D. Xu

Identification of P-type ATPase as a bacterial transporter for host-derived small RNA

This study identifies a bacterial P-type ATPase transporter, PtaT, that specifically binds and mediates the uptake of host-derived tsRNAs in Fusobacterium nucleatum.

Conformational Landscapes of a Class I Ribonucleotide Reductase Complex during Turnover Reveal Intrinsic Dynamics and Asymmetry

This study uses cryo-EM and deep learning to analyze conformational changes in ribonucleotide reductase during turnover, revealing dynamic asymmetry and transient states essential for catalysis.

Heparan sulfate selectively inhibits the collagenase activity of cathepsin K

This study shows heparan sulfate inhibits cathepsin K collagenase activity while preserving peptidase activity, revealing HS as a potential therapeutic target for bone resorption diseases.

CRISPR screens reveal convergent targeting strategies against evolutionarily distinct chemoresistance in cancer

This study identifies convergent therapeutic targets for chemoresistance in cancer using CRISPR screens across multiple drug conditions and cancer models.

Medium Composition Affects Microbial Corrosion Rates

The paper shows that medium composition affects microbial corrosion rates, with D. vulgaris outperforming D. ferrophilus in marine conditions despite initial assumptions about their mechanisms.

Elucidating Microbial Iron Corrosion Mechanisms with a Hydrogenase-Deficient Strain of Desulfovibrio vulgaris

This study investigates Fe0 corrosion by a hydrogenase-deficient mutant of Desulfovibrio vulgaris, showing H2 oxidation indirectly promotes corrosion via sulfide generation, not direct electron transfer.

A PTER-dependent pathway of taurine metabolism linked to energy balance

This study identifies PTER as the taurine N-acetyltransferase/hydrolase, showing its role in regulating N-acetyltaurine levels and linking it to energy balance and metabolic phenotypes.

Arabidopsis GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation

This study identifies GUN1's molecular function as RNA binding and maturation by analyzing plastid transcriptomes and validating targets through RNA immunoprecipitation.

Single-cell Sequencing Highlights Heterogeneity and Malignant Progression in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma

This study uses single-cell RNA-seq to analyze the progression from actinic keratosis to cutaneous squamous cell carcinoma, identifying key driver genes and tumor microenvironment interactions.

Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information

The paper improves CNN-based cryo-EM micrograph filtering by using fine-tuning and Fourier space information, resulting in higher prediction accuracy.

Inhibition of KLK8 promotes pulmonary endothelial repair by restoring VE-cadherin/Akt/FOXM1 pathway

This study shows that inhibiting KLK8 restores the VE-cadherin/Akt/FOXM1 pathway, promoting endothelial repair and reducing sepsis-induced lung injury and mortality.

Identification of a highly drought-resistant pp7l hda6 mutant

The paper identifies a pp7l hda6 mutant with enhanced drought resistance, showing reduced drought-responsive gene changes and alleviated growth penalties compared to the pp7l single mutant.

pathCLIP: Detection of Genes and Gene Relations from Biological Pathway Figures through Image-Text Contrastive Learning

The paper introduces pathCLIP, a system that identifies genes and gene relations from biological pathway figures using image-text contrastive learning, outperforming single-modality approaches.

Design of universal Ebola virus vaccine candidates via immunofocusing

This paper designs universal Ebola virus vaccine candidates using hyperglycosylation to focus antibody responses on conserved epitopes, showing cross-neutralizing activity against multiple orthoebolavirus species.

Geometric constraint of mechanosensing in bone marrow stromal cell cultures prevents stiffness-induced differentiation

This study shows that in bone marrow stromal cells, matrix deformations and differentiation are influenced by ECM stiffness, geometry, and cell density, with high cell density reducing deformation differences between stiff and soft substrates.

Comparative omics reveals unanticipated metabolic rearrangements in a high-oil mutant of plastid acetyl-CoA carboxylase

The paper investigates metabolic changes in an Arabidopsis mutant with altered ACCase activity, revealing shifts in carbon flux and protein accumulation.

Heparan sulfate promotes TRAIL-induced tumor cell apoptosis

This study identifies heparan sulfate as a key regulator of TRAIL-induced apoptosis, showing that HS enhances TRAIL's apoptotic activity by promoting oligomerization and DR5 internalization.

From Asymptomatic to Symptomatic: Multiomics profiling of the temporal response of grapevine viral-mixed infection

This study profiles multiomics data from grapevine plants with mixed viral infections to identify factors influencing the timing of virus-like symptoms.

A non-canonical function of LDHB promotes SLC7A11-mediated glutathione metabolism and protects against glutaminolysis-dependent ferroptosis in KRAS-driven lung cancer

This study identifies a non-canonical role of LDHB in protecting KRAS-driven lung cancer from ferroptosis by promoting SLC7A11-mediated glutathione metabolism.

rRNA intermediates coordinate the multilayered nucleolar phase transition in C. elegans

This study identifies two types of nucleoli in C. elegans and shows that rRNA processing factors regulate their structure and dynamics.

Designing epitope-focused vaccines via antigen reorientation

This paper introduces an antigen reorientation strategy using oligoD insertion to shift immune responses toward conserved epitopes, demonstrating improved cross-reactivity in influenza vaccines.

Inhibition of proline tyrosine kinase 2 (Pyk2) phosphorylation during adherent-invasive Escherichia coli infection inhibits intra-macrophage replication and inflammatory cytokine release

This study shows that inhibiting Pyk2 reduces AIEC replication in macrophages and inflammatory cytokine release, suggesting a potential therapeutic target for Crohn's Disease.

Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought stress

This study examines (post)transcriptional changes in Arabidopsis under drought stress using long non-coding RNA-sequencing, revealing that alternative splicing significantly affects gene expression and proteome diversity.

Uncovering Lasonolide A biosynthesis using genome-resolved metagenomics

This paper identifies the biosynthetic pathway for lasonolide A in a marine sponge-associated bacterium using genome-resolved metagenomics.

Adipokine C1q/Tumor necrosis factor-related protein 3 (CTRP3) Attenuates Intestinal Inflammation via Histone Deacetylase Sirtuin 1 (SIRT1)/NF-κB Signaling

This study shows that CTRP3 reduces intestinal inflammation in colitis models and IBD patients by modulating SIRT1/NF-κB signaling to suppress pro-inflammatory cytokines.

The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells

This study shows DDX4, a germline factor, enhances chemoresistance and motility in SCLC cells by altering metabolism and EMT-like features.

Antiviral roles of interferon regulatory factor (IRF)-1, 3 and 7 against human coronavirus infection

This study investigates the antiviral roles of IRF1, IRF3, and IRF7 against human coronavirus infection, finding that IRF3 is critical for restricting 229E and OC43 infections.

Heparan Sulfate-dependent RAGE oligomerization is indispensable for pathophysiological functions of RAGE

This study shows that heparan sulfate-dependent RAGE oligomerization is essential for RAGE signaling and demonstrates a monoclonal antibody that blocks this interaction.

Structural and mechanistic insights into the MCM8/9 helicase complex

This study reports the structure of the MCM8/9 helicase complex using cryo-EM, revealing its DNA unwinding mechanism through conformational changes and rotary motions.

Recapitulation of patient-specific 3D chromatin conformation using machine learning and validation of identified enhancer-gene targets

The paper develops a machine learning model to predict enhancer-gene connections from ATAC-seq and RNA-seq data, validated using multi-omics data and CRISPRi in cancer patients.