proteomics

How to design 1000-plex mass tags using the differential mass defect

This paper explores designing high-plex mass tags using differential mass defect to enable large-scale multiplexing in proteomics.

β-cyclocitral elicits rapid signaling distinct from the excess-light response in Arabidopsis

This study shows that β-cyclocitral triggers rapid cellular responses in Arabidopsis, distinct from the delayed transcriptional changes associated with excess light stress.

Ribosome-Associated GTPase Drg1 Links Cytosolic Translation to Mitochondrial Homeostasis

This study identifies Drg1 as a ribosome-associated GTPase that links cytosolic translation to mitochondrial homeostasis by supporting the synthesis of mitochondrial proteins.

An intrinsically disordered proline-rich domain acts in synergy with AGP-type glycosylation to control the protein fate of FLA4

This study shows that a proline-rich domain and AGP-type glycosylation work together to control FLA4 protein stability and localization.

Informatics Methods to Enhance Bacterial Peptide Detection

The paper develops and benchmarks an in silico spectral library workflow to detect low-abundance bacterial peptides in human-dominated samples, finding it has complementary performance to conventional database searches.

Fully integrative species delimitation with machine learning and diverse data types in delimSOM 2.0

delimSOM 2.0 integrates diverse data types using machine learning to improve species delimitation, showing strong performance with larger samples and robustness to missing data.

Achieving near single-molecule sensitivity in separation-free protein detection using engineered kinetic proofreading

This paper introduces SPEAR, a separation-free protein detection method that achieves sub-100-molecule sensitivity using engineered kinetic proofreading, outperforming existing methods for Alzheimer's and SARS-CoV-2 biomarkers.

An Optimized Stem Cell Secretome Proteomics Platform: Application to Progranulin-Deficient iPSCs

This paper optimizes a secretome proteomics platform for iPSCs and applies it to study progranulin deficiency's effects on extracellular and intracellular proteomes.

NEK1 autophosphorylation is disrupted by amyotrophic lateral sclerosis-associated missense variants: activity biomarkers and structural insights

Kinase-dead controls, XIC quantification and phosphospecific antibodies establish pSer14, pThr156 and pSer418 as NEK1 autophosphorylation sites; a pThr156 assay shows ALS missense variants differ, with R261C reducing it most.

Proteomes reflect size-based growth constraints across diverse microbes

The paper uses proteomic data to show that microbial growth rates are constrained by size-related factors, with intermediate-sized cells having the highest growth potential.

In-Depth Immune Profiling Reveals Cell-Type, Sex and Infection-Stage Dependent Differences for Tuberculosis Control

This study profiles the immune environment in male and female mice following TB infection and vaccination, identifying sex-specific immune markers and known protective responses.

Comparative proteomic quantification reveals novel longevity regulators

The paper compares five quantitative proteomic methods to identify high-confidence longevity regulators in C. elegans by analyzing IIS mutants.

Endothelial Cell Secretome Alterations Induced by Inflammatory Stress

This study identifies conventionally and unconventionally secreted proteins from HUVECs under inflammatory stress, revealing novel UCPS cargo and their functional roles.

Herpes simplex virus pUL56 abolishes neuronal activity by removing voltage-gated ion channels from the plasma membrane

This study identifies HSV-1 protein pUL56 as responsible for removing voltage-gated ion channels from neuronal plasma membranes, disrupting calcium signaling and neuronal activity.

Basal Ganglia Dopamine Availability and Immune Activation Interact and Relate to Anhedonia Severity among Youth with Depression

This study examines how dopamine availability and immune activation interact to influence anhedonia severity in youth with depression.

Intrinsic IL-6 expression reduces rhIL-6-induced JAK/STAT activation and promotes glucose and oleic acid oxidation in cultured human myoblasts

Synaptic synergy of T cell receptor and interleukin 2 receptor in CD8+ T cells

The paper shows that TCR and IL2 receptor signaling synergize at the immunological synapse of CD8+ T cells, enhancing T-T synapse formation and function.

Inter-strain diversity among coastal picocyanobacteria across salinity gradients

The paper examines how picocyanobacterial strains from different salinities adapt their growth and metabolism across varying salinity and light conditions.

Human CD4 T cells coordinate antitumor immunity through indirect antigen presentation

This study shows human CD4 T cells can drive antitumor immunity in MHC class II-negative cancers through indirect antigen presentation via APCs.

Sphingolipid-Driven Lipotoxicity Promotes Calcific Aortic Valve Disease Through ER-Stress-NF-κB-EndMT Signaling and Is Therapeutically Targetable Through Serine Palmitoyltransferase Inhibition

This study identifies ceramide-driven lipotoxicity as a driver of calcific aortic valve disease and shows that SPT inhibition can reverse disease progression in vivo.

Conserved RGF1 peptide signaling regulates root meristem development through ROS in Arabidopsis and rice

This study shows that RGF1 peptide signaling via ROS regulates root meristem development in Arabidopsis and rice, with conserved function across dicots and monocots.

A bistable UV-sensitive opsin from a reef building coral showing a switchable and tunable regulation of Gs-signaling by different wavelengths of light

The paper characterizes and engineers a bistable cnidopsin from a coral that can switch between states using different light wavelengths, showing potential as an optogenetic tool for regulating Gs-signaling.

A First-in-Class, Brain-Penetrant Small Molecule Inhibitor of the NOS1AP-Tau Interaction Rescues Tau Pathology In Vivo and Improves Cognition

CAPTOR-1, a small molecule inhibitor of NOS1AP-tau interaction, reduces tau pathology and improves cognition in AD models.

Identification of Expressed Endogenous Retroviral Element Associated Long Terminal Repeats in Devil Facial Tumour Cells

The paper identifies expressed endogenous retroviral element long terminal repeats (ERV LTRs) in devil facial tumour cells and validates them as potential vaccine targets.

sORF-Trans2MS: a two-module deep learning framework for sORF translation and MS-supported microprotein prediction

sORF-Trans2MS is a two-module deep learning framework that predicts Ribo-supported sORFs and MS-supported microproteins, improving prediction and extending discovery to underrepresented candidates.

A tonic PDGFA-dependent niche organizer maintains alveolar homeostasis

This study identifies PDGFA-expressing alveolar type 1 cells as a tonic niche organizer that maintains alveolar homeostasis by restraining fibroblast activation and promoting tissue repair.

A broadly conserved phytoplasma α/β-hydrolase effector, SGP-7, is a catalytically active esterase that hydrolyses strigolactone analogues and alters shoot architecture

This paper identifies SGP-7, a phytoplasma effector with esterase activity that hydrolyzes strigolactone analogues and alters plant shoot architecture.

Diet-conditioned microbiota enhances fecal microbiota transplantation efficacy in alcoholic liver disease through caproic acid-PPARα signaling

This study shows that a high-protein donor diet enhances fecal microbiota transplantation efficacy in alcoholic liver disease by increasing caproic acid and PPARα signaling.

Interferon-induced OASL restricts ADAR1 p150 RNA binding and A-to-I RNA editing

This study identifies OASL as an inhibitor of ADAR1 p150, showing it limits RNA binding and A-to-I editing while modulating antiviral immunity.

lisaR: An LLM-Inferred Semantic Annotation of biological categories for gene set enrichment analysis

lisaR organizes gene set enrichment analysis results into semantic categories using LLM-inferred dictionaries, improving interpretability of biological findings.