A5105217575- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Virus-based gene therapy research
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Herpesvirus Infections and Treatments
- Plant Virus Research Studies
- Epigenetics and DNA Methylation
- Animal Virus Infections Studies
- Genetic Mapping and Diversity in Plants and Animals
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Plant and Fungal Interactions Research
- Machine Learning in Bioinformatics
- Algal biology and biofuel production
- Gene expression and cancer classification
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Viral gastroenteritis research and epidemiology
- Ocular Diseases and Behçet’s Syndrome
- Tissue Engineering and Regenerative Medicine
- Aquaculture Nutrition and Growth
- interferon and immune responses
- Plant Disease Resistance and Genetics
- Genetics and Plant Breeding
Kyushu University
2025
Hokkaido University
2011-2023
Institute of Agrobiological Sciences
2008
National Institute of Informatics
2007
Japan Biological Informatics Consortium
2007
Bank of Japan
2007
National Institute of Genetics
2007
Nara Institute of Science and Technology
2003-2004
Kyoto University
2000
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of International Genome Sequencing (IRGSP), manually curated annotation sequence, and other genomics information that could be useful for comprehensive understanding rice biology. Since last publication RAP-DB, IRGSP has been revised reassembled. In addition, a large number rice-expressed tags have released, functional resources produced worldwide. Thus, we thoroughly updated our by manual...
The human genome sequence defines our inherent biological potential; the realization of biology encoded therein requires knowledge function each gene. Currently, in this area is still limited. Several lines investigation have been used to elucidate structure and genes genome. Even so, gene prediction remains a difficult task, as varieties transcripts may vary great extent. We thus performed an exhaustive integrative characterization 41,118 full-length cDNAs that capture complete functional...
We present here the annotation of complete genome rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions identified or inferred in 19,969 (70%) proteins, 131 possible npRNAs (including 58 antisense transcripts) found. Almost 5000 annotated protein-coding genes found to be disrupted insertional mutant lines, which will accelerate future experimental validation annotations....
Nerve injuries pose numerous challenges and adversely affect the quality-of-life (QOL) of patients. Artificial nerve guidance conduits (aNGCs) are fabricated using natural synthetic polymers alongside bioactive cues. The objective this study is to simultaneously leverage biophysical biochemical cues develop aNGCs. fabricates core/shell aligned electrospun fibers polycaprolactone (PCL) brain-derived extracellular matrix/gelatin (B-ECM/Gel) as core shell components, respectively, then...
Here we report the new features and improvements in our latest release of H-Invitational Database (H-InvDB; http://www.h-invitational.jp/ ), a comprehensive annotation resource for human genes transcripts. H-InvDB, originally developed as an integrated database transcriptome based on extensive large sets full-length cDNA (FLcDNA) clones, now provides 120 558 mRNAs extracted from International Nucleotide Sequence Databases (INSD), addition to 54 978 FLcDNAs, H-InvDB_4.6. We mapped those...
ABSTRACT For 4 months from September 2008, 102 conjunctival swab specimens were collected for surveillance purposes patients across Japan suspected of having epidemic keratoconjunctivitis (EKC). Human adenovirus (HAdV) DNA was detected in 61 samples by PCR, though the HAdV type 6 PCR-positive could not be determined phylogenetic analysis using a partial hexon gene sequence. Moreover, 2 January 2009, strains with identical sequences isolated five obtained EKC different regions Japan. analyses...
Plant breeding programs in local regions may generate genetic variations that are desirable to populations and shape adaptability during the establishment of populations. To elucidate bases for this process, we proposed a new approach identifying traits improved rice programs; association mapping focusing on population. In present study, performed population, consisting 63 varieties, Hokkaido, northernmost region Japan one northern limits cultivation worldwide. Six seventeen QTLs were...
Human adenovirus type 53 (HAdV-53) has commonly been detected in samples from epidemic keratoconjunctivitis (EKC) patients Japan since 1996. HAdV-53 is an intermediate virus, containing hexon-chimeric, penton base and fiber structures similar to HAdV-22 -37, HAdV-37 HAdV-8, respectively. HAdV-53-like strains were first isolated EKC the 1980s. Here, complete genome sequences of three such (870006C, 880249C 890357C) four determined, their relationships analysed. The seven HAdV classified into...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis full-length cDNAs. Applying both manual computational analyses for 56 419 completely sequenced precisely annotated cDNAs selected H-Invitational transcriptome annotation meetings, we identified 6877 genes with 18 297 different variants. A total 37 670 exons were involved these events. The encoded protein sequences affected 6005 genes. Notably, motifs 3015...
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data various species, more reliable orthology information is prerequisite for further studies. However, detection orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, utilized. Thus, sub-database H-InvDB, an integrated database annotated human ( http://h-invitational.jp/ ), we constructed fully...
In plant genomes, the incorporation of DNA segments is not a common method artificial gene transfer. Nevertheless, various pararetroviruses have been found in genomes recent decades. The rice genome contains number endogenous tungro bacilliform virus-like sequences (ERTBVs), many which are present between AT dinucleotide repeats (ATrs). Comparison genomic two closely related subspecies, japonica and indica, allowed us to verify preferential insertion ERTBVs into ATrs. addition ERTBVs,...
Alternative usage of transcription start sites (TSSs) is one the key mechanisms to generate gene variation in eukaryotes. Here, we show diversified molecular evolution TSSs remotely related flowering plants, rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), by comprehensive analyses large collections full-length cDNAs genome sequences. We determined 45,917 representative within 23,445 loci 35,313 16,964 Arabidopsis, about two per locus either species. The nucleotide features around...
Human mastadenovirus D (HAdV-D) is exceptionally rich in type among the seven human adenovirus species. This feature attributed to frequent intertypic recombination events that have reshuffled orthologous genomic regions between different HAdV-D types. However, this trend appears be paradoxical, as it has been demonstrated replacement of some interacting proteins for a specific function with other orthologues causes malfunction, indicating may deleterious. In order understand why paradoxical...
Retroposition, one of the processes copying genetic material, is an important RNA-mediated mechanism leading to emergence new genes. Because transcription controlling segments are usually not copied location in this mechanism, duplicated gene copies (retrocopies) become pseudogenized. However, few can still survive, e.g. by recruiting novel regulatory elements from region insertion. Subsequently, these genes contribute formation lineage-specific traits and phenotypic diversity. Despite...
Recently, new genotypes of human adenoviruses (HAdVs) have been reported and many them found to be recombinant forms different known types HAdV species D (HAdV-D). The objective this study was document the evolutionary features a novel isolate (HAdV_Chiba_E086/2012) obtained from eye swab patient with conjunctivitis in Japan. Viral DNA extracted sequence whole genome by Sanger method aligned available sequences HAdV-Ds. phylogenetic trees nucleotide penton base, hexon, fiber genes E3 region...
Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the relationships rice varieties in Hokkaido, Japan, one northern limits cultivation around world. Furthermore, artificial selection during programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across genotype-by-sequencing for analyses. Phylogenetics, population...
Endomorphins are neuropeptides that bind strongly to μ-opioid receptors and considered play important roles in pain modulation other biological functions. Two endomorphins have been identified, date, endomorphine-1 -2; both tetrapeptides differ by only a single amino acid the third position. Both peptides were isolated from bovine brains; however, their precursor genes not identified. In this study, nucleotide sequence corresponding endomorphin-1 peptide an expressed tag database has found...