A5103158633- Bioinformatics and Genomic Networks
- Plant-Microbe Interactions and Immunity
- Legume Nitrogen Fixing Symbiosis
- Genomics and Phylogenetic Studies
- Lung Cancer Research Studies
- Plant biochemistry and biosynthesis
- Metabolomics and Mass Spectrometry Studies
- Natural Language Processing Techniques
- Adhesion, Friction, and Surface Interactions
- Gene expression and cancer classification
- Topic Modeling
- Genetic Associations and Epidemiology
- Gut microbiota and health
- Genomics, phytochemicals, and oxidative stress
- Tribology and Lubrication Engineering
- Soybean genetics and cultivation
- Photosynthetic Processes and Mechanisms
- Nematode management and characterization studies
- Genomics and Rare Diseases
- Plant Gene Expression Analysis
- Oral microbiology and periodontitis research
- Genomic variations and chromosomal abnormalities
- Epigenetics and DNA Methylation
- Plant nutrient uptake and metabolism
- Liver Disease Diagnosis and Treatment
Kiryu University
2024
Gunma University
2024
Tohoku Medical Megabank Organization
2017-2024
Tohoku University
2015-2024
Jichi Medical University
1979-2024
Toyo Ink (Japan)
2021
Community Medical Center
2016
Japan Science and Technology Agency
2015
Tokyo Metropolitan Institute of Medical Science
2012
Hitachi (Japan)
2008-2011
ATTED-II (http://atted.jp) is a coexpression database for plant species to aid in the discovery of relationships unknown genes within species. As an advanced analysis method, multispecies comparisons have potential detect alterations gene evolutionary context. However, determining validity comparative studies difficult without quantitative assessments quality data. (version 9) provides 16 platforms nine species, including seven supported by both microarray- and RNA sequencing (RNAseq)-based...
Abstract In the Tohoku Medical Megabank project, genome and omics analyses of participants in two cohort studies were performed. A part data is available at Japanese Multi Omics Reference Panel (jMorp; https://jmorp.megabank.tohoku.ac.jp) as a web-based database, reported our previous manuscript published Nucleic Acid Research 2018. At that time, jMorp mainly consisted metabolome data; however, now genome, methylome, transcriptome have been integrated addition to enhancement number samples...
Abstract ATTED-II (https://atted.jp) is a gene coexpression database for nine plant species based on publicly available RNAseq and microarray data. One of the challenges in constructing condition-independent data expression managing inherent sampling bias. Here, we report version 11, wherein adopted calculation methodology to balance samples using principal component analysis ensemble calculation. This approach has two advantages. First, omitting components with low contribution rates...
Modern medicine is increasingly focused on personalized medicine, and multi-omics data crucial in understanding biological phenomena disease mechanisms. Each ethnic group has its unique genetic background with specific genomic variations influencing risk drug response. Therefore, from populations are essential for the effective implementation of medicine. Various prospective cohort studies, such as UK Biobank, All Us Lifelines, have been conducted worldwide. The Tohoku Medical Megabank...
ATTED-II ( http://atted.jp ) is a coexpression database for plant species with parallel views of multiple data sets and network analysis tools. The user can efficiently find functional gene relationships design experiments to identify functions by reverse genetics general molecular biology techniques. Here, we report updates (version 8.0), including new updated now includes eight microarray- six RNA sequencing-based seven dicot (Arabidopsis, field mustard, soybean, barrel medick, poplar,...
The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of database, mainly focusing on following two points. For first point, added RNAseq-based data three species (human, mouse and fly), largely increased number microarray experiments to nine increase expression with multiple platforms could enhance reliability data. second refined assessment procedures, each coexpressed list total performance a platform. now uses more...
The advent of RNA-sequencing and microarray technologies has led to rapid growth transcriptome data generated for a wide range organisms, under various cellular, organ individual conditions. Since the number possible combinations intercellular extracellular conditions is almost unlimited, cataloging all would be an immeasurable challenge. Gene coexpression refers similarity gene expression patterns conditions, such as disease states, tissue types, developmental stages. quality depends on...
Natural rubber (NR) is stored in latex as particles (RPs), molecules surrounded by a lipid monolayer. Rubber transferase (RTase), the enzyme responsible for NR biosynthesis, believed to be member of cis-prenyltransferase (cPT) family. However, none recombinant cPTs have shown RTase activity independently. We show that HRT1, cPT from Heveabrasiliensis, exhibits distinct vitro only when it introduced on detergent-washed HeveaRPs (WRPs) cell-free translation-coupled system. Using this system,...
Opioids, such as morphine and fentanyl, are widely used effective analgesics for the treatment of acute chronic pain. In addition, opioid system has a key role in rewarding effects morphine, ethanol, cocaine various other drugs. Although sensitivity is well known to vary among individual subjects, several candidate genetic polymorphisms reported so far not sufficient fully understanding wide range interindividual differences human sensitivity. By conducting multistage genome-wide association...
We developed jMorp, a new database containing metabolome and proteome data for plasma obtained from >5000 healthy Japanese volunteers the Tohoku Medical Megabank Cohort Study, which is available at https://jmorp.megabank.tohoku.ac.jp. Metabolome were measured by proton nuclear magnetic resonance (NMR) liquid chromatography-mass spectrometry (LC-MS), while nanoLC-MS. released concentration distributions of 37 metabolites identified NMR, peak intensities 257 characterized LC-MS, observed...
Abstract Land plants produce diverse flavonoids for growth, survival, and reproduction. Chalcone synthase is the first committed enzyme of flavonoid biosynthetic pathway catalyzes production 2′,4,4′,6′-tetrahydroxychalcone (THC). However, it also produces other polyketides, including p -coumaroyltriacetic acid lactone (CTAL), because derailment chalcone-producing pathway. This promiscuity CHS catalysis adversely affects efficiency biosynthesis, although believed to have led evolution...
Plant roots nurture a wide variety of microbes via exudation metabolites, shaping the rhizosphere's microbial community. Despite importance plant specialized metabolites in assemblage and function communities rhizosphere, little is known how far effects these extend through soil. We employed fluid model to simulate spatiotemporal distribution daidzein, an isoflavone secreted from soybean roots, validated using soybeans grown rhizobox. then analysed daidzein affects bacterial soils...
ATTED-II (http://atted.jp) is a database of coexpressed genes that was originally developed to identify functionally related in Arabidopsis and rice. Herein, we describe an updated version ATTED-II, which expands this resource include additional agriculturally important plants. To improve the quality coexpression data for rice, included more gene expression from microarray RNA sequencing studies. The sequencing-based now cover 94% protein-encoding genes, representing substantial increase...
Abstract Chronic consumption of excess ethanol increases the risk colorectal cancer. The pathogenesis ethanol-related cancer (ER-CRC) is thought to be partly mediated by gut microbes. Specifically, bacteria in colon and rectum convert acetaldehyde (AcH), which carcinogenic. However, effects chronic on human microbiome are poorly understood role microbes proposed AcH-mediated ER-CRC remains elaborated. Here we analyse compare microbiota structures non-alcoholics alcoholics. microbiotas...
Abstract Saponins are the group of plant specialized metabolites which widely distributed in angiosperm plants and have various biological activities. The present study focused on α-tomatine, a major saponin tissues tomato (Solanum lycopersicum) plants. α-Tomatine is responsible for defense against pathogens herbivores, but its function rhizosphere remains unknown. Secretion tomatine was higher at early growth than green-fruit stage hydroponically grown plants, concentration field-grown that...
Developmental plasticity is one of the most striking features plant morphogenesis, as plants are able to vary their shapes in response environmental cues. Biotic or abiotic stimuli often promote organogenesis events not observed under normal growth conditions. Root-knot nematodes (RKNs) known parasitize multiple species rooting and induce characteristic tissue expansion called galls root-knots on roots hosts by perturbing cellular machinery. Galls contain giant cells (GCs) neighboring cells,...
Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, genetics and prospective cohort studies develop a critical infrastructure for establishment PHC. To date, TMM CommCohort (adult general population) BirThree Cohort (birth+three-generation families) have conducted recruitments baseline surveys. Genome analyses as part will aid in...
In the era of energy and food shortage, microalgae have gained much attention as promising sources biofuels ingredients. However, only a small fraction microalgal genes been functionally characterized. Here, we developed Algae Gene Coexpression database (ALCOdb; http://alcodb.jp), which provides gene coexpression information to survey modules for function interest. ALCOdb currently supports two model algae: green alga Chlamydomonas reinhardtii red Cyanidioschyzon merolae. Users can retrieve...
Abstract Aberrant activation of NRF2 is as a critical prognostic factor that drives the malignant progression various cancers. Cancer cells with persistent heavily rely on activity for therapeutic resistance and aggressive tumorigenic capacity. To clarify metabolic features NRF2‐activated lung cancers, we conducted targeted metabolomic (T‐Met) global (G‐Met) analyses non–small‐cell cancer (NSCLC) cell lines in combination exome transcriptome analyses. Exome analysis 88 (49 adenocarcinoma, 14...
The fundamental performance of contact/clearance sensor, namely embedded contact sensor (ECS), is addressed in this paper. Both simulation and experiment results revealed that ECS a promising for low clearance high reliability at subnanometer regime. dc signal intrinsically comes from multiple sources including TFC heater, air-bearing surface cooling, friction heating head/disk contact. ac signals detect the resistance change due to contact, but dominated by spacing modulation caused...
Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In Tohoku Medical Megabank Project, we have been developing a series Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data Japanese Here, designed novel version array population, called Array NEO (JPA NEO), comprising total 666,883 markers. Among them, 654,246 tag SNPs autosomes and X...
A baseline oral microbiome study of the Tohoku Medical Megabank Organization (TMM) was planned to characterize profile in Japanese population. The also aimed clarify risk factors for multifactorial diseases by integrated analysis and host genome/omics information. From 2013 2016, we collected three types biospecimens, saliva, supragingival plaque, tongue swab, from a total 25,101 participants who had dental examination TMM. In this study, used two independent cohorts; Community-Based Cohort...
Properties of delta-aminolevulinic acid synthetase in erythroblasts patients with pyridoxine-responsive anemia were investigated special reference to the protease mitochondria erythroblasts. delta-Aminolevulinic activity this disease before treatment was extremely decreased, whereas it gradually increased parallel improvement by therapy pyridoxal phosphate. The amount apo-delta-aminolevulinic also diminished. Apparent affinity phosphate obtained from almost same as that normal controls. a...