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Spatially resolved transcriptomics (SRT) is a promising new technology that enables simultaneous analysis of gene expression and spatial information for biomedical research. However, the existing statistical and deep learning algorithms used for analyzing SRT data …
Read PDFPoplar (<i>Populus</i> spp.) has a short growth cycle and considerable economic value. Also, it is highly susceptible to various diseases. Of these, the canker disease has a significant impact on the health and productivity of …
Read PDFMonoterpene indole alkaloids encompass a diverse class of plant natural products. Many of these valuable compounds, including the anticancer medicines vinblastine and vincristine (<i>Catharanthus roseus</i>) and the antiaddiction treatment ibogaine (<i>Tabernanthe iboga</i>) utilize a common …
Read PDFChloromethane, a toxic gas primarily produced naturally, contributes to stratospheric ozone destruction. The anaerobic acetogen Acetobacterium dehalogenans can utilise chloromethane as a carbon and energy source, but the associated dehalogenase/methyltransferase has remained elusive. Through comparative …
Read PDF<h4>Introduction and aims</h4>Oral lichen planus (OLP) is a chronic inflammatory disease of unknown etiology. Recent studies have implicated microbial dysbiosis in its pathogenesis. Our previous research revealed an increased abundance of Fusobacterium nucleatum (F.nucleatum) in …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) exhibits pronounced spatial heterogeneity that limits therapeutic efficacy. The contribution of epithelial-mesenchymal transition (EMT) to regional tumor progression and immune evasion remains incompletely understood.<h4>Methods</h4>We integrated bulk transcriptomic datasets (TCGA, GSE14520), 34 single-cell …
Read PDFExocrine glands have evolved several times independently in Coleoptera to produce defensive chemical compounds with repellent, antimicrobial, or toxic effects. Research on such glands had focused on morphological or chemical ecology methods. However, modern genetic …
Read PDFCells are organized to form three-dimensional structures of complex tissues. To map the complete 3D organization of a tissue, technologies based on tissue microdissections provide deep bulk RNA sequencing of orthogonally arranged cryosections of a …
Read PDFThe intestinal microbiota influences host susceptibility to <i>Campylobacter jejuni</i> (<i>C. jejuni</i>) infection. However, the interaction between specific intestinal bacteria and the <i>C. jejuni-</i>mediated host response is unclear. We established a defined consortium of bacteria to …
Read PDFSpatial transcriptomics (ST) measures gene expression at a set of spatial locations in a tissue. Communities of nearby cells that express similar genes form spatial domains. Specialized clustering algorithms have been developed to identify spatial …
Read PDFExtensive studies have shown that cerebrovascular dysfunction is a critical factor in the onset and progression of Alzheimer's disease (AD). Neurovascular unit (NVU) is impaired in AD brains, including damage of tight junction between endothelial …
Read PDFCancer is the leading cause of death around the world. While some types of cancer have become manageable due to advancements in medicine, most cancers still lack available cures and treatments. Recent studies have shown …
Read PDFMyalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system disease characterized by a multitude of symptoms across various organ systems. Diagnosis has relied heavily on heterogeneous clinical symptom presentation and evolving case definitions, with treatment …
Read PDF<h4>Objective</h4>The main goal of this study is to explore the link between herpes simplex virus 1 (HSV-1) infection and Parkinson's disease (PD) from the genome-wide association studies (GWAS) data and find the shared molecular signature …
Read PDF<h4>Background</h4>Colorectal cancer (CRC) is a heterogeneous malignancy shaped by genetic alterations and immune microenvironmental interactions. While single-cell RNA sequencing (scRNA-seq) has uncovered diverse epithelial and T cell subsets, the spatial architecture of their crosstalk remains …
Read PDFRNA velocity provides a powerful scope for understanding cell state dynamics by modeling spliced and unspliced mRNA captured by single-cell or spatial transcriptomic technologies. However, prevailing methods relying on restrictive kinetic assumptions often fail in …
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