proteomics

Integrative taxonomy using traits and genomic data for Species Delimitation with Deep learning

This paper introduces a deep learning method that integrates genomic and trait data to improve species delimitation in complex speciation scenarios.

NAD+ Replenishment Reduces Cardiomyocyte Senescence and Improves Diastolic Function in the Aged Male Heart

This study shows that NAD+ replenishment with NR or NRH reduces cardiomyocyte senescence and improves diastolic function in aged male mice but not females.

Intestinal epithelial Casd1 influences mucus sialic acid O-acetylation and tissue damage susceptibility toward large-intestinal mucosal insults.

This study investigates the role of Casd1 in sialic acid O-acetylation of intestinal mucus and its impact on tissue damage susceptibility in mice.

Proteomic profiling of experimental acute alcohol intoxication reveals FGF21 as a specific ethanol-induced hormone

This study identifies FGF21 as a specific ethanol-induced hormone through proteomic profiling of acute alcohol intoxication in humans.

Targeted proteomics informed by long-read RNA-sequencing reveals protein isoform expression associated with bone mineral density

This study uses genetics-guided targeted mass spectrometry to detect protein isoforms associated with bone mineral density, confirming their expression in clinical samples.

Viral tRNA-like structure hijacks host ribosomes for poly(A)-independent translation

This study shows how a viral tRNA-like structure recruits host ribosomes for poly(A)-independent translation by binding to ribosomal subunits and substituting for poly(A) tails.

Customizable bead-based platform for EV surface protein immunocapture and detection in plasma

This paper introduces a customizable bead-based platform for isolating and detecting specific EV populations in plasma, demonstrating sensitivity and the ability to distinguish clinically relevant biomarker expressions.

Preserved Type 2 Immune Cell Plasticity in Human Obesity and Differential Immune Reconstitution After Bariatric Surgery

This study examines immune cell changes in obesity and after bariatric surgery, finding preserved type 2 immune cell plasticity and differential immune recovery.

Sorghum Metabolic Atlas: Large-Scale Subcellular Localization Resource for Sorghum Metabolic Enzymes

The paper experimentally determines subcellular localization of 234 metabolic enzymes in sorghum, providing a resource for metabolic organization studies.

A High-Sensitivity and High-Throughput LC-MS Workflow for Low-Input and Single-Cell Proteomics

This paper develops a high-sensitivity and high-throughput LC-MS workflow for low-input and single-cell proteomics, achieving high proteome depth and throughput without specialized equipment.

Glioblastoma Hijacks Astrocyte Ribosomes to Feul Malignancy through Translatome Reprogramming

This study shows glioblastoma hijacks astrocyte ribosomes via tunneling nanotubes, reprograms the tumor translatome to promote malignancy, and identifies INTS12 as a therapeutic target.

Out-of-the-box bioinformatics capabilities of large language models (LLMs)

This study evaluates the performance of three large language models on basic bioinformatics tasks compared to human performance, finding LLMs match human accuracy in some areas but struggle with complex tasks like sequence alignment.

Illuminating phage dark matter beyond the reach of structural alignments with PhageFlare

PhageFlare predicts functions for phage proteins with no structural matches, outperforming baselines and annotating many previously unresolved proteins.

Phagocytosis of SARS-CoV-2 Nucleocapsid- and RNA-Containing Immune Complexes Drives Inflammatory Cytokine Production and Endothelial Dysfunction

This study investigates how SARS-CoV-2 RNA and nucleocapsid-containing immune complexes drive inflammation and endothelial dysfunction through Fcγ receptor and TLR-8 pathways.

Multi-omics uncover interactions in the vaginal microbiome and a type II secretion/Tad pilus system in Gardnerella species

This study uses multi-omics to uncover Gardnerella genomic features linked to biofilm formation and interspecies interactions in the vaginal microbiome, identifying potential therapeutic targets for bacterial vaginosis.

Yra2 regulates proteolysis of Cse4 to prevent its mislocalization to non-centromeric regions for chromosomal stability in budding yeast

This paper identifies Yra2's role in ubiquitin-mediated proteolysis of Cse4 to prevent its mislocalization and maintain chromosomal stability in budding yeast.

Naturally arising de novo open reading frames as potential zinc chelators in Drosophila melanogaster

The paper identifies de novo open reading frames in Drosophila melanogaster that show sequence signatures indicative of metal-binding potential through bis-histidine motifs.

Proximity labeling of the Listeria monocytogenes surface reveals pathogen control of a host deubiquitinase

The paper identifies CYLD as a host deubiquitinase recruited to Listeria monocytogenes surface via InlC and RNF213, which facilitates cell-to-cell spread in epithelial cells.

A commensally regulated immune rheostat fine-tunes skin barrier fitness

This study identifies a microbial-immune-epithelial feedback mechanism that regulates stem cell activity and skin barrier function through prostaglandin E2 signaling.

A matrikine organizes the dendritic cell- T cell triads that build tertiary lymphoid structures

This study identifies versikine, a matrikine derived from VCAN proteolysis, as essential for organizing dendritic cell-T cell triads in tertiary lymphoid structures and enhancing antitumor immunity.

Selective tRNA charging defects reshape ribosomal pausing and stress adaptation

The paper investigates how selective tRNA charging defects affect translation and stress responses using inhibitors in different cell types.

Synthetic auxotrophy reveals metabolic regulation of plasma cell generation, affinity maturation, and cytokine receptor signaling

The paper shows that glutaminolysis and mitochondrial metabolism are conditionally crucial for B cell differentiation and cytokine signaling, revealing metabolic regulation of plasma cell generation and cytokine receptor signaling.

AP2-L-Dependent Processes Promote PVM Maintenance and Plasmodium Liver-stage Development

This study shows AP2-L is essential for Plasmodium liver-stage development by regulating PVM formation and host-cell interactions.

Lysinoalanine crosslinking in the extracellular flagellar hook of Synergistota

The paper identifies lysinoalanine crosslinking in the extracellular flagellar hook of Synergistota, expanding the known range of bacteria with this modification beyond spirochetes.

USP18-STAT2 axis enhances hepatic resilience under proteotoxic stress

This study identifies the USP18-STAT2 axis as a critical factor enhancing hepatic resilience under proteotoxic stress by modulating interferon signaling and ISG solubility.

The TREM-receptor family interactome in the human brain

The paper identifies novel interactors of TREML1 and TREML2 using proteomics, highlighting their roles in lipid trafficking and immunity.

Bacterial exo-α-sialidases subvert the complement system through desialylation

This study shows bacterial sialidases remove sialic acids from complement proteins, reducing complement activation and helping bacteria evade immune detection.

Lateral opening site of human oligopeptide transporter 2 plays a key role in the interaction with polymyxins

This study identifies key residues in hPepT2 involved in polymyxin interaction, showing that modifying these residues reduces nephrotoxicity while maintaining antibacterial activity.

Survey of the human proteostasis network: the ubiquitin-proteasome system

The paper provides a comprehensive survey of the ubiquitin-proteasome system (UPS) and estimates its size and scope within the human proteostasis network.

MCL1 may not mediate chemoresistance

This study challenges the role of MCL1 in chemoresistance by showing no evidence of nuclear accumulation or DNA repair interactions in live cancer cells.