J. Zhu

THiRST: Computer Vision Empowered Three-dimensional High-Resolution Spatial Transcriptomics Analytics

THiRST reconstructs 3D spatial transcriptomic data from serial 2D sections, improving cross-section consistency and enabling 3D gene expression analysis.

π-SPECFormer: A Mass Spectrometry-based Foundation Model for Decoding the Dark Proteome

This paper introduces π-SPECFormer, a foundation model for mass spectrometry-based proteomics that decodes the dark proteome by pre-training on unannotated spectra and outperforms baselines in peptide sequencing and modification detection.

Cystinosin/Ers1 functions in redox homeostasis in the early secretory pathway

This study identifies a conserved role of cystinosin/Ers1 in the early secretory pathway, revealing new insights into cystinosis pathology beyond lysosomal cystine transport.

PRADA-DTI: A Prototype-Retrieval Augmented Domain-Adaptation Framework for Drug-Target Interaction Prediction

PRADA-DTI improves drug-target interaction prediction by enabling continual learning from new protein domains with minimal parameter updates and reduced forgetting.

Metabolic regulation of misfolded protein import into mitochondria

This study shows that Snf1/AMPK inhibits misfolded protein import into mitochondria and promotes mitochondrial biogenesis under glucose starvation, protecting mitochondrial fitness in yeast and human cells.

pH-Controlled chemoselective rapid azo-coupling reaction (CRACR) enables global profiling of serotonylation proteome in cancer cells

The paper develops a chemical proteomic method to globally profile serotonylation in cancer cells, identifying over 1,000 serotonylated proteins and their modification sites.

Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells

The paper identifies 425 dopaminylated proteins in colorectal cancer cells using a chemical probe, revealing their involvement in nucleic acid metabolism and transcription, and suggests targeting protein dopaminylation as a potential anti-cancer strategy.

Delta-5 elongase knockout reduces DHA and TAG synthesis coupled with an increase of heat sensitivity in a marine diatom

This study shows that knocking out delta-5 elongase in a marine diatom reduces DHA and TAG synthesis and increases heat sensitivity.

Disruption of Epithelium Integrity by Inflammation-Associated Fibroblasts through Prostaglandin Signaling

This study shows inflammation-associated fibroblasts disrupt colon epithelial barrier integrity and genome stability via PGE2-EP4 signaling, and EP4 inhibitors can reverse these effects.

HOIL1 mediates MDA5 activation through ubiquitination of LGP2

This study shows HOIL1 ubiquitinates LGP2 to activate MDA5 and induce IFN responses, highlighting a mechanism distinct from RIG-I sensing.

Bioorthogonal labeling and enrichment of histone monoaminylation reveal its accumulation and regulatory function in cancer cell chromatin

This study develops chemical probes to label and enrich histone monoaminylation, revealing its enrichment in cancer tissues and its role in chromatin architecture regulation.

Structural and biophysical characterisation of ubiquitin variants that specifically inhibit the ubiquitin conjugating enzyme Ube2d2

The paper identifies ubiquitin variants that inhibit Ube2d2, showing structural and biophysical properties that suggest potential for developing selective E2 enzyme inhibitors.

Unicellular cyanobacteria rely on sodium energetics to fix N2

This study shows that unicellular cyanobacteria rely on sodium energetics for N2 fixation, which may explain their low abundance in coastal waters due to insufficient NaCl levels.

A tale of two fusion proteins: understanding the metastability of human respiratory syncytial virus and metapneumovirus and implications for rational design of uncleaved prefusion-closed trimers

The study analyzes metastability in fusion proteins of RSV and hMPV to design stable uncleaved prefusion-closed trimers for vaccine development.

Robust Neutralization of SARS-CoV-2 Variants Including JN.1 and BA.2.87.1 by Trivalent XBB Vaccine-Induced Antibodies

The paper compares antibody responses from individuals with XBB reinfection and those vaccinated with WSK-V102C, showing the vaccine induces stronger neutralization against SARS-CoV-2 variants including JN.1 and BA.2.87.1.

Enhanced Antibody Response to the Conformational Non-RBD Region via DNA Prime-Protein Boost Elicits Broad Cross-Neutralization Against SARS-CoV-2 Variants

This study shows that DNA prime-protein boost elicits enhanced antibodies against non-RBD regions of SARS-CoV-2, improving cross-neutralization against variants in mice.

Functional validation of EIF2AK4 (GCN2) missense variants associated with pulmonary arterial hypertension

The paper functionally validates EIF2AK4 variants in PAH patients, finding some variants are non-pathogenic and others are hypomorphic and responsive to a kinase inhibitor.

TDP43 aggregation at ER-exit sites impairs ER-to-Golgi transport

The paper identifies TDP43 aggregation at ER-exit sites as a cause of impaired ER-to-Golgi transport in ALS.

Cross-species genomic survey reveals a single origin of the soft-shelled turtles

This study reveals that soft-shelled turtles have a single origin of their ZW-type sex chromosomes, coinciding with the Paleocene-Eocene thermal maximum.

Effects of different feeding methods on serum biochemical indexes, metabolic indexes, immune indexes, and intestinal microorganisms of Nanjiang yellow goats

This study examines how different feeding methods affect serum biochemical, immune, and metabolic indicators and intestinal microbiota in Nanjiang Yellow goats, finding significant differences in metabolites, immune factors, and microbial composition.

Plant-associated fungi co-opt ancient antimicrobials for host manipulation

The paper identifies antimicrobial effectors in plant-associated fungi, suggesting they evolved from ancient antimicrobials to manipulate host microbiota and immunity.

Development of attenuated coxsackievirus B3 vectored intranasal pre-emptive pan-coronavirus vaccine

The paper designs an intranasal pan-coronavirus vaccine using epitopes from SARS-CoV-2 and zoonotic coronaviruses, showing immune responses in mice but needing further cross-reactivity testing.

Development of an Engineered Mycobacterium tuberculosis Strain for a Safe and Effective Tuberculosis Human Challenge Model

This paper develops an engineered Mycobacterium tuberculosis strain with kill switches for a safe TB human challenge model, showing rapid clearance and low escape rates.

An exploration of mechanisms underlying Desemzia incerta colonization resistance to methicillin-resistant Staphylococcus aureus on the skin

This study identifies Desemzia incerta as a skin commensal that reduces MRSA colonization through secreted antimicrobial proteins and decreased biofilm formation in a murine model.

Hybrid hydrogel-extracellular matrix scaffolds identify distinct ligand and mechanical signatures in cardiac aging

The paper develops tunable hybrid scaffolds to study how ligand presentation and mechanical stiffness in ECM influence cardiac fibroblast behavior during aging.

Differential effects of aneuploidy on growth and differentiation in human intestinal stem cells

This study investigates how different types of aneuploidy affect growth and differentiation in human intestinal stem cells, finding that complex aneuploidy triggers p53 activation and cell-cycle arrest, while simple aneuploidy allows continued proliferation and impaired differentiation.

Voxelated bioprinting of modular double-network bio-ink droplets

This paper introduces a voxelated bioprinting method to create double-network hydrogel droplets with precise 3D assembly and mechanical properties.

Bet hedging in a unicellular microalga

The paper demonstrates bet hedging in the microalga Haematococcus pluvialis through reversible phenotypic diversification into mobile and non-mobile subunits, enhancing population persistence under environmental stress.

Oxidized LDL regulates efferocytosis through the CD36-PKM2-mtROS pathway

This study identifies the CD36-PKM2-mtROS pathway as a mechanism by which oxidized LDL disrupts efferocytosis, contributing to atherosclerosis progression.

Stabilization of RRBP1 mRNA via an m6A-dependent manner in prostate cancer constitutes a therapeutic vulnerability amenable to small-peptide inhibition of METTL3

This study identifies METTL3-mediated stabilization of RRBP1 mRNA via m6A in prostate cancer and develops small-peptide inhibitors to target this pathway.