R. Zhao

A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits

The paper presents a reusable TWAS workflow for cattle to identify gene-trait associations using GWAS and transcriptomic data, improving variant calling and detecting novel associations.

Airway basal stem cells are necessary for the maintenance of functional intraepithelial airway macrophages.

This study shows that airway basal stem cells maintain intraepithelial airway macrophages via Notch signaling, enabling localized allergic inflammation in the trachea but not distal lung tissues.

Cold seeps are hotspots of deep-sea nitrogen-loss driven by microorganisms across 21 phyla

This study identifies cold seeps as significant nitrogen-loss hotspots, revealing diverse microbial communities and active nitrogen-loss genes across multiple phyla.

Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast

The paper humanizes yeast U1 snRNP components to study 5 ss recognition, finding that U1C ZnF substitution causes splicing defects and mitochondrial dysfunction.

AHR activation accelerates the resolution of TGF-β1 induced fibroblast activation and promotes alveolar type 1 cell regeneration in alveolar organoids

The paper identifies DB-11-BE87 as a compound that promotes AT1 cell regeneration by reducing TGF-β1-induced fibroblast activation through AHR activation in alveolar organoids.

Kilohertz volumetric imaging of in-vivo dynamics using squeezed light field microscopy

This paper introduces squeezed light field microscopy (SLIM), a method for high-speed 3D volumetric imaging, and demonstrates its application in tracking blood cell motion and neural activity in vivo.

T cell polarization and NFAT translocation are stiffness-dependent and are differentially regulated by Piezo1 and Orai1

This study shows that T cell polarization and NFAT translocation are stiffness-dependent and are regulated by different Ca2+ influx pathways, Piezo1 and Orai1.

Heterogeneous hybrid immunity against Omicron variant JN.1 at 11 months following breakthrough infection

This study evaluates hybrid immunity against the Omicron variant JN.1 11 months after breakthrough infection, showing heterogeneous responses and increased neutralization following reinfection.

SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML

This study shows SUMO promotes DNA repair protein collaboration for telomere maintenance in ALT cancer cells without PML bodies.

SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

SingleM and Sandpiper improve microbial taxonomic profiling in metagenomic data by detecting novel species and showing most environments are dominated by unrepresented taxa.

Tumor-selective effects of active RAS inhibition in pancreatic ductal adenocarcinoma

This study evaluates the therapeutic potential of RMC-7977, a broad-spectrum RAS inhibitor, in pancreatic ductal adenocarcinoma models, showing strong anti-tumor effects with minimal impact on normal tissues.

Regenerative Signatures in Bronchioalveolar Lavage of Acute Respiratory Distress Syndrome

This study identifies differentially expressed exosomal proteins in ARDS patients that may serve as regenerative niches for lung recovery.

Origin, age, and metabolisms of dominant anammox bacteria in the global oxygen deficient zones

The paper identifies two novel Scalindua genomes from oxygen deficient zones, revealing their metabolic versatility and evolutionary adaptation to anoxic environments.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential

This study reports 33 new metagenome-assembled genomes of DPANN archaea from marine oxygen deficient zones, revealing their abundance, distribution, and potential roles in biogeochemical cycles.

Force sensing GPR133 is essential for normal balance and modulates vestibular hair cell membrane excitability via Gi signaling and CNGA3 coupling

This study identifies GPR133 as a force-sensing GPCR essential for balance, showing it modulates vestibular hair cell excitability via Gi signaling and CNGA3 coupling.

A new abundant nitrite-oxidizing phylum in oligotrophic marine sediments

The paper identifies a new bacterial phylum, Candidatus Nitrosediminicolota, which oxidizes nitrite and resolves the abundance imbalance between ammonia-oxidizing archaea and canonical nitrite-oxidizing bacteria in marine sediments.

SASH1 interacts with TNKS2 and promotes human melanocyte stem cell maintenance

This study identifies SASH1 as a regulator of melanocyte stem cell maintenance, showing that the S519N variant disrupts its function and links to pigmentation disorders.

Human receptive endometrial assembloid for deciphering the implantation window

This study develops a human endometrial assembloid model that mimics the receptive endometrium during the implantation window, showing structural and molecular features and hormone responsiveness.

Modeling Mechanical Activation of Macrophages During Pulmonary Fibrogenesis for Targeted Anti-Fibrosis Therapy

This study models mechanical activation of macrophages in fibrotic lung tissue and shows pirfenidone inhibits this activation, offering a new mechanism for anti-fibrosis therapy.

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.

A high-throughput 3D kinetic killing assay

This paper introduces a high-throughput 3D kinetic killing assay to evaluate immune killer cell function and tumor cell viability under in vivo-like conditions.

PIEZO1-mediated mechanosensing governs NK cell killing efficiency and infiltration in three-dimensional matrices

This study shows that PIEZO1-mediated mechanosensing affects NK cell killing efficiency and infiltration in 3D matrices by responding to tumor cell stiffness.

Coupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment

This paper develops a combined proteomic workflow to enable deep spatial proteome profiling of small tissue samples, achieving over 5,000 protein quantifications from a human pancreatic tissue pixel.

Crystal structure of mRNA cap (guanine-N7) methyltransferase E12 subunit from monkeypox virus and discovery of its inhibitors

The paper reports the crystal structure of MPXV E12 and identifies potential inhibitors through docking studies.

Knockout of endoplasmic reticulum localized molecular chaperone HSP90.7 impairs seeding development and cellular auxin homeostasis in Arabidopsis

This study identifies a knockout mutant of HSP90.7 in Arabidopsis, showing its essential role in seedling development and auxin homeostasis through transcriptome and proteome analyses.

Novel mRNA vaccines encoding Monkeypox virus M1R and A35R protect mice from a lethal virus challenge

This paper develops mRNA vaccines against Monkeypox virus that protect mice from lethal infection, with fusion protein vaccines showing better immune responses than separate protein vaccines.

SARS-CoV-2 spike-induced syncytia are senescent and contribute to exacerbated heart failure

This study links SARS-CoV-2 spike-induced syncytia to cellular senescence and exacerbated heart failure, showing that senolytic drugs and WNK1 inhibitors can mitigate cardiac damage.

Nitrite accumulation and the associated anammox bacteria niche partitioning in marine sediments

This study identifies niche partitioning of anammox bacteria in marine sediments based on nitrite accumulation and substrate utilization differences.

A Deep Redox Proteome Profiling Workflow and Its Application to Skeletal Muscle of a Duchene Muscular Dystrophy Model

The paper introduces a deep redox proteome profiling workflow and applies it to skeletal muscle from mdx mice, revealing increased thiol oxidation and pathway-specific effects.

Linking collective migration/growth to differentiation boosts global shaping of the transcriptome and exhibits a grasshopper effect for driving maturation

The paper links collective migration to differentiation in hPSC-derived hepatocytes, showing a significant increase in maturation through a deep-learning gene circuit.