T. Yu

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products

The paper analyzes metagenomes from cold seeps to create a database showing microbial diversity and potential natural products.

Simulations reveal unique roles for the FXR hinge in the FXR-RXR nuclear receptor heterodimer

The paper uses simulations to study the FXR-RXR heterodimer's structure and shows the hinge's role in DNA binding and interdomain allostery.

A Community Challenge to Predict Clinical Outcomes After Immune Checkpoint Blockade in Non-Small Cell Lung Cancer

The paper evaluates predictive models for immune checkpoint inhibitor outcomes in NSCLC using clinical trial data from two RCTs, finding that models combining PD-L1, TMB, and immune signatures outperform single biomarkers.

Nuclear receptor interdomain communication is mediated by the hinge with ligand specificity

This study uses computational and experimental methods to show that the hinge region of FXR mediates ligand-induced interdomain communication.

Hypermigration of macrophages through the concerted action of GRA effectors on NF-κB/p38 signaling and host chromatin accessibility potentiates Toxoplasma dissemination

This study identifies how Toxoplasma gondii uses GRA effectors to manipulate host signaling and chromatin accessibility, promoting macrophage migration and parasite dissemination.

Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis

The paper introduces a novel PIP-FUCCI reporter to study endothelial cell cycle stages in postnatal retinal vessels and identifies G2 stalling in tip cells.

E3 ligase ASB3 downregulates antiviral innate immunity by targeting MAVS for ubiquitin-proteasomal degradation

This study identifies ASB3 as an E3 ligase that suppresses antiviral immunity by ubiquitinating and degrading MAVS, thereby inhibiting IFN-I responses and promoting viral replication.

NLRP3 Cys126 palmitoylation by ZDHHC7 Promotes Inflammasome Activation

This study identifies ZDHHC7-mediated palmitoylation of NLRP3 at Cys126 as critical for inflammasome activation, with implications for therapeutic targeting of inflammatory diseases.

Biosynthesis of H-GDGTs linked to ocean oxygen deficiency

The paper identifies the gene responsible for biosynthesizing H-GDGTs and shows its association with oxygen-deficient environments.

A peptide-centric local stability assay to unveil protein targets of diverse ligands

This paper introduces PELSA, a peptide-centric local stability assay that identifies ligand-binding regions across the proteome with high sensitivity and without ligand modification.

Exposure to titanium dioxide nanoparticles accelerates abnormal fat deposition through the mediation of the ROS via the AGE-RAGE signaling pathway in mice

This study shows that titanium dioxide nanoparticles induce fat deposition in mice by increasing ROS and activating the AGE-RAGE pathway, with NAC as a potential therapeutic.

Endothelial cell flow-mediated quiescence is temporally regulated and utilizes the cell cycle inhibitor p27

This study shows that endothelial cell quiescence under flow is temporally regulated and depends on p27, with arterial flow leading to deeper quiescence requiring HES1 and ID3.

Experimental study of modified human tendon stem cells to promote graft ligamentation and tendon-bone healing after anterior cruciate ligament reconstruction

This study modifies human tendon stem cells to enhance graft ligamentation and tendon-bone healing after ACL reconstruction, showing improved recovery in animal models.

13C ENDOR Spectroscopy-Guided MD Computations Reveals the Structure of the Enzyme-Substrate Complex of an Active, N-linked Glycosylated Lipoxygenase

This paper uses 13C/1H ENDOR spectroscopy-guided MD simulations to determine the structure of an active fungal lipoxygenase-substrate complex, revealing evolutionary insights into enzyme function.

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its co-evolution history with the early Earth surface environment

This study investigates the evolutionary history and metabolic diversity of Bathyarchaeia, linking their diversification to geological events and environmental changes.

Cultivation of widespread Bathyarchaeia reveals a novel methyltransferase system utilizing lignin-derived aromatics

This study cultivates a Bathyarchaeia strain capable of degrading lignin via a novel methyltransferase system, suggesting its role in global anaerobic lignin remineralization.

SynBOLD-DisCo: Synthetic BOLD images for distortion correction of fMRI without additional calibration scans

This paper introduces SynBOLD-DisCo, a method to correct fMRI distortion using synthetic BOLD images generated from structural images, without needing additional calibration scans.

Tree and shrub richness modify subtropical tree productivity by modulating the diversity and community composition of soil bacteria and archaea

The paper examines how tree and shrub richness affects tree productivity by altering soil bacterial and archaeal diversity and composition in a subtropical forest experiment.

Severe fever with thrombocytopenia syndrome virus and parthenogenetic Asian longhorned tick Haemaphysalis longicornis (Acari: Ixodidae)

The paper investigates the role of parthenogenetic Asian longhorned ticks in spreading SFTSV, finding they contribute to rapid spread and long-range movement.

Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Dextran Sodium Sulfate-Induced Ulcerative Colitis

This study shows that Celastrol reduces colitis by modulating gut microbiota, improving immune balance, and increasing metabolites like pyruvate and adenosine.

Peptide fusion improves prime editing efficiency

This study identifies peptide fusions that enhance prime editing efficiency using a high-throughput screening approach.

Profiling tumor immune microenvironment of non-small cell lung cancer using multiplex immunofluorescence

This study profiles the tumor immune microenvironment of NSCLC using multiplex immunofluorescence, identifying three immune subtypes and an immune-related risk score for prognosis prediction.

20-HETE-promoted cerebral blow flow autoregulation is associated with enhanced α-smooth muscle actin positive cerebrovascular pericyte contractility

This study shows that 20-HETE enhances pericyte contractility and cerebral blood flow autoregulation in rats by modulating vascular smooth muscle cell function.

Neural mechanisms underlying regulation of empathy and altruism by beliefs of others' pain

This study investigates how beliefs about others' pain influence empathy and altruism through neural mechanisms, showing reduced empathy and altruism when beliefs of others' pain are decreased.

Bathyarchaeota Occurence in Shallow Marine Methane-rich Sediments (Saco Do Mamangua, Rio de Janeiro, Brazil)

The paper investigates the spatial and vertical distribution of microbial communities in methane-rich sediments of Saco do Mamangua, Brazil, highlighting the prevalence of Bathyarchaeota.

Network-enabled efficient image restoration for 3D microscopy of turbid biological specimens

This paper introduces ScatNet, a deep-learning method for restoring 3D fluorescence microscopy images of turbid biological specimens, improving resolution and signal-to-noise ratio.

Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy

This paper introduces a computational light-sheet microscopy method that rapidly images entire organs at subcellular resolution, achieving high isotropic spatial resolution and significantly improved throughput.

Molecular basis of ubiquitination catalyzed by the bacterial transglutaminase MavC

This study determines the structure of the MavC-UBE2N-Ub complex, revealing the mechanism of MavC's transglutaminase and deamidase activities and its opposing activity to MvcA.

Inference of sexual selection from pairwise contests

The paper applies the Bradley-Terry model to Drosophila mate-choice experiments to infer sexual selection by quantifying contestant merits and predicting contest outcomes.

Prognostic significances of interleukin-17-producing cells and Th17 cells in malignant cancers: a meta-analysis of the literatures

This meta-analysis evaluates the prognostic role of IL-17+ cells and Th17 cells in cancer, finding high IL-17+ cells correlate with worse survival, while Th17 cells show no significant effect.