosales: Moraceae) has been shown to cease isoprene emissions when exposed temperatures 12 °C or lower re-induce synthesis upon subsequent exposure 30 higher for 24 h. To elucidate regulation genes underlying disabling then induction emission during acclimatization ambient temperature, we conducted...