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In aquaculture nutrition, alternative protein sources, such as those derived from bacteria, have recently garnered significant attention as safe and viable replacements for traditional protein sources, including fish meal (FM) and soybean meal (SBM). This …
Read PDFThe rhopalium, an early specialized centralized nervous structure in medusozoans, exhibits a remarkable regenerative capacity after removal, offering a unique model for investigating the ancestral regulatory logic of neural regeneration. However, the cellular and molecular …
Read PDFAlzheimer's disease (AD) progression involves complex molecular interactions across multiple biological layers, yet integrating high-dimensional single-cell multi-omics data remains computationally challenging. While Graph Convolutional Networks (GCNs) effectively model cell-gene interaction topologies, they face three critical …
Read PDFColorectal cancer (CRC) presents considerable therapeutic challenges due to its diverse cellular composition and intricate microenvironment. Our study utilized single-cell RNA sequencing (scRNA-seq) on CRC tissues, examining 18,741 individual cells, which were grouped into six …
Read PDFFunctional imaging using genetically encoded indicators (GEIs) allows researchers to understand neuronal-, circuit-, and organism-level mechanisms that govern sensory processing and brain function. Here, we present a protocol to extract calcium signals and significant changes …
Read PDFCurrent single-cell RNA sequencing (scRNA-seq) methods suffer from biases that restrict the detection of cellular transcripts to 10-40% of total RNAs. This hinders the identification of transcripts of interest. Additionally, information retrieved from most high-throughput …
Read PDFThe metabolic activity of stallion spermatozoa was assessed using flow cytometry to detect NAD(P)H and FAD fluorescence without labels. Sperm were incubated with different energy sources-glucose, lactate, and pyruvate-individually or combined, and measurements of NAD(P)H, …
Read PDFChronic neuroinflammation driven by activated microglia is a critical hallmark of Alzheimer's disease (AD) progression. Metabolic dysregulation, particularly iron metabolism, has been implicated in neurodegeneration, yet the role of iron-responsive element-binding protein 2 (IREB2) in …
Read PDFTooth development is a continuous, highly orchestrated process that serves as an ideal model for dissecting the cellular and molecular mechanisms of organogenesis. In recent years, advances in single-cell transcriptomics have provided unprecedented insights into …
Read PDFCellular heterogeneity is an inherent feature of biological systems, and living single-cell metabolomics (SCM) has emerged as a powerful approach to probe this diversity-a dimension often lost in conventional bulk analyses. Currently, mass spectrometry (MS)-based …
Read PDFSingle-cell omics data are high-dimensional, sparse, and noisy, and learning embeddings that simultaneously preserve local cell-state structure, global hierarchy, and smooth developmental trajectories remains an open problem. Existing approaches typically achieve only one of these …
Read PDFIntratumoral heterogeneity complicates the interpretation of single-test biomarkers. Microsatellite instability (MSI) is one such biomarker, which is used to guide immune checkpoint inhibitor treatment by classifying samples as having high microsatellite instability (MSI-H) or as …
Read PDFSenescent cells accumulate with age following stress-induced cell cycle arrest triggered by DNA damage, oncogene activation, and replicative exhaustion. While they contribute to tissue repair and tumor suppression, their persistent senescence-associated secretory phenotypes (SASPs) drive …
Read PDF<h4>Background</h4>Radiotherapy resistance limits colorectal cancer (CRC) treatment efficacy, with only 15%-20% of patients achieving a complete response. Validated biomarkers predicting treatment response and serving as therapeutic targets are critically needed.<h4>Methods</h4>We performed integrative multiomics analysis of …
Read PDFVibrational frequency profiling (VFP) using optical tweezers has emerged as a promising technique to characterize single-cell behavior for diagnostic applications. These applications include cancer screening, identifying bacterial resistance to antibiotics, and assessing cellular response to …
Read PDFPancreatitis constitutes a serious global health challenge characterized by a multicellular pathogenesis and limited therapeutic options. The recent discovery of different cellular pathogenic mechanisms and the emerging effectiveness of nanotechnology-based, cell-targeted therapies have provided promising …
Read PDFSingle-cell ATAC-seq (scATAC-seq) enables the interrogation of chromatin accessibility at cellular resolution, yet its practical utility is often constrained by limited sequencing depth, extreme sparsity, and pervasive technical missingness, which collectively hamper robust cell-state delineation …
Read PDFBACKGROUND: Intracerebral hemorrhage (ICH) lacks effective neuroprotective therapies. We integrated cell type–resolved genetic inference with single-cell profiling to map putative causal programs and multicellular circuitry relevant to ICH. METHODS: Cis-eQTLs from eight human brain cell …
Read PDFData preprocessing is critical for single-cell omics analyses, but default pipelines often underperform on diverse datasets, especially from emerging platforms like spatial transcriptomics. We introduce Lense, a language-model-guided method that automatically selects optimal preprocessing by …
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