Collective cell dynamics is essential for tissue morphogenesis and various biological functions. However, it remains incompletely understood how mechanical forces and chemical signaling are integrated to direct collective cell behaviors underlying tissue morphogenesis. Here, we propose a three-dimensional (3D) mechanochemical theory accounting for biochemical reaction-diffusion and cellular mechanotransduction to investigate the dynamics of multicellular lumens. We show that the interplay between biochemical signaling and mechanics can trigger either pitchfork or Hopf bifurcation to induce diverse static mechanochemical patterns or generate oscillations with multiple modes both involving marked mechanical deformations in lumens. We uncover the crucial role of mechanochemical feedback in emerging morphodynamics and identify the evolution and morphogenetic functions of hierarchical topological defects including cell-level hexatic defects and tissue-level orientational defects. Our theory captures the common mechanochemical traits of collective dynamics observed in experiments and could provide a mechanistic context for understanding morphological symmetry breaking in 3D lumen-like tissues.
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http://dx.doi.org/10.1126/sciadv.adn0172 | DOI Listing |
Med Image Anal
January 2025
Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands; Amsterdam University Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
Histopathological analysis of whole slide images (WSIs) has seen a surge in the utilization of deep learning methods, particularly Convolutional Neural Networks (CNNs). However, CNNs often fail to capture the intricate spatial dependencies inherent in WSIs. Graph Neural Networks (GNNs) present a promising alternative, adept at directly modeling pairwise interactions and effectively discerning the topological tissue and cellular structures within WSIs.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China.
Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance. In this study, we investigate the potential role of RNA-binding proteins (RBPs) in TAD organization.
View Article and Find Full Text PDFEnviron Monit Assess
January 2025
School of Mathematical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia.
This study investigates the effectiveness and efficiency of two topological data analysis (TDA) techniques, the conventional Mapper (CM) and its variant version, the Ball Mapper (BM), in analyzing the behavior of six major air pollutants (NO, PM, PM, O, CO, and SO) across 60 air quality monitoring stations in Malaysia. Topological graphs produced by CM and BM reveal redundant monitoring stations and geographical relationships corresponding to air pollutant behavior, providing better visualization than traditional hierarchical clustering. Additionally, a comparative analysis of topological graph structures was conducted using node degree distribution, topological graph indices, and Dynamic Time Warping (DTW) to evaluate the sensitivity and performance of these TDA techniques.
View Article and Find Full Text PDFComput Methods Biomech Biomed Engin
January 2025
Université de Lyon, VetAgro Sup, UPSP ICE 2021.A104, France.
Extrusion-based 3D printing is a widely utilized tool in tissue engineering, offering precise 3D control of bioinks to construct organ-sized biomaterial objects with hierarchically organized cellularized scaffolds. Topological properties in flowing polymers are determined by macromolecule conformation, namely orientation and stretch degree. We utilized the micro-macro approach to describe hydrogel macromolecule orientation during extrusion, offering a two-scale fluid behavior description.
View Article and Find Full Text PDFInorg Chem
December 2024
Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India.
Design of hierarchical hollow nanoheterostructure materials through interfacial and defect engineering is an innovative approach for achieving optimal charge separation dynamics and photon harvesting efficiency. Herein, we have described a facile technique to fabricate hollow MOF-derived C, N-doped-CoO (C, N-CoO) dodecahedral particles enwrapped with MgInS nanosheets for enhanced N reduction performance. ZIF-67 was initially used as a sacrificial template to prepare hollow C, N-CoO using a carbonization route followed by low-temperature calcination treatment.
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