Yoshiyuki Ogata
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View article: Analyses of S Protein Homology Using the Genomes of SARS-CoV-2 Specimens Unveil Missing Links in the Temporal Order of Mutations in Its Variants
Analyses of S Protein Homology Using the Genomes of SARS-CoV-2 Specimens Unveil Missing Links in the Temporal Order of Mutations in Its Variants Open
(1) Background: Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the evolutionary traits of its variants have been revealed. However, the temporal order of the majority of mutations harbored by variants …
View article: A database for retrieving information on SARS-CoV-2 S protein mutations based on correlation network analysis
A database for retrieving information on SARS-CoV-2 S protein mutations based on correlation network analysis Open
Background Over a million genomes and mutational analyses of SARS-CoV-2 are available in public databases, which reveal the phylogenetic tree of the virus. Although these data have enabled scientists to closely track the evolution and tran…
View article: Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi
Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi Open
(1) Background: Fungi contain several millions of species, and the diversification of fungal genes has been achieved by speciation, gene duplication, and horizontal gene transfer. Although several databases provide information on orthologo…
View article: Genetic Mapping of the HLA1 Locus Causing Hybrid Lethality in Nicotiana Interspecific Hybrids
Genetic Mapping of the HLA1 Locus Causing Hybrid Lethality in Nicotiana Interspecific Hybrids Open
Hybrid lethality, a postzygotic mechanism of reproductive isolation, is a phenomenon that causes the death of F1 hybrid seedlings. Hybrid lethality is generally caused by the epistatic interaction of two or more loci. In the genus Nicotian…
View article: Chemical genetic approach using β-rubromycin reveals that a RIO kinase-like protein is involved in morphological development in Phytophthora infestans
Chemical genetic approach using β-rubromycin reveals that a RIO kinase-like protein is involved in morphological development in Phytophthora infestans Open
View article: An Artificial Conversion of Roots into Organs with Shoot Stem Characteristics by Inducing Two Transcription Factors
An Artificial Conversion of Roots into Organs with Shoot Stem Characteristics by Inducing Two Transcription Factors Open
View article: Gcorn Plant: A Database for Retrieving Functional and Evolutionary Traits of Plant Genes
Gcorn Plant: A Database for Retrieving Functional and Evolutionary Traits of Plant Genes Open
Gene homology helps us understand gene function and speciation. The number of plant genes and species registered in public databanks is continuously increasing. It is useful to associate homologous genes of various plants to better underst…
View article: Suppressive Effects of Vermicomposted-Bamboo Powder on Cucumber Damping-Off
Suppressive Effects of Vermicomposted-Bamboo Powder on Cucumber Damping-Off Open
The suppressive effect of vermicomposted-bamboo powder (VB) derived from waste bamboo shoots on cucumber damping-off when VB is used as a nursery medium was characterized. A greenhouse inoculation experiment showed that the damping-off cau…
View article: A Novel Conversion of Roots into Organs with Shoot Stem Characteristics by Inducing Two Transcription Factors
A Novel Conversion of Roots into Organs with Shoot Stem Characteristics by Inducing Two Transcription Factors Open
View article: ConfeitoGUI: A toolkit for size-sensitive community detection from a correlation network
ConfeitoGUI: A toolkit for size-sensitive community detection from a correlation network Open
Analysis of the large amounts of data accumulated in public databanks can facilitate a more comprehensive understanding of molecular biological processes. Community detection from molecular biological data is paramount in characterizing ev…
View article: Gene cloning, expression, and X-ray crystallographic analysis of a β-mannanase from Eisenia fetida
Gene cloning, expression, and X-ray crystallographic analysis of a β-mannanase from Eisenia fetida Open
View article: Pathway-specific metabolome analysis with 18O2-labeled Medicago truncatula via a mass spectrometry-based approach
Pathway-specific metabolome analysis with 18O2-labeled Medicago truncatula via a mass spectrometry-based approach Open
Our finding indicated that 18O2 labeling was effective not only for the mining of unknown metabolites which were biosynthesized by oxygenase-related pathway but also for the identification of metabolites whose oxygen …
View article: The longitudinal effect of the aldehyde dehydrogenase 2*2 allele on the risk for nonalcoholic fatty liver disease
The longitudinal effect of the aldehyde dehydrogenase 2*2 allele on the risk for nonalcoholic fatty liver disease Open
View article: Relationship of airflow limitation severity with work productivity reduction and sick leave in a Japanese working population
Relationship of airflow limitation severity with work productivity reduction and sick leave in a Japanese working population Open
Ayumi Onoue,1 Hisamitsu Omori,1 Takahiko Katoh,2 Kenichi Kubota,3 Yoshio Nonami,3 Yasuhiro Ogata,3 Hiromasa Inoue4 1Department of Biomedical Laboratory Sciences, 2Department of Public Health, Faculty of Life Sciences, Kumamoto University, …
View article: Quantitative Proteomic Analysis of the Response to Zinc, Magnesium, and Calcium Deficiency in Specific Cell Types of Arabidopsis Roots
Quantitative Proteomic Analysis of the Response to Zinc, Magnesium, and Calcium Deficiency in Specific Cell Types of Arabidopsis Roots Open
The proteome profiles of specific cell types have recently been investigated using techniques such as fluorescence activated cell sorting and laser capture microdissection. However, quantitative proteomic analysis of specific cell types ha…
View article: The ECOMICS schematic concept for analysis of relationships between the environment and omics datasets.
The ECOMICS schematic concept for analysis of relationships between the environment and omics datasets. Open
Since the global ecosystem is composed of biodiversity in plant, animal and bacterial systems, our research target is not focused to single species, but accepts matrix datasets measured from complex systems. Experimental data should be com…
View article: Identification of putative target genes of bZIP19, a transcription factor essential for Arabidopsis adaptation to Zn deficiency in roots
Identification of putative target genes of bZIP19, a transcription factor essential for Arabidopsis adaptation to Zn deficiency in roots Open
Summary Zinc (Zn) depletion adversely affects plant growth. To avoid lethal depletion of cellular Zn, plants have evolved mechanisms to adjust the expression of genes associated with Zn homeostasis, the details of which are poorly understo…
View article: A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads Open
We demonstrated that reliable identification of differentially expressed transcripts in undissected interface region of the parasite-host association is feasible and informative with respect to differential-expression patterns.
View article: Potential Biomarkers of Fatigue Identified by Plasma Metabolome Analysis in Rats
Potential Biomarkers of Fatigue Identified by Plasma Metabolome Analysis in Rats Open
In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capillary electrophoresis-mass sp…
View article: Multiomics in Grape Berry Skin Revealed Specific Induction of the Stilbene Synthetic Pathway by Ultraviolet-C Irradiation
Multiomics in Grape Berry Skin Revealed Specific Induction of the Stilbene Synthetic Pathway by Ultraviolet-C Irradiation Open
Grape (Vitis vinifera) accumulates various polyphenolic compounds, which protect against environmental stresses, including ultraviolet-C (UV-C) light and pathogens. In this study, we looked at the transcriptome and metabolome in grape berr…