A5043367527- Mosquito-borne diseases and control
- Viral Infections and Vectors
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Influenza Virus Research Studies
- Viral gastroenteritis research and epidemiology
- Malaria Research and Control
- Antibiotic Resistance in Bacteria
- Respiratory viral infections research
- Tuberculosis Research and Epidemiology
- HIV Research and Treatment
- Monoclonal and Polyclonal Antibodies Research
- Legume Nitrogen Fixing Symbiosis
- Mycobacterium research and diagnosis
- Salmonella and Campylobacter epidemiology
- Eicosanoids and Hypertension Pharmacology
- Vector-borne infectious diseases
- Dengue and Mosquito Control Research
- HIV/AIDS drug development and treatment
- Streptococcal Infections and Treatments
- Viral Infections and Outbreaks Research
- Pharmaceutical and Antibiotic Environmental Impacts
- Hepatitis Viruses Studies and Epidemiology
- Venomous Animal Envenomation and Studies
- Insect symbiosis and bacterial influences
National Institute of Infectious Diseases
2013-2019
Tohoku University
2011-2018
Genomics (United Kingdom)
2014-2017
Osaka University
2003-2014
National Institutes of Health
2014
Sapporo Kosei General Hospital
1993
With the severe acute respiratory syndrome epidemic of 2003 and renewed attention on avian influenza viral pandemics, new surveillance systems are needed for earlier detection emerging infectious diseases. We applied a "next-generation" parallel sequencing platform in nasopharyngeal fecal samples collected during seasonal virus (Flu) infections norovirus outbreaks from 2005 to 2007 Osaka, Japan. Random RT-PCR was performed amplify RNA extracted 0.1–0.25 ml aspirates (N = 3) specimens 5),...
To determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistant Escherichia coli isolates from aquatic environment in India, water samples were collected rivers sewage treatment plants five Indian states. A total 446 E. randomly obtained. Resistance to ESC and/or carbapenem was observed 169 (37.9%) isolates, which further analyzed. These showed numerous antimicrobials; more than half...
Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of health but also various diseases such as obesity, diabetes, inflammatory bowel disease, and allergy. However, most intestinal bacteria are considered 'unculturable' bacteria, their functions remain unknown. Although culture-independent genomic approaches have enabled us to gain insight into potential roles, culture-based still required understand characteristic features...
Influenza virus has the ability to evade host immune surveillance through rapid viral genetic drift and reassortment; therefore, it remains a continuous public health threat. The development of vaccines producing broadly reactive antibodies, as well therapeutic strategies using human neutralizing monoclonal antibodies (HuMAbs) with global reactivity, been gathering great interest recently. Here, three hybridoma clones HuMAbs against influenza B virus, designated 5A7, 3A2 10C4, were prepared...
Whole-genome sequencing (WGS) with next-generation DNA (NGS) is an increasingly accessible and affordable method for genotyping hundreds of Mycobacterium tuberculosis (Mtb) isolates, leading to more effective epidemiological studies involving single nucleotide variations (SNVs) in core genomic sequences based on molecular evolution. We developed all-in-one web-based tool Mtb, referred as the Total Genotyping Solution TB (TGS-TB), facilitate multiple platforms using NGS spoligotyping...
Although next-generation sequencing (NGS) technology provides a comprehensive means with which to identify potential pathogens from clinical specimens, simple and user-friendly bioinformatics pipelines are expected obtain the entire viral genome sequence, subsequently providing traceability, based on extensive molecular phylogenetic analyses. We have developed web-based integrated NGS analysis tool for (virus genome-targeted assembly pipeline: VirusTAP), includes sequence subtraction of...
Kawasaki disease (KD) is an acute febrile illness of early childhood. Previous reports have suggested that genetic susceptibility factors, together with a triggering infectious agent, could be involved in KD pathogenesis; however, the precise etiology this remains unknown. Additionally, previous culture-based studies possible role intestinal microbiota pathogenesis. In study, we performed metagenomic analysis to comprehensively assess longitudinal variation twenty-eight patients. Several...
Abstract Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved evolution, we decoded here the ~1.4-Gb genome habu, Protobothrops flavoviridis . We identified 60 genes (SV) and 224 non-venom paralogs (NV), belonging 18 gene families. Molecular phylogeny reveals early divergence SV NV genes, suggesting that one four copies...
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although phylogenetically close to japonicum USDA110, a legume symbiont, it unable induce root nodules in siratro, often used for testing Nod factor-dependent nodulation. The genome of single circular chromosome, 7,231,841 bp length, with average GC content 64.3%. contains 6,898 potential protein-encoding genes, one set rRNA and 45 tRNA genes. Comparison the structure between USDA110 showed strong...
Abstract A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of PilV protein, a minor component thin pilus. is one most difficult regions for de novo genome assembly because its structural diversity even an isolated bacterial clone. We determined complete sequences, including those IncI2 plasmids carrying mcr-1 , three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing Illumina sequencing....
We screened mcr-1 and mcr-2 genes in 9,306 Escherichia coli strains isolated from healthy animals the Japanese Veterinary Antimicrobial Resistance Monitoring (JVARM) system. was detected 39 (5, 20, 14 cattle, swine, broilers, respectively), whereas not detected. also with investigation sequence homology search against our curated GenEpid-J database.
The rhcJ and ttsI mutants of Bradyrhizobium japonicum USDA122 for the type III protein secretion system (T3SS) failed to secrete typical effector proteins gained ability nodulate Rj2 soybean plants (Hardee), which are symbiotically incompatible with wild-type USDA122. This suggests that effectors secreted via T3SS trigger incompatibility between these two partners.
Human norovirus (HuNoV) is a leading cause of viral gastroenteritis worldwide, which GII.4 the most predominant genotype. Unlike other genotypes, has created various variants that escaped from previously acquired immunity host and caused repeated epidemics. However, molecular evolutionary differences among all variants, including recently discovered strains, have not been elucidated. Thus, we conducted series bioinformatic analyses using numerous, globally collected, full-length major capsid...
Next-generation DNA sequencing technologies have led to a new method of identifying the causative agents infectious diseases. The analysis comprises three steps. First, DNA/RNA is extracted and extensively sequenced from specimen that includes pathogen, human tissue commensal microorganisms. Second, reads are matched with database known sequences, organisms which individual were derived inferred. Last, percentages organisms' genomic sequences in (i.e., metagenome) estimated, pathogen...
Spontaneously hypertensive rats (SHR) and stroke-prone SHR (SHRSP) are frequently used as rat models not only of essential hypertension stroke, but also attention-deficit hyperactivity disorder (ADHD). Normotensive Wistar-Kyoto (WKY) the control in these cases. An increasing number studies has demonstrated critical role central nervous system development maintenance hypertension. In a previous study, we analyzed gene expression profiles adrenal glands SHR. Thus, this brains order to identify...
The global clustering of gene families through network analysis has been demonstrated in whole genome, plasmid, and microbiome analyses. In this study, we carried out a plasmidome all available complete bacterial plasmids to determine plasmid associations. A blastp search at 100% aa identity cut-off sharing least one between plasmids, followed by multilevel community revealed that surprisingly large number the were connected largest component (LCC), with dozens sub-groupings. LCC consisted...
Dengue viruses (DENVs) and their vectors are widely distributed throughout the tropical subtropical regions of world. An autochthonous case DENV was reported in Tokyo, Japan, 2014, for first time 70 years. A comprehensive database sequences containing both serotype genotype data epidemiological is crucial to trace outbreak isolates promptly respond outbreaks. We constructed a serotype, genotype, year country/region collection by collecting all publically available sequence information from...
Severe flooding, which is associated with numerous outbreaks of a wide range infectious diseases, particularly those caused by enteric viruses, occurred in all areas Thailand 2011. To determine the prevalence five human namely enterovirus, rotavirus (RV), norovirus (NV), hepatitis A virus (HAV), and E virus, flood water, 100 water samples were collected from flood-damaged central Thailand. Viral RNA was extracted concentrated analyzed RT-PCR sequencing. NV most commonly detected pathogen...
Background The majority of dengue patients infected with any serotype virus (DENV) are asymptomatic, but the remainder may develop a wide spectrum clinical symptoms, ranging from mild fever (DF) to severe hemorrhagic (DHF). Severe cases occur more often in who experience secondary infection different serotype. A phenomenon called antibody-dependent enhancement (ADE) has been proposed explain onset these cases, exact mechanism ADE remains unclear. Methodology/Principal Finding Virus...
Streptococcus intermedius is known to cause periodontitis and pyogenic infections in the brain liver. Here we report complete genome sequence of strain TYG1620 (genome size, 2,006,877 bp; GC content, 37.6%; 2,020 predicted open reading frames [ORFs]) isolated from a abscess an infant. Comparative analysis S. sequences suggested that carries notable type VII secretion system (T7SS), two long repeat regions, 19 ORFs for cell wall-anchored proteins (CWAPs). To elucidate genes responsible...
Spontaneously hypertensive rats (SHR) and stroke-prone SHR (SHRSP) are frequently used as model not only in studies of essential hypertension stroke, but also attention deficit hyperactivity disorder (ADHD). Normotensive Wistar-Kyoto (WKY) normally controls these studies. In this study, using rats, we aimed to identify the genes causing well involved ADHD. Since adrenal gland products can directly influence cardiovascular, endocrine sympathetic nervous system functions, gene expression...
Pyrosequence targeting of the 16S rRNA gene has been adopted for microbial communities associated with field-grown plants. To examine phylogenetic drifts according to read length and bioinformatic tools, original chopped sequences (250–570 bp) covering V1–V4 regions genes were compared using pyrosequence Sanger reads rice root microbiomes. The assignment at genus level depended on length, especially in Bradyrhizobium, which is one ecologically important bacterial genera We discuss...