On biophysical aspects of growth and dynamics of epithelial tissues

A fundamental and unresolved question of life is how organs are formed. The shape and form of organs emerges by spatio temporally controlled division and motility of cells. As both processes are tightly coordinated, interactions amongst cells are required to ensure stability and integrity. Many genetic networks controlling the polarised cell motility or promoting cell division have been identified. Action between cells results in an increased complexity. Yet cells give rise to regular patterned organs. The form of objects and their motion is subject to physical laws. Cells are of an active character, divide and move, interesting properties for a material, with potentially new knowledge emerging from their study. Here, we perform a quantitative characterisation of two experimental models for tissue morphogenesis. Using cultured epithelial sheets we address the mechanical properties of growth control and identify regulatory mechanisms. Based on this study, we propose a phenomenological description of tissue dynamics, reproducing the observed data. Using the methods developed to understand the cultured sheet, we approach the role of mechanics in the migration of an embryonic tissue. We measure the directed motion of the tissue and show that the findings can be reproduced by coupling the biophysical model of motile cells to a dynamically regulated polarisation mechanism.Formgebung von Organen ist ein grundlegendes, ungelöstes Problem des Lebens. Ihre Gestalt resultiert aus raumzeitlich kontrollierten Zellteilungen sowie Bewegungen von Zellen. Um mechanische Stabilität sowie Integrität des Gewebes zu gewährleisten, werden Zell-Zell Wechselwirkungen benötigt. Viele genetische Netzwerke kontrollieren die polarisierte Zellbeweglichkeit oder fördern die Zellteilung. Interaktion zwischen Zellen führt zu einer erhöhten Komplexität. Dennoch bilden sich reguläre Muster. Die Form von Objekten und deren Bewegung unterliegt physikalischen Gesetzen. Zellen sind von aktiver Art, teilen und bewegen sich, interessante Eigenschaften für ein Material, welche in neuen Erkenntnissen münden könnten. In dieser Arbeit führen wir eine quantitative Charakterisierung von zwei Modellsystemen der Morphogenese von Geweben durch. Anhand von kultivierten Epithelien behandeln wir die mechanischen Eigenschaften der Wachstumskontrolle und identifizieren Regulationsmechanismen. Darauf aufbauend, schlagen wir eine phänomenologische Modellbeschreibung für Gewebedynamik vor, welche die Beobachtungen reproduziert. Wir machen Gebrauch von diesen Methoden um die Mechanik der Migration eines embryonalen Epithels zu verstehen. Dabei messen wir die gerichtete Bewegung des Gewebes und zeigen, dass die resultierenden Daten durch Kopplung der biophysikalischen Motilitätsbeschreibung an einen dynamisch regulierten Polarisationsmechanismus reproduziert werden

Global morphogenetic flow is accurately predicted by the spatial distribution of myosin motors.

During embryogenesis tissue layers undergo morphogenetic flow rearranging and folding into specific shapes. While developmental biology has identified key genes and local cellular processes, global coordination of tissue remodeling at the organ scale remains unclear. Here, we combine in toto light-sheet microscopy of the Drosophila embryo with quantitative analysis and physical modeling to relate cellular flow with the patterns of force generation during the gastrulation process. We find that the complex spatio-temporal flow pattern can be predicted from the measured meso-scale myosin density and anisotropy using a simple, effective viscous model of the tissue, achieving close to 90% accuracy with one time dependent and two constant parameters. Our analysis uncovers the importance of a) spatial modulation of myosin distribution on the scale of the embryo and b) the non-locality of its effect due to mechanical interaction of cells, demonstrating the need for the global perspective in the study of morphogenetic flow

Identification of a neural crest stem cell niche by Spatial Genomic Analysis

The neural crest is an embryonic population of multipotent stem cells that form numerous defining features of vertebrates. Due to lack of reliable techniques to perform transcriptional profiling in intact tissues, it remains controversial whether the neural crest is a heterogeneous or homogeneous population. By coupling multiplex single molecule fluorescence in situ hybridization with machine learning algorithm based cell segmentation, we examine expression of 35 genes at single cell resolution in vivo. Unbiased hierarchical clustering reveals five spatially distinct subpopulations within the chick dorsal neural tube. Here we identify a neural crest stem cell niche that centers around the dorsal midline with high expression of neural crest genes, pluripotency factors, and lineage markers. Interestingly, neural and neural crest stem cells express distinct pluripotency signatures. This Spatial Genomic Analysis toolkit provides a straightforward approach to study quantitative multiplex gene expression in numerous biological systems, while offering insights into gene regulatory networks via synexpression analysis

Identification of a neural crest stem cell niche by Spatial Genomic Analysis

The neural crest is an embryonic population of multipotent stem cells that form numerous defining features of vertebrates. Due to lack of reliable techniques to perform transcriptional profiling in intact tissues, it remains controversial whether the neural crest is a heterogeneous or homogeneous population. By coupling multiplex single molecule fluorescence in situ hybridization with machine learning algorithm based cell segmentation, we examine expression of 35 genes at single cell resolution in vivo. Unbiased hierarchical clustering reveals five spatially distinct subpopulations within the chick dorsal neural tube. Here we identify a neural crest stem cell niche that centers around the dorsal midline with high expression of neural crest genes, pluripotency factors, and lineage markers. Interestingly, neural and neural crest stem cells express distinct pluripotency signatures. This Spatial Genomic Analysis toolkit provides a straightforward approach to study quantitative multiplex gene expression in numerous biological systems, while offering insights into gene regulatory networks via synexpression analysis

Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy

Due to low light emission of fluorescent samples, live fluorescence microscopy imposes a tradeoff between spatiotemporal resolution and signal-to-noise ratio. This can result in images and videos containing motion blur or Poisson-type shot noise, depending on the settings used during acquisition. Here, we propose an algorithm to simultaneously denoise and temporally super-resolve movies of repeating microscopic processes that is compatible with any conventional microscopy setup that can achieve imaging at a rate of at least twice that of the fundamental frequency of the process (above 4 frames per second for a 2 Hz process). Our method combines low temporal resolution frames from multiple cycles of a repeating process to reconstruct a denoised, higher temporal resolution image sequence which is the solution to a linear program that maximizes the consistency of the reconstruction with the measurements, under a regularization constraint. This paper describes, in particular, a parallelizable superresolution reconstruction algorithm and demonstrates its application to live cardiac fluorescence microscopy. Using our method, we experimentally show temporal resolution improvement by a factor of 1.6, resulting in a visible reduction of motion blur in both on-sample and off-sample frames

Topological structure and dynamics of three-dimensional active nematics.

Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination loops that undergo complex dynamics and recombination events. Our work suggests a framework for analyzing the nonequilibrium dynamics of bulk anisotropic systems as diverse as driven complex fluids, active metamaterials, biological tissues, and collections of robots or organisms

Active Tension Network model suggests an exotic mechanical state realized in epithelial tissues.

Mechanical interactions play a crucial role in epithelial morphogenesis, yet understanding the complex mechanisms through which stress and deformation affect cell behavior remains an open problem. Here we formulate and analyze the Active Tension Network (ATN) model, which assumes that the mechanical balance of cells within a tissue is dominated by cortical tension and introduces tension-dependent active remodeling of the cortex. We find that ATNs exhibit unusual mechanical properties. Specifically, an ATN behaves as a fluid at short times, but at long times supports external tension like a solid. Furthermore, an ATN has an extensively degenerate equilibrium mechanical state associated with a discrete conformal - "isogonal" - deformation of cells. The ATN model predicts a constraint on equilibrium cell geometries, which we demonstrate to approximately hold in certain epithelial tissues. We further show that isogonal modes are observed in the fruit y embryo, accounting for the striking variability of apical areas of ventral cells and helping understand the early phase of gastrulation. Living matter realizes new and exotic mechanical states, the study of which helps to understand biological phenomena