proteomics

Scp160 deletion suppresses TDP-43 aggregation and toxicity in Saccharomyces cerevisiae

This study shows that deleting Scp160 reduces TDP-43 aggregation and toxicity in yeast, while Bfr1 has a lesser effect.

Divergent genotype-phenotype maps determine the capacity for adaptation to antibiotics among Enterobacteria

This study compares the adaptation of E. coli and K. aerogenes to antibiotics, finding that their differing genotype-phenotype maps determine their capacity to evolve resistance.

Behavioral, Cardiovascular, and Neuroinflammatory Effects of 3-Aminobenzamide in a Rodent Model of Chronic Psychological Stress

This study investigates the effects of 3-aminobenzamide (3-AB), a PARP inhibitor, on chronic stress-induced behavioral, cardiovascular, and neuroinflammatory changes in rats, finding protective effects against behavioral deficits and neuroinflammation.

Nutrient-sensitive histone propionylation regulates T cell fate and function

This study shows that histone propionylation, influenced by nutrient availability, regulates T cell fate and antitumor immunity.

Monitoring the translation initiation process in prokaryotes via large-scale examination using optimized SSU-seq technique

The paper develops an optimized SSU-seq protocol for E. coli to study ribosome-mRNA interactions, revealing patterns of small subunit distribution linked to rRNA-mRNA hybridization.

Protein-level mapping reveals novel Immune State Types (ISTs) associated with Chlamydia trachomatis infection, inflammatory remodeling, and scarring in trachoma-hyperendemic Amhara Ethiopia

The paper identifies four immune state types (ISTs) in trachoma patients using protein profiling, linking them to infection, inflammation, and scarring outcomes.

IgG4 antibody repertoire diversity is stable over several years in health and autoimmune disease

The paper examines IgG4 antibody repertoire stability over time in health and autoimmune diseases, finding that most clones remain stable despite treatment.

Tubule extension by plastids is due to increase in bilayer-forming galactolipids at the outer envelope membrane

The paper identifies increased bilayer-forming galactolipids on the outer envelope membrane as the mechanism driving plastid tubule extension under stress.

Disentangling maternal pregnancy and fetal-specific plasma signatures through integrated proteomics and site-specific N-glycoproteomics

The paper identifies pregnancy-specific and fetal-specific plasma proteomic and N-glycoproteomic signatures by comparing maternal, cord blood, and non-pregnant control samples.

An Aphid Protein Interferes with Plant endomembrane Trafficking Machinery to Promote Aphid Survival and Plant Growth

This study identifies an aphid protein, AAF1, that manipulates plant autophagy to enhance aphid survival and plant growth.

Extracellular vesicle cross-linking coupled with solid-phase purification facilitates discovery of ribonucleoprotein complexes assembled on EV RNAs.

This paper introduces two methods, EV-CLASP and EV(r)-CLASP, to study RNP complexes on EV RNAs, revealing post-transfer interactions and intra-vesicular compositions.

Polyploid Achromatium sp. expresses protein variants based on environmental cues

The paper investigates how Achromatium sp. expresses protein variants in response to temperature changes using proteomics and a newly assembled protein atlas.

Similar fertility losses in response to heat are followed by distinct recovery trajectories across seven Drosophila species

This study examines heat-induced fertility loss and recovery across seven Drosophila species, finding similar initial losses but distinct recovery patterns.

Inadequate antibody validation places substantial numbers of animal and human tissue samples at risk of waste

Of 760 papers using 35 antibodies that failed knockout-controlled testing in every application, 15.8% showed validation; the other 640 used at least 8,064 animal and 4,424 human tissue samples.

The Hunt for Cholesteryl Ester Hydrolases: Identification of Lipoprotein Lipase as a Cholesterylesterase

This study identifies lipoprotein lipase (LPL) as a neutral cholesteryl ester hydrolase in mammals through biochemical and pharmacological analyses.

Metabolic commitment to human motor neurons is characterized by mitochondrial depletion and pyruvate rewiring

The paper characterizes metabolic changes in human motor neuron differentiation, showing mitochondrial depletion and a shift in pyruvate metabolism.

A circRNA-derived IRES-like element enables programmable translational activation of the endogenous chaperone HSP90

The paper describes a synthetic circRNA-derived IRES-like element, SynFarsa, that enhances translation of an endogenous protein, HSP90, in trans by targeting its 3'UTR.

SARS-CoV-2 Nucleocapsid Protein forms biomolecular condensates and interacts with ALS-associated RNA binding proteins in vitro

This study investigates how SARS-CoV-2 N-protein forms biomolecular condensates and interacts with ALS-associated RNA-binding proteins in vitro and human cell models.

Bioreactor cultures of brain endothelial cells produce extracellular vesicles with comparable characteristics as that of batch cultures

This study compares extracellular vesicles from bioreactor and batch cultures of brain endothelial cells, finding similar functional properties and protein content, with bioreactor cultures producing higher yields.

YY1 phosphorylation links non-apoptotic caspase-8 signaling to MASH fibrosis

This study identifies YY1 phosphorylation as a key mechanism linking non-apoptotic caspase-8 signaling to METRN induction and MASH fibrosis.

PREpiBind: Protein Representation-integrated Epitope-MHC Class II Binding Prediction

PREpiBind evaluates ten protein representations for pMHC-II binding prediction across multiple datasets, showing varying performance depending on the task and evaluation method.

Development and Analytical Validation of a Smartphone-Based Quantitative Lateral Flow Immunoassay for Serum Cystatin-C

This paper develops and validates a smartphone-based lateral flow immunoassay for serum Cystatin-C, showing high accuracy and reliability in clinical samples.

Development of NanoBRET cellular target engagement assays in primary neurons for activating mutants of p21-activated kinase 1

This paper develops NanoBRET assays for PAK1 and its mutant in primary neurons to evaluate inhibitor target engagement.

Phenotypic characterization of Prevotella melaninogenica ATCC 25845

This study characterizes the phenotypic and growth properties of Prevotella melaninogenica ATCC 25845, revealing its morphology, antibiotic susceptibility, and carbon source preferences.

Intraindividual longitudinal changes of the proteome reveal dynamic markers of biological aging

The paper develops a proteomic aging clock using longitudinal plasma proteomics data to show that biological aging is dynamically influenced by modifiable risk factors.

RNA and protein are not interchangeable in single-cell spatial multi-omics

This study shows that spatial RNA and protein measurements are largely overlapping for lineage markers and abundance but discordant for specific molecules and spatial features, indicating they are complementary rather than interchangeable.

Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models

A structure-conditioned nucleotide-level Potts model designs protein and coding sequences jointly, enabling tRNA adaptation and RNA motif embedding beyond synonymous codons with designability comparable to Caliby.

Neutrophil degranulation and extracellular ROS production are inactivated by Yersinia pseudotuberculosis YopE through a SKAP2 independent pathway

This study identifies how Yersinia pseudotuberculosis uses YopE and YopH to inhibit neutrophil degranulation and ROS production through distinct pathways.

TriPort tangential flow filtration: a lab-assembled system for EV isolation across diverse cell-culture sources

The paper describes a low-cost, lab-assembled TFF system for EV isolation from diverse cell culture sources and evaluates its performance with and without SEC.

Protein secretion by the type IV pilus machinery in Francisella tularensis

This study identifies proteins secreted by Francisella tularensis using BONCAT and proteomics, validating T4P-mediated secretion of ChiA, ChiD, and KatG.