Y. Ge

Free energy profiles of temozolomide crossing brain plasma membranes

This paper investigates how temozolomide crosses brain plasma membranes using molecular dynamics simulations, finding that it cannot cross by pure diffusion at normal body temperature but requires higher temperatures or assistance from cholesterol and cerebroside lipids.

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

The paper analyzes microbial content in 5,734 whole-genome sequencing samples from TCGA to provide a comprehensive reference dataset for future cancer microbiome studies.

Pre-existing Immunity to Influenza Aids Ferrets in Developing Stronger and Broader Vaccine-induced Antibody Responses

This study shows that pre-existing immunity in ferrets enhances vaccine-induced antibody responses, reducing the need for booster shots and broadening protection against homologous and heterologous influenza strains.

The stability of lower genital tract microbiota correlates with reproductive system function and in vitro fertilization and frozen embryo transfer outcomes in women with polycystic ovarian syndrome

This study investigates the relationship between lower genital tract microbiota and reproductive outcomes in PCOS patients, finding that higher Lactobacillus abundance correlates with better IVF-FET outcomes.

Dietary tryptophan and genetic susceptibility expand gut microbiota that promote systemic autoimmune activation

The paper shows that dietary tryptophan and genetic factors shape gut microbiota, which in turn influence autoimmune activation in lupus.

WTAP, transcriptionally regulated by p65, promotes inflammation through m6A modification and phase separation

This study identifies WTAP as a p65-regulated m6A writer that promotes inflammation via phase separation and m6A modification, offering a therapeutic target for hyperinflammation.

The essential genome of Xanthomonas citri

This study identifies essential genes and genomic features of Xanthomonas citri using transposon mutagenesis, revealing insights into its genome organization and potential therapeutic targets.

Mass spectrometry-based multi-omics identifies metabolic signatures of sarcopenia in rhesus monkey skeletal muscle

This study uses mass spectrometry-based multi-omics to identify metabolic signatures of sarcopenia in rhesus monkey skeletal muscle, revealing age-related changes in energy metabolism and muscle function.

Major data analysis errors invalidate cancer microbiome findings

The paper re-analyzes a cancer microbiome study and identifies two major data and methodological errors that invalidate its findings and those of subsequent studies.

Structure and dynamics of endogenous protein complexes in human heart tissue captured by native nanoproteomics

This study develops a native nanoproteomics method to characterize the structure and dynamics of endogenous cardiac troponin complexes in human heart tissue using native top-down mass spectrometry.

Spatially-resolved single-cell atlas of ascidian endostyle provides insights into the origin of vertebrate pharyngeal organs

The paper constructs a spatially-resolved single-cell atlas of the ascidian endostyle, identifying new cell types and evolutionary insights into vertebrate pharyngeal organs.

Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics

This paper develops a top-down proteomics method to characterize endogenous phospholamban proteoforms in cardiac tissue, revealing site-specific PTMs.

Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates

This study benchmarks molecular dynamics force fields for simulating biological condensates, finding that combined protein and RNA force fields with a common water model best describe RNA-protein interactions and protein conformations.

In situ architecture of Opa1-dependent mitochondrial cristae remodeling

This study uses cryo-electron tomography to visualize how different Opa1 forms affect mitochondrial cristae architecture and function in mouse cells.

Identification and Characterization of a Novel Major Facilitator Superfamily (MFS) Efflux Pump SA09310 Mediating Tetracycline Resistance in Staphylococcus aureus

This study identifies and characterizes SA09310 as a novel tetracycline resistance efflux pump in Staphylococcus aureus, showing it mediates drug resistance through H+-dependent extrusion.

High Sensitivity Top-down Proteomics Captures Single Muscle Cell Heterogeneity in Large Proteoforms

This study develops a sensitive top-down proteomics method to analyze large proteoforms in single muscle cells, revealing heterogeneity and linking it to muscle fiber types.

Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel

The paper quantifies variation in sorghum's morphological, physiological, and metabolic responses to nitrogen stress and links these to grain yield under different conditions.

cGAS/STING-DEPENDENT SENSING OF ENDOGENOUS RNA

The paper shows that loss of SAMHD1 leads to chronic DNA damage and cGAS/STING-dependent type I interferon production in mice, linking it to autoimmunity and cancer.

One-Pot Exosome Proteomics Enabled by a Photocleavable Surfactant

This paper introduces a one-pot exosome proteomics method using a photocleavable surfactant, enabling rapid and effective exosomal lysis, protein extraction, and digestion, with high reproducibility and coverage.

Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry

This study uses top-down mass spectrometry to analyze O-glycoform changes in the Omicron S-RBD variant compared to wild-type and Delta, revealing novel glycosites and structural heterogeneity.

A Chemical Mutagenesis Approach to Insert Post-Translational Modifications in Aggregation-Prone Proteins

The paper introduces a method to maintain amyloidogenic proteins soluble during chemical mutagenesis, demonstrating it by mimicking phosphorylation and acetylation of amyloid-beta peptide.

Histone neutralization in a rat model of acute lung injury induced by double-hit lipopolysaccharide

This study shows that histone neutralization with STC3141 reduces circulating histones, improves oxygenation, and decreases lung edema in a rat model of LPS-induced ALI, similar to dexamethasone.

Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance

This study identifies plant genetic loci associated with rhizobiome composition in maize and shows host selection influences microbial abundance under different nitrogen conditions.

Absence of cardiolipin from the outer leaflet of a mitochondrial inner membrane mimic restricts Opa1-mediated fusion

The paper investigates how cardiolipin distribution affects mitochondrial inner membrane fusion mediated by Opa1, finding that cardiolipin in the outer leaflet is crucial for tethering and fusion.

Predictive framework of macrophage activation

The paper establishes a common framework for macrophage activation by identifying conserved transcriptional profiles across tissues and conditions.

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques

The paper compares MD simulation techniques for rehydrating buried water sites in protein-ligand binding, finding that grand outperforms BLUES and normal MD, but water sampling remains challenging.

A UAV-based high-throughput phenotyping approach to assess time-series nitrogen responses and identify traits associated genetic components in maize

This study uses UAV-based phenotyping to analyze maize nitrogen responses over time, identifying genetic regions and candidate genes associated with phenotypic traits.

De novo identification of universal cell mechanics gene signatures

This study identifies a conserved gene module involved in cell mechanics regulation using a mechanomics approach combining mechanical characterization and machine learning analysis of transcriptomic data.

Cell Surface Multimeric Assemblies Regulate Canonical and Noncanonical EphA2 Receptor Tyrosine Kinase Signaling

This study identifies molecular interfaces that mediate EphA2 receptor assembly and distinguishes between canonical and noncanonical signaling pathways.

Unbalanced dietary patterns contribute to the pathogenesis of precocious puberty by affecting gut microbiota and host metabolites

This study identifies unbalanced dietary patterns as contributors to precocious puberty by altering gut microbiota and host metabolites, with biomarkers showing high diagnostic accuracy.