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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 PDFExploring the plant lipidome: techniques, challenges, and prospects.
Adv Biotechnol (Singap)
March 2024
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
Plant lipids are a diverse group of biomolecules that play essential roles in plant architecture, physiology, and signaling. To advance our understanding of plant biology and facilitate innovations in plant-based product development, we must have precise methods for the comprehensive analysis of plant lipids. Here, we present a comprehensive overview of current research investigating plant lipids, including their structures, metabolism, and functions.
View Article and Find Full Text PDFUncovering novel KCC2 regulatory motifs through a comprehensive transposon-based mutant library.
Front Mol Neurosci
January 2025
Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland.
Introduction: The neuron-specific K-Cl cotransporter KCC2 maintains low intracellular chloride levels, which are crucial for fast GABAergic and glycinergic neurotransmission. KCC2 also plays a pivotal role in the development of excitatory glutamatergic neurotransmission by promoting dendritic spine maturation. The cytoplasmic C-terminal domain (KCC2-CTD) plays a critical regulatory role in the molecular mechanisms controlling the cotransporter activity through dimerization, phosphorylation, and protein interaction.
View Article and Find Full Text PDFApelin/APJ system: a novel promising target for anti-oxidative stress in stroke.
Front Pharmacol
January 2025
Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
The apelin/APJ system has garnered increasing attention in recent years. In this review, we comprehensively discuss the physiological and pathological mechanisms of the apelin/APJ system in stroke. The apelin/APJ system is widely expressed in the central nervous system (CNS).
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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