Biology subjects

Wopat, S.

Publications and source records attributed to Wopat, S..

3 recordsLinked to original sources

bioRxiv2025

Stationary and germ layer-specific cellular flows shape the zebrafish gastrula

During gastrulation, a sequence of complex processes transforms the blastula into a multi-layered embryo. Fixed sample analysis has revealed much about how genetic signaling cascades determine the major body axes and organize cell fate patterns into the germ layers: ectoderm, mesoderm, and endoderm. In toto live imaging of vertebrate development highlights that embryogenesis is a dynamic process that involves on the order of ten thousand cells, but hurdles related to data handling have hampered quantitative analysis. Therefore, our understanding of the rich physical aspects of multilayered tissue reconfigurations remains incomplete. Here, we reveal that modules of stationary and germ-layer-specific tissue flows shape the zebrafish gastrula. We combine in toto live imaging with tissue-specific markers and image analysis to reveal the global shape of the enveloping layer (EVL), epiblast, and mesoderm over time. A user-friendly tissue cartography pipeline based on the Blender 3D software moves into the reference frame of individual tissue layers. We find distinct tissue flow patterns in the enveloping layer (EVL), epiblast, and mesoderm, respectively. The instantaneous tissue flow of these germ layers is organized in a temporal sequence of hours-long, constant flow patterns. This suggests that a sequence of stationary tissue flow modules transports cells to their destination during gastrulation. Mathematical decomposition suggests that epiblast flow is strongly influenced by a superposition of rotational flow in the mesoderm, and divergent flow in the EVL. Molecular and cellular complexity notwithstanding, these results hint at surprisingly, tractable physical processes that underlie vertebrate gastrulation, and set the stage for investigations of how morphogens orchestrate dynamics.

developmental biology↗

bioRxiv2025

Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data

Volumetric microscopy can image complex 3D tissues, but 3D image data remains difficult to visualize and quantify. Many biological systems are organized as thin, curved sheets (for example, epithelia). Tissue cartography extracts and cartographically projects these curved surfaces from volumetric images. This converts 3D into 2D image data, greatly facilitating visualization, analysis, and computational processing. Existing tools, however, demand advanced coding expertise and are limited to simple tissue geometries. Here, we present blender issue cartography (btc), an interactive add-on for the 3D editor Blender that makes tissue cartography user-friendly by a graphical interface, and handles complex biological shapes using powerful computer graphics algorithms. An accompanying Python library supports faithful 3D measurements in 2D cartographic projections and custom analysis pipelines. Time-lapse data can be batch-processed by algorithmically aligning all time points to a single key frame. We demonstrate btc on diverse and complex tissue shapes from Drosophila, stem-cell organoids, Arabidopsis, and zebrafish. btc enables quantitative cartographic analysis of complex 3D tissues, broadening access to methods previously restricted to specialists, while leveraging tools from computer graphics to unlock new capabilities.

bioinformatics↗

bioRxiv2023

Axial segmentation by iterative mechanical signaling

In bony fishes, formation of the vertebral column, or spine, is guided by a metameric blueprint established in the epithelial sheath of the notochord. Generation of the notochord template begins days after somitogenesis and even occurs in the absence of somite segmentation. However, patterning defects in the somites lead to imprecise notochord segmentation, suggesting these processes are linked. Here, we reveal that spatial coordination between the notochord and the axial musculature is necessary to ensure segmentation of the zebrafish spine both in time and space. We find that the connective tissues that anchor the axial skeletal musculature, known as the myosepta in zebrafish, transmit spatial patterning cues necessary to initiate notochord segment formation, a critical pre-patterning step in spine morphogenesis. When an irregular pattern of muscle segments and myosepta interact with the notochord sheath, segments form non-sequentially, initiate at atypical locations, and eventually display altered morphology later in development. We determine that locations of myoseptum-notochord connections are hubs for mechanical signal transmission, which are characterized by localized sites of deformation of the extracellular matrix (ECM) layer encasing the notochord. The notochord sheath responds to the external mechanical changes by locally augmenting focal adhesion machinery to define the initiation site for segmentation. Using a coarse-grained mathematical model that captures the spatial patterns of myoseptum-notochord interactions, we find that a fixed-length scale of external cues is critical for driving sequential segment patterning in the notochord. Together, this work identifies a robust segmentation mechanism that hinges upon mechanical coupling of adjacent tissues to control patterning dynamics.

developmental biology↗