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Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways.
Brief Bioinform
November 2024
School of Artificial Intelligence, Jilin University, Qianjin Street 2699, 130010 Changchun, China.
Imaging-based spatial transcriptomics (iST), such as MERFISH, CosMx SMI, and Xenium, quantify gene expression level across cells in space, but more importantly, they directly reveal the subcellular distribution of RNA transcripts at the single-molecule resolution. The subcellular localization of RNA molecules plays a crucial role in the compartmentalization-dependent regulation of genes within individual cells. Understanding the intracellular spatial distribution of RNA for a particular cell type thus not only improves the characterization of cell identity but also is of paramount importance in elucidating unique subcellular regulatory mechanisms specific to the cell type.
View Article and Find Full Text PDFTranscriptomic insight into zinc dependency of vindoline accumulation in Catharanthus roseus leaves: relevance and potential role of a CrZIP.
Plant Cell Rep
January 2025
CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, Uttar Pradesh, India.
Foliar-applied Zn on Catharanthus roseus enhanced production of vindoline, the main impediment precursor for costly anticancer bisindoles. A leaf-abundant CrZIP was characterized for likely role in modulating vindoline metabolism. The leaf-localized Catharanthus roseus alkaloid, vindoline, is the major impediment precursor in the production of scanty and expensive anticancer bisindoles, vinblastine and vincristine.
View Article and Find Full Text PDFSynaptic enrichment and dynamic regulation of the two opposing dopamine receptors within the same neurons.
Elife
January 2025
Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
Dopamine can play opposing physiological roles depending on the receptor subtype. In the fruit fly , and encode the D- and D-like receptors, respectively, and are reported to oppositely regulate intracellular cAMP levels. Here, we profiled the expression and subcellular localization of endogenous Dop1R1 and Dop2R in specific cell types in the mushroom body circuit.
View Article and Find Full Text PDFSingle-organelle visualization tracking natural glycosaminoglycans within mitochondria-lysosome crosstalk for inflammatory homeostasis.
Int J Biol Macromol
January 2025
School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, Shandong 266237, China. Electronic address:
Glycosaminoglycans (GAGs), as natural products with diverse biological activities, play a significant role in regulating inflammatory homeostasis. Nevertheless, the mechanism underlying their intracellular anti-inflammatory properties remains unclear. Herein, we propose a single-organelle visualization tracking framework, leveraging an advanced fluorescent imaging technology combined with labeling methods to dynamically trace the subcellular regulatory mechanisms of GAGs in eliminating inflammatory markers, such as reactive oxygen species (ROS).
View Article and Find Full Text PDFThe Shab family potassium channels are highly enriched at the presynaptic terminals of human neurons.
J Biol Chem
January 2025
Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; Molecular, Cellular & Integrated Neurosciences, Colorado State University, Fort Collins, CO 80523, USA; Cell & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA. Electronic address:
The Shab family voltage-gated K channels (i.e., Kv2.
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