Biology subjects

Mitchell, N. P.

Publications and source records attributed to Mitchell, N. P..

4 recordsLinked to original sources

bioRxiv2022

Morphodynamic Atlas for Drosophila Development

During morphogenesis, diverse cell-scale and tissue-scale processes couple to dynamically sculpt organs. In this coupling, genetic expression patterns and biochemical signals regulate and respond to mechanical deformations to ensure reproducible and robust changes in tissue geometry. A long-standing approach to characterize these interactions has been the construction of expression atlases, and these atlases have necessarily relied on fixed snapshots of embryogenesis. Addressing how expression profiles relate to tissue dynamics, however, requires a scheme for spatiotemporal registration across different classes of data that incorporates both live samples and fixed datasets. Here, we construct a morphodynamic atlas that unifies fixed and live datasets - from gene expression profiles to cytoskeletal components - into a single, morphological consensus timeline. This resource and our computational approach to global alignment facilitate hypothesis testing using quantitative comparison of data both within and across ensembles, with resolution in both space and time to relate genes to tissue rearrangement, cell behaviors, and out-of-plane motion. Examination of embryo kinematics reveals stages in which tissue flow patterns are quasi-stationary, arranged as a sequence of morphodynamic modules. Temperature perturbations tune the duration of one such module - during body axis elongation - according to a simple, parameter-free scaling in which the total integrated tissue deformation is achieved at a temperature-dependent rate. By extending our approach to visceral organ formation during later stages of embryogenesis, we highlight how morphodynamic atlases can incorporate complex shapes deforming in 3D. In this context, morphodynamic modules are reflected in some, but not all, measures of tissue motion. Our approach and the resulting atlas opens up the ability to quantitatively test hypotheses with resolution in both space and time, relating genes to tissue rearrangement, cell behaviors, and organ motion.

developmental biology↗

bioRxiv2022

TubULAR: Tracking deformations of dynamic tissues and interfaces in 3D

A common motif in biology is the arrangement of cells into tube-like sheets, which further transform into more complex shapes. Traditionally, analysis of the dynamic surfaces of growing tissues has relied on inspecting static snapshots, live imaging of cross-sections, or tracking isolated cells in 3D. However, capturing the interplay between in-plane and out-of-plane behaviors requires following the full surface as it deforms and integrating cell-scale motions into collective, tissue-scale deformations. The advent of methods for whole-organ live imaging ushers the need for in toto analysis methods to understand these collective tissue dynamics. Here, we introduce an approach that builds in toto maps of surface deformation by following tissue parcels in the material frame of reference. Mapping the full 3D surface to 2D images such that the tissue motion in 2D is minimal enables the user to easily follow the tissue and discern its 3D motion. We then provide a computational framework for linking in-plane and out-of-plane behaviors and decomposing complex deformation maps into elementary contributions. The Tube-like sUrface Lagrangian Analysis Resource (TubULAR) provides an open-source MATLAB implementation whose functionality is accessible either as a standalone toolkit or as an extension of the ImSAnE package used in the developmental biology community. We underscore the power of our approach by analyzing shape change in the embryonic Drosophila midgut and beating zebrafish heart. Following deformations in the tissue/material frame reveals the signatures of tissue flow and a reduced-dimensional mode decomposition of the dynamics. The method naturally generalizes to in vitro and synthetic systems and provides ready access to the mechanical mechanisms relating genetic patterning to organ shape change.

developmental biology↗

bioRxiv2022

Geometric control of Myosin-II orientation during axis elongation

The actomyosin cytoskeleton is a crucial driver of morphogenesis. Yet how the behavior of large-scale cytoskeletal patterns in deforming tissues emerges from the interplay of geometry, genetics, and mechanics remains incompletely understood. Convergent extension flow in D. melanogaster embryos provides the opportunity to establish a quantitative understanding of the dynamics of anisotropic non-muscle myosin II. Cell-scale analysis of protein localization in fixed embryos suggests that there are complex rules governing how the control of myosin anisotropy is regulated by gene expression patterns. However, technical limitations have impeded quantitative and dynamic studies of this process at the whole embryo level, leaving the role of geometry open. Here we combine in toto live imaging with quantitative analysis of molecular dynamics to characterize the distribution of myosin anisotropy and corresponding genetic patterning. We found pair rule gene expression continuously deformed, flowing with the tissue frame. In contrast, myosin anisotropy orientation remained nearly static, aligned with the stationary dorsal-ventral axis of the embryo. We propose myosin recruitment by a geometrically defined static source, potentially related to the embryo-scale epithelial tension, and account for transient deflections by the interplay of cytoskeletal turnover with junction reorientation by flow. With only one parameter, this model quantitatively accounts for the time course of myosin anisotropy orientation in wild-type, twist, and even-skipped embryos as well as embryos with perturbed egg geometry. Geometric patterning of the cytoskeleton suggests a simple physical strategy to ensure a robust flow and formation of shape.

developmental biology↗

bioRxiv2021

Visceral organ morphogenesis via calcium-patterned muscle contractions

How organs achieve their final shape is a problem at the interface between physics and developmental biology. Organs often involve multiple interacting tissue layers that must be coordinated to orchestrate the complex shape changes of development. Intense study uncovered genetic, and physical ingredients driving the form of mono layer tissue. Yet, tracing dynamics across tissue layers, and scales - from cell to tissue, to entire organs - remains an outstanding challenge. Here, we study the midgut of Drosophila embryos as a model visceral organ, to reconstruct in toto the dynamics of multi-layer organ formation in vivo. Using light-sheet microscopy, genetics, computer vision, and tissue cartography, we extract individual tissue layers to map the time course of shape across scales from cells to organ. We identify the kinematic mechanism driving the shape change due to tissue layer interactions by linking out-of-plane motion to active contraction patterns, revealing a convergent extension process in which cells deform as they flow into deepening folds. Acute perturbations of contractility in the muscle layer using non-neuronal optogenetics reveals that these contraction patterns are due to muscle activity, which induces cell shape changes in the adjacent endoderm layer. This induction cascade relies on high frequency calcium pulses in the muscle layer, under the control of hox genes. Inhibition of targets of calcium involved in myosin phosphorylation abolishes constrictions. Our study of multi-layer organogenesis reveals how genetic patterning in one layer triggers a dynamic molecular mechanism to control a physical process in the adjacent layer, to orchestrate whole-organ shape change.

developmental biology↗