proteomics

Improving real-time search through deep learning-enhanced fragment ion indexing

The paper develops a deep learning-enhanced fragment ion indexing method to reduce memory usage in tandem mass spectrometry searches while maintaining search accuracy and speed.

Filament assembly confers the mechanical resilience of the IFI16 restrictosome

This study shows that IFI16 filament assembly provides mechanical stability to condensates by compacting DNA into ultra-stable tangles, contrasting with the sensitivity of HIN200-dsDNA complexes.

Engineering and characterisation of AAVS1 FRT cell lines for inducible and dose-dependent gene expression

This paper develops a stable RPE1 cell line with inducible and dose-dependent transgene expression using CRISPR/Cas9 and FRT/Tet-On systems, validated through multi-omics analysis.

Mapping Endogenous Psychedelic Chemistry: Indolethylamine N-Methyltransferase (INMT) Localizes Proximal to the Golgi Apparatus of Human Neurons

This study identifies INMT's localization near the Golgi apparatus in human neurons and suggests it creates a region for psychedelic tryptamine biosynthesis.

Endothelin-1 from Tongue Glands Gates 1 Sodium Taste and Intake

This study shows that endothelin-1 from tongue glands modulates sodium taste and intake by inhibiting salt-sensing neurons, with effects reversed under sodium deficiency.

Immuno-Proteomic Age of Cardiovascular Etiology (iPACE) Signature Predicts Cardiovascular Risk in Elderly Patients

The paper develops an immune proteomic signature (iPACE) from serum proteins in elderly patients that predicts cardiovascular risk and mortality.

Long-PDE4D degradation attenuates left ventricular cardiomyocyte hypertrophic remodelling

This study shows that targeted degradation of long PDE4D isoforms reduces cardiac hypertrophy without affecting contractile function in rat and human cardiomyocytes.

Megakaryocytic proteomic signatures define myeloproliferative neoplasms

The paper performs proteomic analysis of megakaryocytes in MPN patients and identifies disease-specific proteomic signatures.

A RecBCD-like enzyme regulates expression of bacterial defense operons in response to DNA damage

The paper identifies a bacterial pathway, Cerberus, that uses DNA damage sensing to regulate defense operon expression through anti-sigma factor cleavage.

The Global Phosphorylation Landscape of Acute Heat Stress in Reef-Building Corals

This study identifies conserved kinase signaling responses in corals under acute heat stress, revealing molecular mechanisms that may contribute to bleaching.

Conformation governs cellular behaviors of LRRK2 Parkinson's disease variants

This study identifies 'unlatching' as a common mechanism for Parkinson's disease-associated LRRK2 variants, showing increased membrane localization and decreased S935 phosphorylation.

A developmentally scheduled inhibitory polarity circuit centers the stomatal pore

The paper identifies a polarity circuit in guard cells that determines stomatal pore position through MUS and OPL2 interactions, revealing a mechanism for coordinated cellular asymmetry.

QC-espresso: Brewing quality in proteomics

QC-espresso provides an automated quality-control workflow for DIA proteomics data, generating structured reports to assess acquisition quality and quantitative reliability.

Quantitative imaging of native tissue architecture combined with deep multi-omics reveals the spatial biology of kidney aging

This paper introduces NORIGAMI, a multi-omics pipeline that combines imaging and deep learning to analyze kidney aging, revealing age-related structural and molecular changes.

Local fractal dimension as an indicator of functional reorganization in molecular interaction networks

The paper introduces DIFFRACT, a framework that uses local fractal dimension changes in protein interaction networks to detect functional reorganization, showing its utility in identifying novel biological roles in RAVER1-deficient cells.

GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.

Characterisation of Saccharomyces cerevisiae and Saccharomyces jurei hybrids for oenological applications

The paper identifies Saccharomyces cerevisiae and Saccharomyces jurei hybrids with improved oenological traits for wine fermentation.

Tropical Peatlands as Hotspots of Hidden Arcellinida Diversity: Insights from Maludam National Park, Borneo (Sarawak, Malaysia)

This study investigates Arcellinida diversity in tropical peatlands, finding higher species richness in zones with developed understory vegetation and distinct community composition compared to extratropical ecosystems.

Multi-modal in situ profiling of human cells using the AVITI24 platform characterizes single-cell responses to acute stress

The paper uses a multi-modal platform to profile single-cell stress responses in human cell lines, finding a shared stress response program with cell-specific magnitude variations.

Foreign Body Responses Adapt to Systemic Immunosuppression to Maintain Local Immune Homeostasis Through Decorin-Associated Signaling

Nanobodies against Plasmodium vivax AMA1 block parasite invasion

The paper identifies nanobodies against PvAMA1 that inhibit Plasmodium vivax and falciparum invasion by binding novel epitopes distinct from known antibodies.

Recognition of the centromere-binding protein Ndc10 by Scm3HJURP directs Cse4CENP-A deposition at native centromeres

The paper shows Scm3HJURP facilitates Cse4CENP-A deposition at native centromeres by interacting with Ndc10, enhancing Cse4 assembly efficiency in yeast.

Autophagy activator AA-20 engages CDK5 to promote lipophagy and improve neurodegeneration-associated phenotypes

AA-20 promotes lipophagy by activating lysosomal acid lipase and CDK5, reducing lipid droplet accumulation and improving neurodegeneration-associated phenotypes in cellular and organoid models.

Single-probe, amplification-free multiplex mRNA PNA-FISH maps bacterial gene expression in intact three-dimensional biofilms

This paper develops a single-probe, amplification-free PNA-FISH method to map bacterial gene expression in 3D biofilms, showing it accurately captures transcriptional changes without amplification.

Putrescine-responsive post-transcriptional feedback regulation of Arabidopsis ADC2 mediated by 5'-UTR elements

This study identifies Putrescine-responsive feedback regulation of ADC2 in Arabidopsis mediated by 5'-UTR elements, showing translational repression and its role in Put homeostasis.

Homoplastic evolution of proximal podomere patterning across Arthropoda

The paper examines proximal podomere patterning in sea spiders and arachnids, finding homoplastic evolution of gene expression patterns that challenges assumptions about leg segment homology.

Cumulus cells mediate the protective effect of the marine carotenoid fucoxanthin against postovulatory oocyte aging via NRF2 signaling

This study shows that fucoxanthin protects mouse oocytes from postovulatory aging by activating NRF2 in cumulus cells, improving mitochondrial function and reducing oxidative stress.

A rational design strategy and validation for protease-resistant fusion-inhibitor antiviral peptides

This study designs and validates protease-resistant antiviral peptides that inhibit SARS-CoV-2 fusion, showing improved efficacy in vitro and in vivo.

From cellular stress to cytokine modulation: An in vitro study of intestinal effects of major Alternaria mycotoxins

This study investigates the effects of Alternaria mycotoxins on intestinal cells using in vitro models, finding low toxicity and absorption, with some immunomodulatory effects on cytokine secretion.

The small ORF (smORF)-encoded polypeptide MIRINE promotes neuronal differentiation in vertebrate brain development

The paper identifies MIRINE, a small ORF-encoded polypeptide that promotes neuronal differentiation in vertebrate brain development by regulating the balance between proliferation and maturation.