proteomics

UVC Irradiation Induces Time-Dependent Proteomic Remodeling in Geodermatophilus obscurus G20

This study examines proteomic changes in Geodermatophilus obscurus G20 under UV stress, showing distinct responses in acute and recovery phases.

Monounsaturated fatty acid depletion is a metabolic pattern of pathogenesis surveilled to activate p38 MAPK innate immunity

The paper identifies oleate depletion as a metabolic signal sensed by C. elegans to activate innate immunity against bacterial infection.

Energetic and functional development of soil food webs along secondary succession

This study examines energy flux changes in soil food webs during secondary succession, finding shifts from herbivory to detritivory and differences between plantation and natural forest types.

Contrastive Learning Improves Generalization on M2OR Olfactory Binding Dataset

The paper evaluates contrastive learning on VOC-OR binding datasets, showing improved generalization and reduced performance inflation from identity leakage.

Host-Derived Lipids Sustain Membrane Biogenesis in an Obligate Endosymbiont

The paper investigates how host-derived lipids sustain membrane biogenesis in the obligate endosymbiont Buchnera aphidicola, showing host lipid metabolism is critical for symbiont survival.

Aging, HIV Status, and Sex Differentially Influence Antiretroviral Therapy Disposition Pathways in Rectosigmoid Tissue and Peripheral Blood Mononuclear Cells

This study identifies how aging and HIV status differentially affect antiretroviral therapy disposition pathways in rectosigmoid tissue and PBMC, with aging causing broader changes in drug-related proteins.

Hypoxia-inducible factor 2-alpha promotes fitness of cytokine-activated human natural killer cells

This study identifies HIF-2 as a critical factor for the survival of cytokine-activated human NK cells, showing it is induced by IL-2/IL-15 and not hypoxia, and its inhibition reduces NK cell viability.

Onsite fixation preserves phosphoprotein profile in human whole blood

This study shows that fixing whole blood at collection preserves phosphoprotein profiles, particularly in neutrophils and monocytes, better than cryopreserved PBMCs.

TACO: An open, interpretable model for microsecond-scale TCR specificity prediction

TACO predicts TCR specificity against HLA-A*02:01-presented peptides using a statistical model, achieving AUROC 0.67 on held-out data and enabling efficient computational evaluation of TCR-peptide interactions.

Joint protein-DNA language modeling enables prediction and engineering of DNA recognition specificity

This paper introduces PDLMs, protein-DNA language models that jointly represent protein and DNA sequences to predict and engineer DNA recognition specificity.

Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

Hijacking Cellular S-Acylation with Molecular Assemblies Rewires Oncogenic Signaling

This paper shows that targeting cellular S-acylation with synthetic compounds can spatially disrupt KRAS signaling and stress responses in cancer cells.

Unlocking Targeted Underwater Delivery of Coral Probiotics

This study develops alginate-based delivery systems for coral probiotics, showing increased probiotic colonization in treated corals.

ACTIVATION OF THE ARYL HYDROCARBON RECEPTOR REDUCES VISCERAL HYPERSENSITIVITY IN A MOUSE MODEL OF COLITIS IN REMISSION

This study shows that activating the AhR in TRPV1+ nociceptors reduces visceral hypersensitivity in post-colitis mice, suggesting AhR as a therapeutic target for IBD-related abdominal pain.

HIV-1 Vpu complements HLA-A downregulation by Nef and impairs TCR-mediated recognition of HIV-infected cells through distinct mechanisms

This study shows HIV-1 Vpu reduces HLA-A expression and impairs TCR recognition, acting independently of Nef and requiring BST2/tetherin.

BNCT Triggers Immunogenic Cell Death in B16 Melanoma Without Accompanying T-Cell Infiltration--Implications for Combination Immunotherapy

This study shows BNCT reduces B16 melanoma growth and survival, induces immunogenic cell death and a Th1 response, but fails to increase CD8+ T-cell infiltration, suggesting immune resistance mechanisms may limit its efficacy.

Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

This study introduces TISCA2 and IncepTIS to map and predict stress-responsive translation initiation sites, revealing tissue-specific patterns and enabling engineered mRNA 5' leaders.

Compartment-Resolved Matrisome Shifts During Postnatal Tendon Maturation in Mice

This study uses compartment-resolved proteomics to analyze changes in the tendon matrisome during postnatal maturation in mice, revealing distinct trajectories in soluble and insoluble ECM components.

Lipidic α-synuclein fibrils catalyze the formation of pathological mature fibrils

This study shows lipidic α-synuclein fibrils catalyze the formation of mature fibrils through a heterogeneous nucleation mechanism, lowering the energy barrier and following Ostwald's Rule of Stages.

Clonally Convergent Tph/Tfh-like CD4+ T Cells are Shared Across Recovery and Recurrence in Experimental Periodontitis

The paper identifies clonally convergent Tfh/Tph-like CD4+ T cells that persist in the mucosa after recovery from periodontitis and contribute to recurrence.

memVar: an integrated resource for interpreting human membrane protein variation in molecular and disease contexts

memVar links human membrane protein variants to molecular contexts and disease, revealing enrichment of pathogenic variants in transmembrane regions and interaction sites.

Platycodin D2 Targets Vimentin to Suppress Fibroblast-Myofibroblast Transition: A Novel Therapeutic Strategy Against Pulmonary Fibrosis

This study identifies Platycodin D2 as a vimentin ligand that suppresses fibroblast-myofibroblast transition, offering a new therapeutic approach for pulmonary fibrosis.

The binding landscape of Ras/effector interactions provides insights on Ras switching and oncogenesis

This study maps the Ras/Nore1A binding landscape under different states and mutations, revealing how oncogenic changes alter interaction dynamics and provide insights for inhibitor design.

Use of Integrative Proteomic Analysis to Uncover Shared Molecular Signatures Across Distinct Forms of Hydrocephalus

This study identifies shared and etiology-specific proteomic signatures across hydrocephalus subtypes using cross-study proteomic analysis of CSF.

Genetic Variation in Photosynthetic Maintenance and Post-Chill Recovery for Early Season Maize Plantings

This study evaluates genetic variation in maize's response to chilling stress and recovery, identifying heritable traits linked to cold resilience.

Improving phosphoproteomic kinase activity inference by contextual refinement of Kinase Library relationships

The paper improves kinase activity inference by refining kinase-substrate relationships with protein-association evidence, enhancing accuracy and coverage in phosphoproteomic data.

RNA Polymerase Backtracking Promotes Type III-A CRISPR DNA Targeting

The paper shows RNA polymerase backtracking promotes type III-A CRISPR DNA targeting by inhibiting GreA anti-backtracking factors, which suppress Cas10-Csm activity.

Jade1S SUMOylates tau and targets oligomers for degradation

This study identifies Jade1S as a SUMO ligase and chaperone that regulates tau stability, prevents oligomerization, and promotes proteasomal degradation of aggregated tau.

PartiDesign: A structure-sequence co-design paradigm for practical all-to-all biomolecules design

PartiDesign is a structure-sequence co-design model that generates molecular structures and sequences for proteins, nucleic acids, and small molecules, achieving high design throughput across benchmarks.

Receptor-proximal phosphoform organization precedes β2 integrin activation

The paper quantifies phosphoform organization near β2 integrins and shows that signaling alters phosphosites while preserving spatial organization of proteins.