L. Zheng

Ketogenic diet synergistic reprogramming of both host and microbiome promotes tissue regeneration

This study shows a ketogenic diet reprograms host and microbiome functions to enhance tissue regeneration through IL-17A activation and microbial riboflavin and sphingomyelinase pathways.

Why the adventitious roots of poplar are so colorful: RNAseq and metabolomic analysis reveal flavonols, flavones, and anthocyanins accumulation in canker pathogens-induced adventitious roots in poplar

This study identifies flavonols, flavones, and anthocyanins as the colorants in poplar adventitious roots induced by fungal pathogens, revealing their biosynthesis regulation by sunlight and transcription factors.

Thymidine Phosphorylase Mediates SARS-CoV-2 Spike Protein Enhanced Thrombosis in K18-hACE2TG Mice

This study identifies thymidine phosphorylase (TYMP) as a mediator of SARS-CoV-2 spike protein-induced thrombosis in mice, showing that TYMP inhibition reduces thrombosis and coagulation.

The MKK3 MAPK cascade integrates temperature and after-ripening signals to modulate seed germination

This study identifies the MKK3 MAPK cascade as a regulator of seed germination temperature range by integrating temperature and after-ripening signals through phytohormone metabolism.

An Evaluation of the Tumor Microenvironment through CALR,IL1R1,IFNB1,and IFNG to Assess Prognosis and Immunotherapy Response in Bladder Cancer Patients

This study evaluates ICD-related genes in bladder cancer to assess prognosis and immunotherapy response, finding higher ICD expression correlates with better survival and response to PD1-targeted therapy.

The transcription factor OsbZIP48 governs rice responses to zinc deficiency

This study identifies OsbZIP48 as a transcription factor critical for rice's response to zinc deficiency, showing it regulates zinc transporter genes through direct promoter binding.

The Mechanism Insight into Bacterial Degradation of Pentachlorobiphenyl

This study identifies a new bacterium capable of degrading pentachlorobiphenyl and characterizes its enzymatic, proteomic, and metabolomic responses to the pollutant.

Hydrophobic bulk conservation and genetic code determine the pattern of prokaryotic genome organization

The paper analyzes prokaryotic genome organization patterns and finds that GC-content, mutational biases, and genetic code influence GC-skew, AT-skew, and gene strand bias through synonymous and nonsynonymous substitutions.

Semantical and Geometrical Protein Encoding Toward Enhanced Bioactivity and Thermostability

This paper introduces a pre-training framework that combines sequential and geometric encoders to improve protein variant prediction for enhanced bioactivity and thermostability.

Protein Engineering with Lightweight Graph Denoising Neural Networks

This study introduces a lightweight graph neural network for protein engineering that predicts fitness and guides the design of effective mutants with improved physicochemical properties.

Tumor- and Nerve-Derived Axon Guidance Molecule Promotes Pancreatic Ductal Adenocarcinoma Progression and Metastasis through Macrophage Reprogramming

This study identifies SEMA3D as a dual driver of pancreatic ductal adenocarcinoma progression and metastasis through tumor- and nerve-derived mechanisms involving macrophage reprogramming.

Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K

The paper investigates the onset of anharmonicity in a protein and its surface water around 200 K, finding they are decoupled, with the protein's transition being intrinsic and the water's being a resolution effect.

Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity

The paper presents cryo-EM structures of human SIDT1 and SIDT2, revealing their dimeric architecture and demonstrating low-pH-dependent RNA binding and oligomerization.

A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity

This paper introduces CPDiffusion, a conditional protein diffusion model that generates artificial endonuclease sequences with enhanced activity without labeled data.

Characterization of N-glycosylation and its Functional Role in SIDT1-Mediated RNA Uptake

This study maps N-glycosylation sites in SIDT1 and SIDT2 and shows their role in RNA uptake, cell surface expression, and protein stability.

Bioinformatic and Experimental Characterization of the RBM15 RNA Binding Protein

This study characterizes RBM15's RNA binding mechanism through bioinformatics and experiments, showing it interacts with stem-loop RNA motifs via RRMs 2 and 3.

Mn2+-Induced Structural Flexibility Enhances the Entire Catalytic Cycle and the Cleavage of Mismatches in Prokaryotic Argonaute Proteins

This study shows that Mn2+ enhances pAgo protein flexibility, improving catalytic efficiency and mismatch cleavage through structural changes.

Structural insights into Rad18 targeting by the SLF1 BRCT domains

The paper presents the crystal structure of SLF1tBRCT bound to Rad18 peptide, revealing mechanisms of Rad18 recognition and BRCT-mediated complex assembly.

SeMOE allows for quantitative glycan perception and exhibits anti-cancer potentiality

SeMOE enables absolute glycan quantification and visualization through selenosugar-based metabolic oligosaccharide engineering, with demonstrated anti-cancer potential.

Doxorubicin inhibits phosphatidylserine decarboxylase and confers broad-spectrum antifungal activity

The paper shows doxorubicin inhibits MoPSD2, a phosphatidylserine decarboxylase in Magnaporthe oryzae, reducing fungal growth and crop disease severity.

Frizzled-9 activates YAP to rescue simulated microgravity induced osteoblasts dysfunction.

This study shows that Fzd9 overexpression rescues SMG-induced osteoblast dysfunction by activating YAP through actin polymerization and nuclear translocation.

HCC-1 accelerates atherosclerosis by inducing endothelial cells and macrophages pyroptosis and serves as an early diagnostic biomarker

This study shows HCC-1 promotes atherosclerosis by inducing pyroptosis in endothelial cells and macrophages and suggests it as an early diagnostic biomarker.

An Antibody-Based Molecular Switch for Continuous Biosensing

This paper introduces an antibody-based molecular switch for continuous biosensing of biomarkers without sample preparation, demonstrating real-time detection of digoxigenin and cortisol with adjustable sensitivity.

Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions

This study uses 3D imaging and genomic analysis to show that human pancreatic precancerous lesions (PanINs) are highly multifocal and genetically heterogeneous.

Structure of human phagocyte NADPH oxidase in the resting state

The paper reports the cryo-EM structure of the human NOX2-p22 complex in the resting state, revealing interactions and conformational features important for its function.

Longitudinal characterization of circulating extracellular vesicles and small RNA during simian immunodeficiency virus infection and antiretroviral therapy

This study tracks changes in extracellular vesicle concentration and small RNA expression during SIV infection and ART in macaques, identifying dynamic shifts in miRNAs and U6 RNA associated with viral load.

Allosteric Regulation of Aptamer Affinity through Mechano-Chemical Coupling

This paper introduces a method to modulate aptamer affinity using a molecular clamp that destabilizes secondary structure through mechanical tension, demonstrating up to 65-fold affinity changes without prior structural knowledge.

Inflammatory Signaling in Pancreatic Cancer Transfers Between a Single-cell RNA Sequencing Atlas and Co-Culture

This paper integrates single-cell RNA sequencing data with organoid co-cultures to study inflammatory signaling in pancreatic cancer and validates findings through transfer learning and mechanistic experiments.

A small DNA virus initiates replication with no more than three genome copies per cell

This study shows DNA viruses like TYLCV undergo intracellular population bottlenecks, limiting replication to no more than three genome copies per cell, ensuring lethal mutations are purged.

Lipid nanoparticle topology regulates endosomal escape and delivery of RNA to the cytoplasm

This study shows that lipid nanoparticle (LNP) topology affects endosomal escape and RNA delivery efficiency, with bicontinuous cubic LNPs (cuboplexes) outperforming lamellar LNPs.