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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 PDFSubcellular mitochondrial heterogeneity enables opposing metabolic demands.
Trends Endocrinol Metab
January 2025
Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:
Mitochondria perform essential metabolic processes that sustain cellular bioenergetics and biosynthesis. In a recent article, Ryu et al. explored how mitochondria coordinate biochemical reactions with opposing redox demands within the same cell.
View Article and Find Full Text PDFMouse-derived Synaptosomes Trypsin Cleavage Assay to Characterize Synaptic Protein Sub-localization.
Bio Protoc
January 2025
Department of Structural Interactomics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
Neurons communicate through neurotransmission at highly specialized junctions called synapses. Each neuron forms numerous synaptic connections, consisting of presynaptic and postsynaptic terminals. Upon the arrival of an action potential, neurotransmitters are released from the presynaptic site and diffuse across the synaptic cleft to bind specialized receptors at the postsynaptic terminal.
View Article and Find Full Text PDFAsGAD1 cloned from creeping bentgrass modulates cadmium tolerance of Arabidopsis thaliana by remodelling membrane lipids and cadmium uptake, transport and chelation.
Physiol Plant
January 2025
College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
The gene GAD1 encodes a glutamate decarboxylase, which is a rate-limiting enzyme for the biosynthesis of endogenous γ-aminobutyrate acid (GABA), but a potential role of GAD1 in regulating cadmium (Cd) tolerance needs to be further elucidated in plants. The objective of this study was to investigate Cd tolerance of creeping bentgrass (Agrostis stolonifera) and transgenic yeast (Saccharomyces cerevisiae) or Arabidopsis thaliana overexpressing AsGAD1. The Cd-tolerant creeping bentgrass cultivar LOFTSL-93 accumulated more endogenous GABA in relation to a significant upregulation of AsGAD1 in leaf and root than the Cd-sensitive W66569 in response to Cd stress.
View Article and Find Full Text PDFCell-free systems: A synthetic biology tool for rapid prototyping in metabolic engineering.
Biotechnol Adv
January 2025
Division of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea. Electronic address:
Microbial cell factories provide sustainable alternatives to petroleum-based chemical production using cost-effective substrates. A deep understanding of their metabolism is essential to harness their potential along with continuous efforts to improve productivity and yield. However, the construction and evaluation of numerous genetic variants are time-consuming and labor-intensive.
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