Human retina can achieve single-photon sensitivity through specialised photoreceptors that convert light into electrical signals via phototransduction. Among microbial light-sensitive proteins, proteorhodopsins stand out for their intrinsic light-driven ion transport and spectral tunability, making them promising candidates for bio-inspired photonic devices. A central challenge for acellular integration, however, is the fragility of most bacterial rhodopsins […]
Carbamylome analysis reveals regulatory roles for lysine carbamylation in β-cell glycolytic and insulin-processing enzymes
In type 1 diabetes (T1D), insulin-producing beta cells are destroyed by an autoimmune response driven by pro-inflammatory cytokines, including interferons. beta-cell cytokine signaling is mediated in part by post-translational modifications, such as phosphorylation and acetylation. However, the role of other post-translational modifications in beta-cell cytokine signaling represents an important knowledge gap. In the context of […]
Comprehensive characterization of skeletal muscle remodeling in hSOD1G93A mice reveals limited functional impact of systemic FOXO1 inhibition
Background Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron (MN) loss, muscle atrophy and paralysis. Although traditionally considered a MN-specific disease, accumulating evidence supports a crucial contribution of skeletal muscle pathology to disease onset and progression. Except for specific mutations, to date there is no effective treatment for ALS. […]
Instance-Wise Contrastive Graph Neural Network Enables the Discovery of Novel Aedes aegypti Larvicidal Compounds
Aedes aegypti remains a major arboviral vector, making larval control a critical strategy to reduce mosquito populations. However, resistance to commercial larvicides has reduced the long-term effectiveness of current interventions, reinforcing the need for new compounds with improved potency and selectivity. Here, we present an instance-wise contrastive graph neural network (GNN) framework to accelerate the […]
Detection of Pancreatic Cancer Using a Methylation-Specific PCR-Based Multi-Cancer Early Detection Test
Context: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy often diagnosed at advanced stages due to the lack of early clinical symptoms. DNA methylation alterations arise early in PDAC tumorigenesis and may serve as promising biomarkers for blood-based cancer detection. Objective: To evaluate the performance of EPISEEK, a laboratory-developed blood-based multi-cancer early detection (MCED) assay, […]
LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery
Most human genes produce multiple RNA isoforms, yet it remains unclear which isoforms are translated into stable, functional proteins. Long-read RNA-sequencing resolves full-length transcript structures and, when paired with mass spectrometry, can provide empirical evidence of isoform translation. Despite this opportunity, comprehensive workflows integrating isoform discovery, open reading frame prediction, peptide identification, and protein inference […]
Osteopontin Upregulation Defines a Pre-Rupture State in Thoracic Aortic Aneurysms in Mice and Humans
Background: Thoracic aortic aneurysm (TAA) is a life-threatening condition with an unpredictable lisk of rupture. Current clinical parameters have limited ability to accurately predict imminent rupture. Osteopontin (OPN) has been implicated in aortic aneurysm pathology, however, it role as a marker of imminent rupture remains. unclear. We investigated the dynamics of OPN expression dynamics in […]
Analytical Choices Drive Toxicogenomic Potency Estimates: A Systematic Evaluation of Transcriptomic Points of Departure
Omics technologies are increasingly integrated into next-generation risk assessment, yet quantitative toxicogenomics outcomes remain highly dependent on analytical choices, motivating a systematic evaluation of how bioinformatics workflows influence hazard characterization and transcriptomic Points of Departure (tPOD). Here, we applied five independent transcriptomics pipelines to a shared dataset of RPTEC-TERT1 kidney cells exposed to cisplatin across […]
GAPVD1 regulates CSNK1D-dependent PER2 FASP phosphorylation
The mammalian circadian clock relies on precisely timed transcriptional and post-translational events to generate ~24-hour rhythms. A key post-translational mechanism is phosphorylation of PER2 by CSNK1D, governed by a phosphoswitch that integrates stabilizing and destabilizing phosphorylation marks at the FASP and Degron sites to control PER2 stability and circadian period. Here, a novel role for […]
Decoding Hierarchical Cell-Cell Communication in Spatial Multi-Omics with CellSTIC
Cell-cell communication helps to coordinate tissue development, homeostasis, and immune responses, but identifying signaling interactions within intact tissues remains difficult. Although single-cell transcriptomics has enabled systematic inference of ligand-receptor interactions, dissociation disrupts spatial context and limits the identification of bona fide local signaling and region-specific communication programs. Spatial transcriptomics and spatial multi-omics offer the opportunity […]
Organoid-T cell co-cultures functionally stratify tumor-reactive T cells and their responses to immune checkpoint inhibitors
Tumor-reactive T cells (TRTs) are critical for anti-tumor immunity but are incompletely captured by current assays, which fail to reproduce tumor-specific antigen diversity. Here, we show that multiplex functional profiling of patient-derived tumor organoid-T cell co-cultures (PDOTs) enables robust identification of TRTs across CD8, CD4, and double-negative (DN) T cell populations. Single activation markers underestimated […]
Antibody maturation increases rigidity in protein-contacting regions and flexibility at glycan interfaces
Antibody design is a challenging task that could be improved by understanding the conformational changes accompanying affinity maturation. Antibody maturation is a critical immune system process by which antibodies gain mutations that improve affinity and specificity for antigen targets. However, how these mutations change antibody dynamics, specifically whether antibodies become more rigid as they mature, […]