Nitrile-containing natural products are produced in all kingdoms of life. Despite the wide application of nitrile-containing peptide scaffolds in medicinal chemistry, the presence of the nitrile group is unprecedented in ribosomally synthesized and post-translationally modified peptides (RiPPs). In this work, we report the identification and characterization of a RiPP biosynthetic gene cluster (BGC), where an […]
PHGDH is a targetable driver of PDAC progression
Pancreatic ductal adenocarcinoma (PDAC) arises in a nutrient-deprived microenvironment through progressive stages from pancreatic intraepithelial neoplasia (PanIN) to invasive carcinoma. While serine metabolism supports tumor growth across multiple cancer types, the stage-specific role of de novo serine synthesis in PDAC evolution remains undefined. Here, we show that expression of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme […]
Differential chromatin looping regulated by two GA-binding transcription factors creates an X-specific chromatin environment for dosage compensation
The mechanisms by which differential occupancy of transcription factors (TFs) at similar binding sites leads to context-specific targeting of large transcription complexes remain poorly understood. X chromosome upregulation (XCU), the most highly conserved step in dosage compensation and best studied in Drosophila, serves as a model for understanding how differential occupancy of similar TFs functions […]
APOE4 Accelerates Menopause-Associated Brain Metabolic Shift and Disrupts Bioenergetic Adaptation
Introduction Disruption of brain glucose and lipid metabolism contributes to Alzheimer’s disease (AD) and often emerges before clinical symptoms. Women are at elevated AD risk due to menopause-associated estrogen decline, which impairs mitochondrial function and glucose metabolism. Women’s risk of AD is further elevated by the APOE4 allele, the strongest genetic risk factor for late-onset […]
AI literacy mediates AI assisted diagnosis participation and critical thinking among medical students under supervision
npj Digital Medicine, Published online: 14 March 2026; doi:10.1038/s41746-026-02521-9 AI literacy mediates AI assisted diagnosis participation and critical thinking among medical students under supervision
HiFi-Helper: A reproducible workflow for genome assembly from HiFi reads alone
The PacBio Revio simplifies genome assembly by generating very long reads with very few errors at an affordable price point. Comparative ease of assembly is democratizing access, leading to a larger niche for assembly workflows. HiFi-Helper is a user-friendly snakemake workflow designed to facilitate genome assembly from HiFi data alone. This tool produces a visual […]
Assessment of adult structural plasticity in Drosophila neurons
Unraveling how adult neurons reshape their architecture is key to understanding post-developmental plasticity. Drosophila clock neurons, which remodel their terminals on a daily basis, offer a unique model to examine the mechanisms underlying structural plasticity. In this study, we examine the impact of the experimental design on the remodeling process. We established a simple fixation […]
DisGeneFormer: Precise Disease Gene Prioritization by Integrating Local and Global Graph Attention
Identifying genes associated with human diseases is essential for effective diagnosis and treatment. Experimentally identifying disease-causing genes is time-consuming and expensive. Computational prioritization methods aim to streamline this process by ranking genes based on their likelihood of association with a given disease. However, existing methods often report long ranked lists consisting of thousands of potential […]
Altered Cardiac Neural Crest Migration Patterning in a Left Atrial Ligation Model of Hypoplastic Left Heart Syndrome
Cardiac neural crest cells (CNCCs) contribute to key cardiac structures during embryonic development. Disruption of CNCC patterning or function can lead to congenital heart defects. Here, we investigate whether hemodynamic perturbation alters CNCC behavior in chick embryos. We use the left atrial ligation model to modify intracardiac blood flow in the early common-atrium, common-ventricle heart […]
A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data
Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of these footprints creates substantial nonspecific mapping against large reference genome collections, leading to spurious taxonomic and functional assignments. Here we present MOPP (Multi-Omics Processing Pipeline), a modular reference-based workflow that denoises metaRibo-Seq data […]
Experimental Data Driven AI Framework for Flexible Protein Conformational Reconstruction
Deep learning has revolutionized structural biology by prediction with near experimental accuracy static protein folds from amino acid sequence alone. However, proteins function as dynamic ensembles of protein conformation states, and current sequence-only models often fail to capture the specific conformational states and heterogeneity dictated by cellular environments or ligand binding. While recent generative models […]
Chronic exposure to low-concentration urban PM2.5 accelerates maladaptive repair after ischemic injury via mitochondrial dysfunction and lysosomal stress.
Background: Long-term exposure to fine particulate matter (PM2.5) is increasingly recognized as a risk factor for chronic kidney disease (CKD). We previously demonstrated that high-dose PM2.5 exposure prior to ischemia/reperfusion injury (IRI) aggravates acute kidney injury (AKI). Here, we investigated how prolonged, low concentration urban PM2.5 exposure affects kidney repair after AKI. Methods: Six-week-old mice […]