B. Zhu

Experimental evolution of gene essentiality in bacteria

The paper generates essential gene deletion mutants in Streptococcus sanguinis and identifies suppressor mutations through experimental evolution, revealing new gene and pathway relationships.

Os-circANK negatively regulates resistance to bacterial blight in rice via Osa-miR398b/OsCSD1/OsCSD2 pathways

The paper identifies Os-circANK as a circRNA that suppresses rice resistance to bacterial blight by sponging Osa-miR398b and modulating OsCSD1/OsCSD2 expression.

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.

SON-dependent nuclear speckle rejuvenation alleviates proteinopathies

This study identifies pyrvinium pamoate as a compound that rejuvenates nuclear speckles, improving protein quality control and reducing YAP1 activity, thereby alleviating proteinopathies in pre-clinical models.

Systematic Discovery of Phage Genes that Inactivate Bacterial Immune Systems

This study identifies phage genes that inactivate bacterial immune systems by testing gene deletions in a phage library against bacterial defense systems.

Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment

This study uses spatial multi-omics to compare EBV-positive and EBV-negative cHL, identifying distinct TME features and immunological signatures linked to EBV.

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

This study introduces MicroCart, a framework for spatial multi-omics analysis of host-microbiome interactions in colitis, revealing tissue-level immune responses and microbial shifts.

Root-specific secondary metabolism at the single-cell level: a case study of theanine metabolism and regulation in the roots of tea plants (Camellia sinensis)

This study uses scRNA-seq to analyze theanine metabolism in tea plant roots, revealing multicellular compartmentation of biosynthesis without high co-expression of transcription factors.

Epsins oversee smooth muscle cell reprogramming by influencing master regulators KLF4 and OCT4.

This study shows Epsins regulate smooth muscle cell reprogramming by modulating OCT4 and KLF4, with implications for coronary artery disease.

A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity

This paper creates a spatial cell atlas of neuroblastoma, revealing tumor heterogeneity through multi-omics data and identifying spatial compartmentalization and signaling patterns.

Targeting endothelial FOXO1 protects diabetic β-cells and improves wound healing

This study shows that targeting endothelial FOXO1 reduces IGF2 levels, improves β-cell function, and enhances wound healing in diabetes.

Paternal genomic resources from the YanHuang cohort suggested a Weakly-Differentiated Multi-source Admixture model for the formation of Hans founding ancestral lineages

The paper analyzes paternal genomic data from the YanHuang cohort to propose a Weakly-Differentiated Multi-source Admixture model for the formation of Han Chinese ancestral lineages.

ListiWiki: a database for the foodborne pathogen Listeria monocytogenes

ListiWiki is a database that provides comprehensive genomic and functional information on Listeria monocytogenes, including gene annotations, protein interactions, and structural data.

Structure and evolution of Alanine/Serine Decarboxylases and the engineering of theanine production

This study solves the structures of AlaDC and SerDC, identifies key residues for activity and specificity, and shows engineered variants improve theanine production.

Characteristics of vaginal microbes and classification of the vaginal microbiome

This study identifies biological characteristics of vaginal microbes and introduces a new classification method, BVT, to better associate vaginal microbiome types with host health traits.

In Vivo Three-dimensional Brain Imaging with Chemiluminescence Probes in Alzheimers Disease Models

This paper develops chemiluminescence probes for in vivo 3D brain imaging in Alzheimer's disease models, showing high photon emission and binding to amyloid beta.

Immune-Epithelial Dynamics and Tissue Remodeling in Chronically Inflamed Nasal Epithelium via Multi-scaled Transcriptomics

This study uses multi-scaled transcriptomics to investigate immune-epithelial dynamics and tissue remodeling in chronic rhinosinusitis, identifying novel cellular interactions and trajectories associated with nasal polyps.

MAPS: Pathologist-level cell type annotation from tissue images through machine learning

MAPS provides pathologist-level cell type annotation from spatial proteomics data using machine learning, outperforming existing methods in speed and accuracy.

Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense

The paper identifies the Gabija complex's mechanism of sensing nucleotide depletion and executing DNA cleavage for antiviral defense, showing its unique synergy between GajA and GajB.

Preservation of ~12-hour ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock

The paper investigates 12-hour ultradian rhythms in gene expression and metabolism in animals lacking a circadian clock, finding evidence for a cell-autonomous 12-hour oscillator.

The central nervous system is a potential reservoir and possible origin of drug resistance in HBV

This study finds HBV can persist in cerebrospinal fluid, showing distinct mutations and resistance patterns compared to serum, and HIV co-infection increases resistance mutations in both compartments.

Potentiation of host defense through sRNA packaged in OMVs of Xanthomonas oryzae pv. oryzicola

This study identifies Xosr001, an sRNA packaged in OMVs of Xoc, as a mediator of stomatal immunity in rice by modulating OsJMT1 and MeJA levels.

Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth

The paper analyzes vaginal microbiome metagenomic data to identify genetic diversity and antimicrobial resistance gene associations with preterm birth.

Molecular insights into the gating mechanisms of voltage-gated calcium channel CaV2.3

This study determines the cryo-EM structure of human CaV2.3 channels and identifies key residues and interactions involved in channel gating and inactivation.

Engineering precise adenine base editor with infinitesimal rates of bystander mutations and off-target editing

This paper engineers a precise adenine base editor, ABE9, with reduced bystander mutations and off-target effects, enabling efficient and accurate A-to-G editing in mouse and rat embryos.

Targeting Epsins by nanotherapy regulates lipid metabolism and promotes ABCG1-mediated cholesterol efflux to fortify atheroma regression

This study shows that targeting Epsins in macrophages with nanotherapy reduces lipid uptake and increases cholesterol efflux, promoting atheroma regression.

Targeting Epsins to Inhibit FGF Signaling while Potentiating TGF-beta Signaling Constrains Endothelial-to-Mesenchymal Transition in Atherosclerosis

This study identifies epsins as promoters of endothelial-to-mesenchymal transition in atherosclerosis and shows that a therapeutic peptide targeting epsin-FGFR1 interaction reduces EndoMT and atherosclerosis progression.

Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance

This paper identifies ZMYND8 as a gene epigenetically regulated by mIDH1 that promotes radioresistance in glioma cells, and shows its knockdown enhances radiosensitivity.

Single cell RNA sequencing reveals mechanisms underlying a senescence-like phenotype of Alveolar Macrophages during Aging

This study uses single-cell RNA sequencing to show that aged alveolar macrophages exhibit a senescence-like phenotype linked to reduced CBFβ expression and impaired self-renewal.

Ubiquitin-like cGAS chain formation by a super enzyme activates anti-phage response

This study identifies a bacterial E2 enzyme that regulates cGAS by mimicking the ubiquitination cascade to activate anti-phage response through poly-cGASylation.