A. Toyoda

Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine

This study identifies gene modules from host-microbiome co-expression networks in marmoset intestines, revealing spatially varying interactions and new bacterial genes mediating host-microbiome relationships.

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia

This study analyzes 42 genomes from Jomon hunter-gatherers to show they adapted to cold environments through positive selection during the Last Glacial Maximum.

Enhanced tameness by Limosilactobacillus reuteri from gut microbiota of selectively bred mice

This study shows that Limosilactobacillus reuteri from tamely bred mice increases tameness and oxytocin levels when administered, suggesting a role in domestication.

Genome sequence and cell biological toolbox of the highly regenerative, coenocytic green feather alga Bryopsis

This paper presents the genome sequence of Bryopsis, a coenocytic green alga, and identifies gene duplications and unique features that may underlie its regeneration ability.

Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex

This study identifies genome size variation in the alga Closterium psl. complex as primarily due to copy number variation, with nonrandom distribution of CNV across gene functions.

ssDNA is not superior to dsDNA as long HDR donors for CRISPR-mediated endogenous gene tagging in human diploid cells

This study compares ssDNA and dsDNA as HDR donors for CRISPR-mediated gene tagging in human diploid cells, finding dsDNA more efficient for precise insertion.

Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes

The paper explores microdiversity in lake bacterioplankton genomes using long-read sequencing and identifies factors driving genomic diversification, finding that viral load drives diversity while population bottlenecks constrain it.

Evolutionary history of sexual differentiation mechanism in insects

The paper investigates the evolutionary history of the doublesex gene in insects, finding it initially promoted male differentiation but later acquired female-specific functions in holometabolan species.

Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine

The paper develops a metatranscriptomic analysis method integrating metagenome and metatranscriptome to study functional changes in the microbiome across intestinal sites in common marmosets, revealing dynamic gene expression patterns.

Evolutionary origin of sex differentiation system in insects

The paper investigates the evolutionary origin of insect sex differentiation systems by analyzing the ancestral function of doublesex in Thermobia domestica, revealing functional discordance between phenotypic and transcriptional levels.

A chromosome-level genome sequence of a model chrysanthemum: evolution and 1 reference for hexaploid cultivated chrysanthemum

The paper presents a chromosome-level genome sequence of a diploid chrysanthemum, identifies recent retrotransposon activity, and demonstrates its utility for positional cloning and breeding.

Diverse DNA modification in marine prokaryotic and viral communities

The paper identifies diverse DNA modifications in marine prokaryotic and viral communities using metaepigenomic analysis and reveals novel MTase-motif pairs and conserved motifs in Alphaproteobacteria.

Unique metabolic strategies in Hadean analogues reveal hints for primordial physiology

The paper investigates metabolic strategies in Hadean analogues, revealing unique non-CO2-reducing pathways that may inform primordial physiology.

Effects of short-term isolation on social animals' behavior: an experimental case study of Japanese macaque

This study examines how short-term isolation affects the movement patterns of Japanese macaques using Bluetooth tracking and machine learning to identify isolation vs. group behavior with high accuracy.

Integrated population genomic analysis and numerical simulation to estimate larval dispersal of Acanthaster cf. solaris between Ogasawara and other Japanese regions

This study estimates larval dispersal of Acanthaster cf. solaris between Ogasawara and Kuroshio regions using genomic analysis and oceanographic simulations, finding limited short-term dispersal but gradual long-term connectivity.

Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory amino acid differences and novel oncoprotein candidates

This study uses GWAS to identify genetic variations in H. pylori strains associated with gastric cancer and duodenal ulcers, revealing amino acid differences and novel oncoprotein candidates.

Evolutionary trajectories of three independent neo-sex chromosomes in Drosophila

The paper compares the evolutionary patterns of neo-sex chromosomes in three Drosophila species, finding accelerated pseudogenization and shared functional constraints across neo-X and neo-Y chromosomes.

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

This study uses single-cell RNA sequencing to identify nine hemocyte subpopulations in shrimp and their differentiation pathways.

Diversification of the restriction modification system of Streptococcus pyogenes through its acquisition of mobile elements

The paper analyzes methyltransferase diversity in Streptococcus pyogenes by comparing RM systems across genomes and suggests phage-derived MTases contribute to methylome diversity and gene regulation.

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus

This study sequenced the genome of a kleptoplastic sea slug and found no evidence of algal gene transfer to the nucleus, showing photosynthesis can occur without nuclear gene transfer.

Host-dependent fungus-fungus competition suppresses fungal pathogenesis in Arabidopsis thaliana

The paper shows that a non-pathogenic fungus inhibits pathogenic fungi in Arabidopsis roots, depending on host phosphate status and defense mechanisms.

Non-Parametric Analysis of Inter-Individual Relations Using an Attention-Based Neural Network

This paper introduces a non-parametric neural network with attention mechanism to analyze inter-individual relations from location data, successfully recovering simulated relations and discovering female-oriented social patterns in Japanese macaques.

A universal subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific

This study identifies a universal bacterial symbiont, COTS27, found in the subcuticular space of crown-of-thorns starfish across the Indo-Pacific, suggesting an ancient symbiotic relationship.

Mate sharing in male stump-tailed macaques as a possible case of coalition-like behavior to modify the group-wise fitness distribution

The paper observes facultative mating sharing among male stump-tailed macaques and models the conditions under which such coalition-like behavior could be evolutionarily advantageous.

Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote

This study shows that a large DNA virus played a key role in the rapid genome reorganization and gene transfer during the endosymbiotic evolution of a photosynthetic amoeba.

Animals exhibit personality traits in their movement: a case study on location trajectories of primates

This study identifies personality traits in movement patterns of Japanese macaques using 3D location data and neural network analysis.

Seasonal stability and dynamics of DNA methylation in plants in a natural environment

The paper examines seasonal DNA methylation patterns in Arabidopsis halleri, finding stable methylation in most regions and identifying seasonally methylated cytosines with distinct seasonal dynamics.

A unicellular relative of animals generates an epithelium-like cell layer by actomyosin-dependent cellularization

The paper studies cellularization in Sphaeroforma arctica, showing it forms an epithelium-like layer via actomyosin-dependent membrane invaginations and regulated gene activation.

Metabolomic analyses of plasma and liver of mice fed with immature Citrus tumida peel

This study investigates the metabolic effects of immature Citrus tumida peel supplementation in mice, showing reduced body weight gain and altered plasma and liver metabolites.

Metaepigenomic analysis reveals the unexplored diversity of DNA methylations in an environmental prokaryotic community

The paper uses metaepigenomic analysis to uncover diverse DNA methylation systems in an environmental prokaryotic community, identifying novel methylated motifs and their associated methyltransferases.