A5039959472- Extracellular vesicles in disease
- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Nuclear Materials and Properties
- RNA modifications and cancer
- Lung Cancer Treatments and Mutations
- Dermatology and Skin Diseases
- Genetic diversity and population structure
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Mass Spectrometry Techniques and Applications
- RNA Research and Splicing
- Colorectal Cancer Treatments and Studies
- Nuclear reactor physics and engineering
- Machine Learning in Bioinformatics
- Evolution and Paleontology Studies
- Urticaria and Related Conditions
- Ferroptosis and cancer prognosis
- Cancer-related Molecular Pathways
- Radioactive element chemistry and processing
- Metabolism, Diabetes, and Cancer
- Fatty Acid Research and Health
- Cancer Genomics and Diagnostics
National Institute of Biomedical Innovation, Health and Nutrition
2016-2025
Kyoto University
2000-2024
Otsuka (Japan)
2024
Kyoto Pharmaceutical University
2022-2023
Institute of Agrobiological Sciences
2003-2023
Hokkaido University of Education
1993-2021
High Energy Accelerator Research Organization
2021
Osaka University
1983-2020
Aisin (Japan)
2020
The Institute of Statistical Mathematics
1992-2016
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There an international collaborative effort to identify all full-length mRNA transcripts from mouse, and ensure that each represented in physical collection clones. Here we report manual annotation 60,770 complementary DNA sequences. These are clustered 33,409 'transcriptional units', contributing 90.1% newly established transcriptome database. Of these transcriptional units, 4,258 new...
We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 (75.86%). Mapping the cDNA genomic revealed that there are 19,000 20,500 transcription units in rice genome. Protein informatics analysis against InterPro database existence proteins presented but not Arabidopsis. Sixty-four percent our cDNAs...
Abstract Background Urine is a desirable material for the diagnosis and classification of diseases because convenience its collection in large amounts; however, all urinary proteome catalogs currently being generated have limitations their depth confidence identification. Our laboratory has developed methods in-depth characterization body fluids; these involve linear ion trap-Fourier transform (LTQ-FT) trap-orbitrap (LTQ-Orbitrap) mass spectrometer. Here we applied to analysis human...
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that regulates genes involved in xenobiotic metabolism, cellular proliferation, and differentiation. Numerous biological compounds are known to interact with AhR, but it remains an orphan receptor, because its physiological ligand unknown. We identified AhR ligands human urine using yeast signaling assay then characterized their properties. Two ligands, indirubin indigo, were both present at average concentrations of...
We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. developed a new computational procedure to identify classify forms splice variation evident in this data organized results into publicly accessible database that can be used for future expression array construction, structural genomics, analyses mechanism regulation alternative splicing. Statistical analysis shows at least 41% possibly as much 60% multiexon genes have multiple...
The Chromosome-Centric Human Proteome Project (C-HPP) is an international effort for creating annotated proteomic catalog each chromosome. first step of the C-HPP project to find evidence expression all proteins encoded on also prioritizes particular protein subsets, such as those with post-translational modifications (PTMs) and found in low abundance. As participants C-HPP, we integrated phosphoproteomic analysis results from chromosome-independent biomarker discovery research create a...
Abstract ALK gene rearrangement was observed in 3%–5% of non-small cell lung cancer patients, and multiple ALK-tyrosine kinase inhibitors (TKIs) have been sequentially used. Multiple ALK-TKI resistance mutations identified from the several compound mutations, such as I1171N + F1174I or L1198H are resistant to all approved ALK-TKIs. In this study, we found that gilteritinib has an inhibitory effect on ALK-TKI–resistant single mutants vitro vivo. Surprisingly, EML4-ALK mutant-expressing tumors...
Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are life-threatening mucocutaneous adverse drug reactions characterized by massive detachment. Cytotoxic T cells associated effector molecules known to drive SJS/TEN pathophysiology, but the contribution of innate immune responses is not well understood. We describe a mechanism which neutrophils triggered inflammation during early phases SJS/TEN. Skin-infiltrating CD8+ produced lipocalin-2 in drug-specific manner, formation...
Extracellular vesicles (EVs) are ubiquitously secreted by almost all tissues and carry many cargoes, including proteins, RNAs, lipids, which related to various biological processes. EVs shed from into the blood expected be used as biomarkers for diseases. Here, we isolated EDTA plasma serum of six healthy subjects an affinity capture isolation method, a total 4,079 proteins were successfully identified comprehensive EV proteomics. Our reliable detailed catalog differential expression...
A partial nucleotide sequence of the mRNA encoding a major part elongation factor 1 alpha (EF1 alpha) from mitochondria-lacking protozoan, Giardia lamblia, was reported, and phylogenetic relationship among lower eukaryotes inferred by maximum-likelihood maximum-parsimony methods protein phylogeny. Both consistently demonstrated that, G. lamblia four protozoan species being analyzed, is earliest offshoot eukaryotic tree. Although EF1 gene showed an extremely high G+C content as compared with...
With the sequencing and annotation of genomes transcriptomes several eukaryotes, importance noncoding RNA (ncRNA)-RNA molecules that are not translated to protein products-has become more evident. A subclass ncRNA transcripts encoded by highly regulated, multi-exon, transcriptional units, processed like typical protein-coding mRNAs increasingly implicated in regulation many cellular functions eukaryotes. This study describes identification candidate functional ncRNAs from among RIKEN mouse...
The yeast estrogen screen was applied to sewage treatment process waters identify the presence of estrogenic activity and investigate fate behavior substances through treatment. Hydrophobic fractions in water phase were extracted concentrated using C18 cartridges for effective extraction 17β-estradiol (E2) other mimics. Clear dose-dependent elevation synthesis β-galactosidase observed with all samples tested, demonstrating that these estrogenic. However, tended reduce during treatment,...
In the process of making full-length cDNA, predicting protein coding regions helps both in preliminary analysis genes and any succeeding process. However, unfinished cDNA contains artifacts including many sequencing errors, which hinder correct evaluation sequences. Especially, predictions short sequences are difficult because they provide little information for evaluating potential. this paper, we describe ANGLE, a new program low quality cDNA. To achieve error-tolerant prediction, ANGLE...
Adipocytes are central players in energy metabolism and the obesity epidemic, yet their protein composition remains largely unexplored. We investigated adipocyte proteome by combining high accuracy, sensitivity identification technology with subcellular fractionation of nuclei, mitochondria, membrane, cytosol 3T3-L1 adipocytes. identified 3,287 proteins while essentially eliminating false positives, making this one largest confidence proteomes reported to date. Comprehensive bioinformatics...
Protein phosphorylation is a key mechanism of cellular signaling pathways and aberrant has been implicated in number human diseases. Thus, approaches phosphoproteomics can contribute to the identification biomarkers assess disease pathogenesis drug targets. Moreover, careful validation large-scale phosphoproteome analysis, which lacking current protein-based biomarker discovery, significantly increases value identified biomarkers. Here, we performed differential analysis using IMAC coupled...
Pyruvate kinase M2 (PKM2) and pyruvate dehydrogenase complex (PDC) regulate production of acetyl-CoA, which functions as an acetyl donor in diverse enzymatic reactions, including histone acetylation. However, the mechanism by acetyl-CoA required for acetylation is ensured a gene context-dependent manner not clear. Here we show that PKM2, E2 subunit PDC acetyltransferase p300 constitute on chromatin with arylhydrocarbon receptor (AhR), transcription factor associated xenobiotic metabolism....