F. Ye

Optical Torque Calculations and Measurements for DNA Torsional Studies

This paper develops a numerical platform and experimental method to calculate and measure optical torque on DNA, showing agreement between simulations and measurements.

Structural insights into sphingosine 1-phosphate receptor 4 activation

The paper determines the cryo-EM structure of activated S1PR4, revealing mechanisms of ligand recognition and Gi coupling to aid in developing safer S1PR4 agonists.

The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity

The paper introduces the Natural Products Discovery Center, releasing 8490 sequenced Actinobacteria strains and highlighting their taxonomic and biosynthetic diversity.

CryoSTAR: Leveraging Structural Prior and Constraints for Cryo-EM Heterogeneous Reconstruction

CryoSTAR uses atomic models as constraints to improve cryo-EM reconstruction of conformational heterogeneity, showing better results across multiple datasets.

Molecular mechanism of acid stress response of A. acidoterrestris DSM 3922T under sublethal pH environment

This study identifies differentially expressed proteins in A. acidoterrestris under sublethal pH stress, revealing key acid resistance mechanisms involving pH homeostasis, metabolism, and DNA repair.

Antibacterial mechanism of inosine against Alicyclobacillus acidoterrestris

This study investigates how inosine inhibits Alicyclobacillus acidoterrestris by damaging its cell membrane and affecting DNA replication and energy metabolism.

Structural Basis of σ54 Displacement and Promoter Escape in Bacterial Transcription

This study presents cryo-EM structures of σ54 with increasing RNA length, revealing the mechanism of σ54 displacement and promoter escape during bacterial transcription initiation.

Cryo-EM structures of the human G-protein coupled receptor 1 (GPR1) - Gi protein complexes bound to the full-length chemerin and to its C-terminal nonapeptide

The paper reports cryo-EM structures of GPR1-Gi complexes bound to full-length chemerin and its C-terminal nonapeptide, revealing a 'two-site' interaction model and structural similarities to CMKLR1-Gi complexes.

Structural insights into ligand recognition and selectivity of the human hydroxycarboxylic acid receptor HCAR2

This study reports cryo-EM structures of HCAR2-Gi1 complexes with agonists, revealing ligand recognition, selectivity, and activation mechanisms for drug design.

Biphasic curvature-dependence of cell migration inside microcylinders: persistent randomness versus directionality

The paper studies how cell migration inside microcylinders depends on curvature, finding a biphasic relationship with changes in speed, anisotropy, and persistence.

HSPB1 facilitates chemoresistance through inhibiting ferroptotic cancer cell death and regulating NF-κB signaling pathway in breast cancer

This study identifies HSPB1 as a driver of chemoresistance in breast cancer by inhibiting ferroptosis and activating NF-κB signaling.

Recovery of structural integrity of epithelial monolayer in response to massive apoptosis-induced defects

This study shows that epithelial monolayers recover structural integrity after apoptosis-induced defects through enhanced cell spreading, migration, and traction forces.

Spatiotemporal heterogeneity and the long-term impact of meteorological , environmental and socio-economic factors of scrub typhus in China from 2012 to 2018

This study analyzes the spatiotemporal patterns of scrub typhus in China from 2012 to 2018, identifying key meteorological, environmental, and socio-economic factors influencing its distribution.

White Adipose Tissue Compositional and Transcriptional Patterns with Progressive Glucose Intolerance in Persons with HIV

The paper examines compositional and transcriptional changes in subcutaneous adipose tissue of HIV-positive individuals with varying glucose intolerance, identifying shared patterns with HIV-negative diabetics.

The Nerve Growth Factor IB-like Receptor Nurr1 (NR4A2) recruits CoREST transcription repressor complexes to silence HIV following proviral reactivation in microglial cells

This study shows that Nurr1 agonists enhance HIV silencing in microglial cells by recruiting CoREST repressor complexes to the HIV promoter, promoting latency and reducing neuroinflammation.

Inhibition of SAR S-CoV-2 infection and replication by lactoferrin, MUC1 and α-lactalbumin identified in human breastmilk

This study identifies lactoferrin, MUC1, and α-lactalbumin in human breastmilk as antiviral components that inhibit SARS-CoV-2 infection and replication, including variants.

Rational Exploration of Fold Atlas for Human Solute Carrier Proteins

The paper identifies three new folds in the solute carrier superfamily, with one validated experimentally in the SLC44 family, providing insights into structure-function relationships.

Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress

The paper shows that glycolysis downregulation is a hallmark of HIV-1 latency and that targeting antioxidant pathways can reactivate latent HIV-1.

Imaging transmembrane dynamics of biomolecules at live cell plasma membranes using quenchers in extracellular environment

The paper develops a method to measure subnanometer position changes of biomolecules in live cell plasma membranes using extracellular quenchers and validates it by studying peptide-induced membrane perforation.

A comparison of Remdesivir versus Au22Glutathione18 in COVID-19 golden hamsters: a better therapeutic outcome of gold compound

This study compares the therapeutic effects of Remdesivir and Au22Glutathione18 in COVID-19 golden hamsters, finding that the gold compound better suppresses viral replication and inflammation.

Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection

This study compares the early host responses to SARS-CoV-2, SARS-CoV, and MERS-CoV infections using transcriptome analysis, revealing distinct patterns of cytokine and antiviral gene expression.

Determining the Depth Limit of Bioluminescent Sources in Scattering Media

This study determines the depth limit of bioluminescent sources in scattering media, finding cellular resolution imaging possible at 5-10 mean free paths.

Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro

This study shows that Scutellaria baicalensis extract and its compound baicalein inhibit SARS-CoV-2 replication and 3CLpro activity in vitro.

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.

Evaluation of biodiversity in estuaries using environmental DNA metabarcoding

The paper evaluates biodiversity in estuaries using environmental DNA metabarcoding, finding higher diversity in less developed rivers and species composition reflecting ecological and environmental factors.

Mutations, Recombination and Insertion in the Evolution of 2019-nCoV

The paper analyzes 120 SARS-CoV-2 genomes to identify genetic subgroups, recombination events, and a unique spike protein insertion that may enhance infectivity.

Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7

This study reveals that the Ocr protein from bacteriophage T7 inhibits host transcription by binding to RNA polymerase and competing with sigma factors, providing a structural basis for its dual role in evading host defenses.

The Pathogenicity of SARS-CoV-2 in hACE2 Transgenic Mice

This study infects hACE2 transgenic mice with SARS-CoV-2 and observes pathogenic effects, confirming Koch's postulates and establishing a model for vaccine and therapeutic development.

Kaposi sarcoma-associated herpesvirus infection in HIV patients: potential role of HIV-associated extracellular vesicles

This study shows HIV-associated extracellular vesicles enhance KSHV infectivity in oral epithelial cells via TAR RNA and EGFR, suggesting EGFR inhibition as a potential therapeutic strategy.

The role of BMP6 in the proliferation and differentiation of chicken cartilage cells

This study investigates BMP6's role in chicken cartilage cell proliferation and differentiation, finding it regulates key signaling pathways and gene expression.