Nonenzymatic template-directed copying of RNA sequences rich in cytidylic acid using nucleoside 5'-(2-methylimidazol-1-yl phosphates) as substrates is substantially more efficient than the copying of corresponding DNA sequences. However, many sequences cannot be copied, and the prospect of replication in this system is remote, even for RNA. Surprisingly, wobble-pairing leads to much more efficient incorporation of G opposite U on RNA templates than of G opposite T on DNA templates.
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http://dx.doi.org/10.1002/1522-2675(20000809)83:8<1678::AID-HLCA1678>3.0.CO;2-P | DOI Listing |
Cell clustering is an essential step in uncovering cellular architectures in single cell RNA-sequencing (scRNA-seq) data. However, the existing cell clustering approaches are not well designed to dissect complex structures of cellular landscapes at a finer resolution. Here, we develop a multi-scale clustering (MSC) approach to construct sparse cell-cell correlation network for identifying de novo cell types and subtypes at multiscale resolution in an unsupervised manner.
View Article and Find Full Text PDFImaging-based spatial transcriptomics (ST) is evolving rapidly as a pivotal technology in studying the biology of tumors and their associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. In this study, we used serial 5-m sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma tumor samples in tissue microarrays to compare the performance of the single cell ST platforms CosMx, MERFISH, and Xenium (uni/multi-modal) platforms in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx Digital Spatial Profiler, and hematoxylin and eosin staining data for the same samples.
View Article and Find Full Text PDF, the causative agent of zoonotic toxocariasis in humans, is a parasitic roundworm of canids with a complex lifecycle. While macrocyclic lactones (MLs) are successful at treating adult infections when used at FDA-approved doses in dogs, they fail to kill somatic third-stage larvae. In this study, we profiled the transcriptome of third-stage larvae derived from larvated eggs and treated with 10 µM of the MLs - ivermectin and moxidectin with Illumina sequencing.
View Article and Find Full Text PDFPlant Cell Environ
January 2025
State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
Allohexaploid wheat (Triticum aestivum L.) is one of the major crops worldwide, however there is very limited research on the transcriptional programmes of underlying cell type specification. Single-cell RNA sequencing (scRNA-seq) was used to unravel the transcriptome heterogeneity of cells and the composition of cell types in broad-spectrum organisms.
View Article and Find Full Text PDFJ Transl Med
January 2025
Tumour Biology and Immunology Laboratory, Research Branch, Sidra Medicine, Doha, Qatar.
Background: FFPE tissue samples are commonly used in biomedical research and are a valuable source for next-generation sequencing in oncology, however, extracting RNA from these samples can be difficult the quantity and quality achieved can impact the downstream analysis. This study compared the effectiveness of seven different commercially available RNA extraction kits specifically designed for use with FFPE samples in terms of the quantity and quality of RNA recovered.
Methods: This study used 9 samples of FFPE tissue from three different types of tissue (Tonsil, Appendix and lymph node of B-cell lymphoma) to evaluate RNA extraction methods.
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