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SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues.
Genome Biol
January 2025
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, 90095, CA, USA.
Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specializations. Applied to retina, brain, and embryonic tissue maps, SMORE identifies novel spatial motifs, including one that offers a new mechanism of action for type 1b bipolar cells.
View Article and Find Full Text PDFStructural basis of human VANGL-PRICKLE interaction.
Nat Commun
January 2025
State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Planar cell polarity (PCP) is an evolutionarily conserved process for development and morphogenesis in metazoans. The well-organized polarity pattern in cells is established by the asymmetric distribution of two core protein complexes on opposite sides of the cell membrane. The Van Gogh-like (VANGL)-PRICKLE (PK) pair is one of these two key regulators; however, their structural information and detailed functions have been unclear.
View Article and Find Full Text PDFDeciphering the fate of replication-induced DNA double-strand breaks.
Mol Cell
January 2025
Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
In this issue of Molecular Cell, studies by Xu et al., Kimble et al., and Elango et al.
View Article and Find Full Text PDFBasic Science and Pathogenesis.
Alzheimers Dement
December 2024
University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Background: The human brain is a complex inter-wired system that emerges spontaneous functional fluctuations. In spite of tremendous success in the experimental neuroscience field, a system-level understanding of how brain anatomy supports various neural activities remains elusive.
Method: Capitalizing on the unprecedented amount of neuroimaging data, we present a physics-informed deep model to uncover the coupling mechanism between brain structure and function through the lens of data geometry that is rooted in the widespread wiring topology of connections between distant brain regions.
Deciphering network dysregulations and temporo-spatial dynamics in disorders of consciousness: insights from minimum spanning tree analysis.
Front Psychol
December 2024
Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
Objectives: The neural mechanism associated with impaired consciousness is not fully clear. We aim to explore the association between static and dynamic minimum spanning tree (MST) characteristics and neural mechanism underlying impaired consciousness.
Methods: MSTs were constructed based on full-length functional magnetic resonance imaging (fMRI) signals and fMRI signal segments within each time window.
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