S. Kimura

Integrating tDNA Epigenomics and Expression with Codon Usage Unravel an Intricate Connection with Protein Expression Dynamics in Trypanosoma cruzi

The paper investigates codon usage bias and its relationship with protein expression in Trypanosoma cruzi by integrating tRNA sequencing and transcriptomic data.

Systematic mutagenesis assay promotes comprehension of the strand-bias laws for mutations induced by oxidative DNA damage

This study uses a mutagenesis assay to show that single DNA lesions from oxidative damage can trigger strand-biased mutations at specific DNA sites.

Transcriptomic Landscape of Hyperthyroidism in Mice Overexpressing Thyroid Stimulating Hormone

This study analyzes the transcriptome of hyperthyroid mice overexpressing TSH, identifying novel genes and pathways associated with goiter development and thyroid hormone secretion.

Cell-specialized chloroplast signaling orchestrates photosynthetic and extracellular reactive oxygen species for stress responses

This study identifies how chloroplast retrograde signals like PAP coordinate ROS production in guard cells to regulate stomatal closure during stress.

A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growth

The paper identifies a tRNA modification in Mycobacterium tuberculosis that supports its intracellular growth by showing that its absence reduces bacterial growth in macrophages.

Peptidyl tRNA hydrolase is required for robust prolyl-tRNA turnover in Mycobacterium tuberculosis

The paper develops Cu-tRNAseq to study peptidyl tRNA turnover in Mtb, finding Pth is essential for prolyl-tRNA recycling and identifies Pth as a potential TB therapeutic target.

PNPO-PLP Axis Senses Prolonged Hypoxia by Regulating Lysosomal Activity

The paper identifies the PNPO-PLP axis as a mechanism for sensing prolonged hypoxia by regulating lysosomal activity in macrophages, leading to altered inflammatory responses.

Cleavage of α-1,4-Glycosidic Linkages by the Glycosylphosphatidylinositol-Anchored α-Amylase AgtA Decreases the Molecular Weight of Cell Wall α-1,3-Glucan in Aspergillus oryzae

This study shows that AoAgtA, a GPI-anchored α-amylase in Aspergillus oryzae, cleaves -1,4-glycosidic bonds in the spacer region of cell wall -1,3-glucan, reducing its molecular weight.

Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

This study sequenced the genome of water wisteria, revealing genes and pathways involved in its environmental adaptation and leaf shape changes.

Chromosome-level genome assembly of Rorippa aquatica revealed its allotetraploid origin and mechanisms of heterophylly upon submergence

This study assembled the chromosome-level genome of Rorippa aquatica to investigate its allotetraploid origin and the molecular mechanisms of heterophylly under submergence.

A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis

The paper identifies MYB93 as a VLCFA-responsive transcription factor that regulates lateral root development in Arabidopsis by modulating cell wall organization gene expression.

Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine

The paper characterizes a sequential C-to-U and U-to-Ψ RNA editing process in Vibrio cholerae tRNA mediated by TrcP, revealing its role in coupling tRNA modification states to iron availability.

Skeletal muscle releases extracellular vesicles with distinct protein and miRNA signatures that accumulate and function within the muscle microenvironment

This study identifies markers for skeletal muscle-derived extracellular vesicles (SkM-EVs) and shows they mainly function within the muscle microenvironment rather than contributing significantly to plasma EVs.

Prospective isolation of mouse and human hematopoietic stem cells using Plexin domain containing 2

This study identifies PLXDC2 as a marker for isolating hematopoietic stem cells (HSCs) in both mouse and human, showing its utility in transplantation and xenograft models.

The two-component response regulator OrrA confers dehydration tolerance by regulating anaKa expression in the cyanobacterium Anabaena sp. strain PCC 7120

Regulation of suberin biosynthesis and Casparian strip development in the root endodermis by two plant auxins

This study shows that PAA and IAA regulate suberin biosynthesis and Casparian strip development differently in root endodermis, with auxin antagonistically affecting CS formation.

Deceleration of cell cycle underpins a switch from proliferative- to terminal division in plant stomatal lineage

The paper identifies SMR4 as a cyclin-dependent kinase inhibitor that decelerates the cell cycle during the transition from asymmetric to symmetric divisions in plant stomatal lineage.

Oxicam-type NSAIDs enhance Agrobacterium-mediated transformation in plants

This study shows oxicam-type NSAIDs like tenoxicam enhance Agrobacterium-mediated transformation in plants by temporarily suppressing immune responses, improving both transient and stable transformation efficiency.

CRK2 and C-terminal phosphorylation of NADPH oxidase RBOHD regulate ROS production in Arabidopsis

This study identifies CRK2 as a regulator of RBOHD-mediated ROS production in Arabidopsis, showing that CRK2 phosphorylates RBOHD's C-terminus to enhance defense against pathogens.

Surveying the landscape of tRNA modifications by combining tRNA sequencing and RNA mass spectrometry

The paper develops a method combining tRNA sequencing and mass spectrometry to identify and characterize tRNA modifications in bacteria, discovering new modifications and editing processes.

Jagged-1 regulates Foxp3 expression and cytokine production in CD4+ T cells

This study investigates how Jagged-1 influences Foxp3 expression and cytokine production in CD4+ T cells during interactions with dendritic cells.

CRK2 enhances salt tolerance by regulating callose deposition in connection with PLDα1

The paper shows CRK2 enhances salt tolerance in Arabidopsis by regulating endocytosis and callose deposition, working with PLDα1.

A new highly sensitive real-time quantitative-PCR method for detection of BCR-ABL1 to monitor minimal residual disease in chronic myeloid leukemia after discontinuation of imatinib

This paper develops a new in-house RQ-PCR method for detecting BCR-ABL1 transcripts in CML patients, showing higher sensitivity than commercial methods for monitoring minimal residual disease.