Y. Xu

Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure

This paper investigates how epiberberine binds to a DNA quadruplex structure and shows how modifying the DNA structure enhances binding affinity, leading to a new method for extracting the compound from plant extracts.

Endogenous and fluorescent sterols reveal the molecular basis for ligand selectivity of human sterol transporters

The paper profiles fluorescent steroid probes across ten STPs to uncover selectivity differences and establishes a screening panel to identify new Aster-B inhibitors.

Additive and partially dominant effects from genomic variation contribute to rice heterosis

This study identifies heterosis-associated genes and metabolites in rice, showing additive and partially dominant genetic effects contribute to 17 agronomic traits and yield heterosis across species.

Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction

This paper shows that Grb2 binding to PTP1B allosterically enhances its catalytic activity through structural changes, revealing a new regulatory mechanism for PTP1B in cell signaling.

Comprehensive Biosynthetic Analysis of Human Microbiome Reveals Diverse Protective Ribosomal Peptides

This study identifies diverse ribosomally synthesized peptides in the human microbiome and shows some inhibit pathogens and reduce inflammation.

Synergically enhanced anti-tumor immunity of in vivo CAR by circRNA vaccine boosting

This study develops circRNA-based in vivo CAR and vaccines that synergistically enhance anti-tumor immunity in mice.

Evaluation of the efficacy of the protopine total alkaloids of Macleaya cordata (Willd.) R. Br. in controlling E. coli infection in broiler chickens

This study evaluates the effectiveness of MPTA extract in reducing E. coli mortality and promoting recovery in infected chickens, finding that 400-1600 mg/kg MPTA-P over 7 days is most effective.

IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation

IsRNAcirc predicts circular RNA 3D structures using coarse-grained molecular dynamics, outperforming template-based methods on a validation set.

Deep learning of protein energy landscape and conformational dynamics from experimental structures in PDB

This study develops DeepConformer, a diffusion model that learns protein conformational dynamics and energy landscapes from PDB structures and coevolution data, reproducing MD simulation results without using MD data.

Single-cell RNA Sequencing Reveals Methamphetamine Inhibits the Liver Immune Response with Involvement of the Dopamine D1 Receptor

This study uses single-cell RNA sequencing to show that chronic methamphetamine exposure alters liver immune cell composition and function, with involvement of the dopamine D1 receptor.

Marseilleviruses biological properties and viral translation-associated proteins based on in silico tertiary structure

This study reports four new marseillevirus strains, analyzes their biological properties, and predicts novel translation-associated proteins through in silico methods.

The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos

The paper shows that spindle length and the cell cycle oscillator regulate the speed of chromosome separation during Drosophila blastoderm cleavage divisions.

Contracted anterior-posterior systematic covariance of cortical thickness in early-onset schizophrenia

This study identifies a contracted anterior-posterior organizational axis of cortical thickness in early-onset schizophrenia using structural MRI data.

APOE Impacts Lipid Trafficking in Retinal Pigment Epithelium Cells

This study investigates how APOE variants affect lipid trafficking in RPE cells, finding that APOE knockout and APOE2-expressing cells show lipid transport deficits, while APOE4-expressing cells upregulate APOE in response to lipid challenges.

Developmental Control of Long-Distance mRNA Transport Involves m5C RNA Methylation and ALYREF Nuclear Export Factors

The paper investigates how m5C RNA methylation and ALY2/ALY4 nuclear export factors regulate mRNA transport during plant development, showing that this regulation changes with developmental stages.

scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains in human and mice

This study uses scRNA-seq to analyze CDR3 length pairing rules in TCR and BCR chains across human and mouse cells, revealing species-specific differences and increased plasticity in humans.

Protective effect of P2Y receptors antagonism on stress-induced retinal degeneration

This study shows that blocking P2Y receptors with suramin prevents stress-induced RPE and photoreceptor degeneration in vitro and in a zebrafish model.

Discovery and binding site identification of a single-stranded DNA-binding protein that interacts with double-stranded DNA

This study identifies a single-stranded DNA-binding protein from E. coli F plasmid that also binds double-stranded DNA, revealing a previously unknown dsDNA-binding capability.

The dual resistance mechanism of CYP325G4 and CYP6AA9 in Culex pipiens pallens legs according to transcriptome and proteome analysis

This study identifies CYP325G4 and CYP6AA9 as key P450 enzymes involved in deltamethrin resistance in Culex pipiens legs through transcriptome and proteome analysis.

Asymmetric binding of coactivator SRC1 to FXR-RXR and allosteric communication within the complex

This study reveals the asymmetric binding of SRC1 to FXR-RXR and the allosteric communication within the complex, providing a structural model for understanding FXR function and its disease implications.

Omicron-specific naive B cell maturation alleviates immune imprinting induced by SARS-CoV-2 inactivated vaccine

The paper investigates how Omicron-specific naive B cell maturation after breakthrough infection alleviates immune imprinting from inactivated SARS-CoV-2 vaccines.

Epithelial NSD2 maintains FMOs-mediated taurine biosynthesis to prevent intestinal barrier disruption

The paper shows NSD2 maintains taurine biosynthesis via FMOs in intestinal epithelial cells, preventing barrier disruption in IBD.

Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Non-structural Proteins Inhibitors

This study uses covalent DNA-encoded libraries to discover inhibitors targeting SARS-CoV-2 proteases 3CLpro and PLpro, identifying novel compounds with potent activity and unique binding modes.

mTOR dysregulation induces IL6 and paracrine AT2 cell senescence impeding lung repair in lymphangioleiomyomatosis

This study shows mTOR dysregulation in LAM causes IL6 production and senescence in AT2 cells, impairing lung repair, and suggests targeting IL6 may help.

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.

Proteomic Dynamics and Heat Stress Response in Arabidopsis Seedlings

The paper investigates proteomic dynamics in Arabidopsis seedlings under heat stress, revealing significant protein turnover changes and tissue-specific adaptations.

Targeting the WSB2-NOXA Axis in Cancer Cells for Enhanced Sensitivity to BCL-2 Family Protein Inhibitors

This study identifies WSB2 as a regulator of mitochondrial apoptosis and shows that targeting the WSB2-NOXA axis enhances sensitivity to BCL-2 inhibitors in cancer cells.

Aquaporins enriched in endothelial vacuole membrane regulate the diameters of microvasculature in hyperglycemia

This study identifies aquaporins in endothelial cells that regulate microvascular diameter in hyperglycemia, suggesting they are potential targets for diabetes-related vascular therapy.

Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation

This study shows neutrophils release nuclear DNA via exosomes to resolve sterile inflammation, with implications for treating inflammatory diseases.

Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1

This study analyzes the humoral immune response to SARS-CoV-2 XBB and JN.1 lineages, showing JN.1 elicits superior neutralization and highlights the need for JN.1-based vaccine boosters.