Q. Ye

Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy

This paper develops a deep learning method to automate measurement of glomerular basement membrane and podocyte foot process widths in TEM images of podocytopathy mouse models, showing comparable accuracy to manual methods.

Molecular Mechanism of Huanglian Jiedu Decoction in Treatment of Alzheimer's Disease based on Network Pharmacology

This study uses network pharmacology to identify the molecular mechanism of Huanglian Jiedu Decoction in treating Alzheimer's disease, revealing its anti-inflammatory effects through multiple targets and pathways.

Human calpain-3 and its structural plasticity: dissociation of a homohexamer into dimers on binding titin

This study investigates the structural plasticity of calpain-3, showing it forms a hexamer that dissociates into dimers upon binding titin.

Global variation in the ratio of sapwood to leaf area explained by optimality principles

The paper explains 60% of global variation in sapwood-to-leaf area ratio using optimality principles linking plant hydraulics and photosynthesis.

Bacterial antiviral defense pathways encode eukaryotic-like ubiquitination systems

This study shows bacteria have a complete ubiquitination pathway similar to eukaryotes, with structural and functional parallels to eukaryotic systems.

E2F1 Mediates SOX17 Deficiency-Induced Pulmonary Hypertension

This study shows that SOX17 deficiency in endothelial cells causes pulmonary hypertension via E2F1 signaling, suggesting E2F1 as a therapeutic target in PAH.

Atlas-Guided Discovery of Transcription Factors for T Cell Programming

The paper identifies transcription factors driving distinct CD8+ T cell states and shows their impact on tumor control and immunotherapy.

Type 2 Inflammation Drives an Airway Basal Stem Cell Program Through Insulin Receptor Substrate Signaling

This study identifies BCAM as a marker of airway basal stem cells and shows that T2 cytokines drive their expansion via IRS signaling in CRSwNP.

Trophoblast and blood vessel organoid cultures recapitulate the role of WNT2B in promoting intravillous vascularization in human intrauterine and ectopic pregnancy

The paper uses organoid models to show that WNT2B promotes vascularization in pregnancies, linking trophoblast function to vascular development in both intrauterine and ectopic pregnancies.

cGASylation by a bacterial E1-E2 fusion protein primes antiviral immune signaling

The paper shows that a bacterial E1-E2 fusion protein, Cap2, primes cGAS for antiviral signaling through a process called cGASylation, which increases cGAMP production by ~50-fold.

Control of bacterial immune signaling by a WYL domain transcription factor

The paper identifies CapW, a transcription factor that regulates CBASS gene expression in bacteria, showing it represses the system in uninfected cells and is activated by phage infection, though not required for anti-phage activity.

Cytoskeletal regulation of a transcription factor by DNA mimicry

The paper reveals DNA mimicry by Kif7 as a mechanism for recruiting Gli transcription factors to microtubules, showing it can be used to inhibit Gli localization in cancer.

FiberSim: a flexible open-source model of myofilament-level contraction

FiberSim simulates myofilament-level contraction mechanics and demonstrates how sarcomeric protein modulation affects contractility.

Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies

This study reports high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein, revealing conserved binding sites for potential diagnostic applications.

Forecasting the effects of water regulation on the population viability of a threatened amphibian

This study models how river regulation affects the extinction risk of southern bell frogs by simulating inundation patterns and population dynamics under different scenarios.

Double Lock of a Potent Human Monoclonal Antibody against SARS-CoV-2

This paper identifies and characterizes a potent human monoclonal antibody, HB27, that blocks SARS-CoV-2 receptor binding and membrane fusion, showing protective effects in mice and non-adverse effects in rhesus macaques.

Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2

A mouse-adapted SARS-CoV-2 strain with RBD mutations caused 100% mortality in aged male BALB/c mice and showed altered receptor binding affinity.

SARS-CoV-2 infection causes transient olfactory dysfunction in mice

This study shows SARS-CoV-2 infection causes temporary olfactory dysfunction in mice by targeting olfactory epithelium cells and disrupting their structure and function.

A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2

A cocktail of neutralizing antibodies targeting SARS-CoV-2 spike protein's NTD and RBD, when used as immunogens in rabbits, elicited strong protective immune responses.

Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody

A potent neutralizing antibody protected against SARS-CoV-2 in an hACE2 mouse model by blocking viral receptor interaction.

The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein

This study shows the SARS-CoV-2 N protein forms distinct condensates with RNA and M protein, aiding viral RNA packaging and virion assembly.

Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein

This study determines the structure and self-assembly of the SARS-CoV-2 nucleocapsid protein, identifies structured regions in disordered domains, and maps amino acid substitutions across viral genomes.

Orthogonal genome-wide screenings in bat cells identify MTHFD1 as a target of broad antiviral therapy

The paper identifies MTHFD1 as a target for broad antiviral therapy by screening bat cells with RNAi and CRISPR libraries against mumps and influenza viruses.

Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity

The paper characterizes NucC, a bacterial endonuclease activated by cyclic tri-AMP to mediate bacteriophage immunity through DNA cleavage or cell death.

HORMA domain proteins and a Pch2-like ATPase regulate bacterial cGAS-like enzymes to mediate bacteriophage immunity

The paper identifies a bacterial immunity pathway involving HORMA domain proteins, a cGAS-like enzyme, and a Pch2-like ATPase that mediates bacteriophage defense by generating a cyclic tri-AMP second messenger.

A conserved mechanism for meiotic chromosome organization through self-assembly of a filamentous chromosome axis core

The paper identifies conserved axis core proteins across species and shows they form filamentous structures essential for meiotic chromosome organization and recombination.

Extensive Expansion of the Speedy gene Family in Homininae and Functional Differentiation in Humans

The paper identifies extensive expansion of the Speedy gene family in Homininae and reports functional differentiation in humans, including distinct expression patterns and prognostic roles in cancer.

Enhancement of Macrophage Function by the Antimicrobial Peptide Sublancin Protects Mice from Methicillin-Resistant Staphylococcus aureus

This study shows that sublancin enhances macrophage function and protects mice from MRSA infection by activating innate immunity and improving T cell responses.