Y. Ito

Comparative genomic analysis of Latilactobacillus sakei strains provides new insights into their association with different niche adaptations

This study analyzes 30 L. sakei genomes to identify genetic mechanisms underlying niche adaptations, revealing core genome conservation, plasmid-mediated metabolic diversity, and potential probiotic applications.

Different molecular recognition by three domains of the full-length GRB2 to SOS1 proline-rich motifs and EGFR phosphorylated sites

This study uses NMR to show that GRB2's SH3 domains bind PRMs with different affinities and that phosphorylated EGFR binding affects GRB2's structure and domain interactions.

Comparative analysis based on shared amplicon sequence variants reveals that cohabitation influences gut microbiota sharing between humans and dogs

This study shows that gut microbes are shared between humans and dogs, with some ASVs being highly abundant and possibly influencing bacterial transfer between hosts.

ER-to-Golgi trafficking via a dynamic intermediate cis-Golgi tubular network in Arabidopsis

This study identifies the ERGIC in Arabidopsis as a dynamic, Golgi-independent tubular network that generates stable cisternae-like Golgi structures through sphingolipid acyl-chain length regulation.

Analysis of chronic host-aspergilloma interactions using a novel mouse model

This paper develops a novel mouse model of aspergilloma to study host-fungal interactions, revealing Th1/Th17 responses and angiogenesis induced by dead fungal hyphae.

Deep mutational scanning of whole SARS-CoV-2 spike in an inverted infection system

The paper develops a DMS platform to analyze SARS-CoV-2 spike mutations, finding that spike expression, not ACE2 affinity, primarily affects infectivity and evolution.

Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression

The paper shows engineered adipocytes can suppress cancer progression by competing for nutrients in multiple cancer types.

Slitflow: a Python framework for single-molecule dynamics and localization analysis

Slitflow is a Python framework for single-molecule dynamics and localization analysis, offering a flexible workflow for image processing, dynamics analysis, and figure creation.

Horizontal transmission of penicillin binding protein 1A caused a nationwide spread of β-lactam resistance in pneumococci

The paper traces the nationwide spread of β-lactam resistance in pneumococci through horizontal transmission of a specific PBP1A variant, highlighting its role in resistance emergence.

Safety margin evaluations for transtympanic laser stimulation of the cochlea from the outer ear in Mongolian gerbils (Meriones unguiculatus)

This study evaluates the safety of prolonged laser stimulation on the cochlea in Mongolian gerbils, finding a safety margin at 6.6 W/cm2 but significant damage at 26.4 W/cm2 after 15 hours.

Structural insights into the complex of oncogenic K-Ras4BG12V and Rgl2, a RalA/B activator

This study investigates the structural interaction between oncogenic KRas4BG12V and Rgl2RA, revealing a unique tetrameric complex formation that explains its hyperactivation of the RalA/B pathway.

Subjective Audibility Modulates the Susceptibility to Sound-Induced Flash Illusion

The paper investigates how changes in sound pressure level affect susceptibility to sound-induced flash illusion, finding a correlation between audibility and illusion occurrence.

Characteristics of intestinal microflora and dysbiosis in relation to the disease duration in patients with Meniere's disease

This study examines intestinal microbiota in Meniere's disease patients, finding dysbiosis correlated with disease duration but not audiometry or DHI scores.

Collection of 2429 constrained headshots of 277 volunteers for deep learning

The paper collects 2429 constrained headshots of 277 volunteers for deep learning, demonstrating its utility for gender recognition with convolutional neural networks.

Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes

The paper shows that nascent peptides with consecutive D/E residues can cause translation discontinuation in eukaryotes, leading to biased amino acid usage in proteomes.

MTCL2 promotes asymmetric microtubule organizationby crosslinking microtubules on the Golgi membrane

This study identifies MTCL2 as a protein that crosslinks microtubules on the Golgi membrane, promoting asymmetric microtubule organization and supporting directional migration.

Prediction of antigen-responding VHH antibodies by tracking evolution of antibody along time course of immunization

The paper predicts antigen-reactive VHH antibodies by analyzing sequence evolution during immunization, achieving 75% accuracy in identifying antigen-responding clusters.

Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells

The paper introduces a method to visualize two endogenous chromatin loci in living cells using synthetic zinc-finger proteins and frankenbodies, revealing their dynamic association and separation upon cohesin disruption.

Visualizing transcription sites in living cells using a genetically encoded probe specific for the elongating form of RNA polymerase II

The paper develops a genetically encoded probe to detect elongating RNA polymerase II in living cells and shows its foci move more dynamically than chromatin domains.

Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase

The paper develops an NMR method to determine multi-state structures of proteins and applies it to yeast ubiquitin hydrolase 1, revealing dynamic motions critical for ubiquitin recognition and proteolysis.

Nascent polypeptide within the exit tunnel ensures continuous translation elongation by stabilizing the translating ribosome

The paper identifies nascent polypeptides as stabilizers of the translating ribosome, preventing elongation abortion by counteracting intrinsic ribosome destabilization sequences.

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

This paper reports the crystal structure of RcaE's bilin-binding domain in the red-absorbing state and provides NMR evidence of bilin protonation states, elucidating the structural basis of the green/red photocycle in CBCRs.

Anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) potency of Mefloquine as an entry inhibitor in vitro

This study identifies Mefloquine as a potent in vitro entry inhibitor of SARS-CoV-2 with higher antiviral activity than Hydroxychloroquine.

MTCL2 promotes asymmetric microtubule organizationby crosslinking microtubules on the Golgi membrane

This study identifies MTCL2 as a protein that crosslinks microtubules on the Golgi membrane, promoting asymmetric microtubule organization and supporting directional migration.

Generation of human bronchial organoids for SARS-CoV-2 research

This paper generates human bronchial organoids that support SARS-CoV-2 infection and drug testing, showing reduced viral load with TMPRSS2 inhibition.

Sphingolipids mediate polar sorting of PIN2 through phosphoinositide consumption at the trans-Golgi Network

The paper shows that sphingolipids regulate phosphoinositide levels at the TGN by mediating PI4P consumption via PI-PLC, affecting PIN2 sorting.

Multidrug treatment with nelfinavir and cepharanthine against COVID-19

This study identifies a new multidrug combination treatment for COVID-19 using nelfinavir and cepharanthine, showing synergistic antiviral effects and improved disease control.

Homologous expression and characterization of gassericin T and gassericin S, a novel class IIb bacteriocin produced by Lactobacillus gasseri LA327

This study identifies and characterizes gassericin S, a novel class IIb bacteriocin produced by Lactobacillus gasseri LA327, and demonstrates its activity and stability.

RUNX3 regulates cell cycle-dependent chromatin dynamics by functioning as a pioneer factor of the restriction point

This study shows RUNX3 regulates chromatin dynamics at the restriction point by opening and closing target loci through recruitment of chromatin modifiers, influencing cell cycle progression and tumor development.

Role of the high-affinity leukotriene B4 receptor signaling in fibrosis after unilateral ureteral obstruction in mice

This study investigates the role of LTB4-BLT1 signaling in kidney fibrosis after unilateral ureteral obstruction in mice, finding that BLT1 inhibition reduces fibrosis markers.