Publications by authors named "Soichi Ozaki"
Targeted blockade of programmed cell death 1 (PD-1), an immune-checkpoint receptor that inhibits T cell activation, provides clinical benefits in various cancers. However, how PD-1 modulates gene expression in T cells remains enigmatic. Here we investigated how PD-1 affects transcriptome changes induced by T cell receptor (TCR) activation.
View Article and Find Full Text PDFArticle Synopsis
- - Sporobolus virginicus is a salt-tolerant grass found globally, with a specific Japanese variant capable of thriving in salt conditions three times saltier than seawater.
- - Researchers generated 3500 transgenic Arabidopsis lines using cDNA from S. virginicus and identified 10 lines with improved salt tolerance, including those containing glycine-rich RNA-binding proteins (SvGRP1 and SvGRP2).
- - Analysis of these transgenic plants showed that SvGRP1 enhances salt tolerance by altering specific metabolic pathways and increasing certain acid levels, shedding light on the potential role of GRPs in helping plants survive salinity stress.
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato.
Plant Cell Physiol
January 2017
Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources.
View Article and Find Full Text PDFIn quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes.
View Article and Find Full Text PDFArticle Synopsis
- The project focuses on integrating large-scale omics data (genomes, transcriptomes, and metabolomes) to enhance our understanding of plant biology by creating a gene expression network (GEN) repository.
- It has currently included data from 745 high-quality mRNA sequencing samples across eight diverse plant species, allowing researchers to analyze gene expression similarities through correspondence analysis.
- The web database, PODC (Plant Omics Data Center), which provides access to these GENs and gene functional annotations, is now publicly available and aims to improve gene annotations using advanced techniques like natural language processing.
Gene-to-gene coexpression analysis is a powerful approach to infer the function of uncharacterized genes. Here, we report comprehensive identification of coexpression gene modules of tomato (Solanum lycopersicum) and experimental verification of coordinated expression of module member genes. On the basis of the gene-to-gene correlation coefficient calculated from 67 microarray hybridization data points, we performed a network-based analysis.
View Article and Find Full Text PDF