From cells to tissues

An essential prerequisite for the existence of multi-cellular life is the organization of cells into tissues. In this thesis, we theoretically study how large-scale tissue properties can emerge from the collective behavior of individual cells. To this end, we focus on the properties of epithelial tissue, which is one of the major tissue types in animals. We study how rheological properties of epithelia emerge from cellular processes, and we develop a physical description for the dynamics of an epithelial cell polarity. We apply our theoretical studies to observations in the developing wing of the fruit fly, Drosophila melanogaster. In order to study epithelial mechanics, we first develop a geometrical framework that rigorously describes the deformation of two-dimensional cellular networks. Our framework decomposes large-scale deformation into cellular contributions. For instance, we show how large-scale tissue shear decomposes into contributions by cell shape changes and into contributions by different kinds of topological transitions. We apply this framework in order to quantify the time-dependent deformation of the fruit fly wing, and to decompose it into cellular contributions. We also use this framework as a basis to study large-scale rheological properties of epithelia and their dependence on cellular fluctuations. To this end, we represent epithelial tissues by a vertex model, which describes cells as elastic polygons. We extend the vertex model by introducing fluctuations on the cellular scale, and we develop a method to perform perpetual simple shear simulations. Analyzing the steady state of such simple shear simulations, we find that the rheological behavior of vertex model tissue depends on the fluctuation amplitude. For small fluctuation amplitude, it behaves like a plastic material, and for high fluctuation amplitude, it behaves like a visco-elastic fluid. In addition to analyzing mechanical properties, we study the reorientation of an epithelial cell polarity. To this end, we develop a simple hydrodynamic description for polarity reorientation. In particular, we account for polarity reorientation by tissue shear, by another polarity field, and by local polarity alignment. Furthermore, we develop methods to quantify polarity patterns based on microscopical images of the fly wing. We find that our hydrodynamic description does not only account for polarity reorientation in wild type fly wings. Moreover, it is for the first time possible to also account for the observed polarity patterns in a number of genetically altered flies.:1 Introduction 1.1 The development of multi-cellular organisms 1.2 Biology of epithelial tissues 1.3 The model system Drosophila melanogaster 1.4 Planar cell polarity 1.5 Physical description of biological tissues 1.6 Overview over this thesis 2 Tissue shear in cellular networks 2.1 Geometry of tissue deformation on the cellular scale 2.2 Decomposition of the large-scale flow field into cellular contributions 2.3 Cellular contributions to the flow field in the fruit fly wing 2.4 Discussion 3 Rheological behavior of vertex model tissue under external shear 3.1 A vertex model to describe epithelial mechanics 3.2 Fluctuation-induced fluidization of tissue 3.3 Discussion 4 Quantitative study of polarity reorientation in the fruit fly wing 4.1 Experimentally quantified polarity patterns 4.2 Effective hydrodynamic theory for polarity reorientation 4.3 Comparison of theory and experiment 4.4 Discussion 5 Conclusions and outlook Appendices: A Algebra of real 2 × 2 matrices B Deformation of triangle networks C Simple shear simulations using the vertex model D Coarse-graining of a cellular Core PCP model E Quantification of polarity patterns in the fruit fly wing F Theory for polarity reorientation in the fruit fly wing G Boundary conditions for the polarity field in the fruit fly wing Table of symbols BibliographyEine wesentliche Voraussetzung für die Existenz mehrzelligen Lebens ist, dass sich einzelne Zellen sinnvoll zu Geweben ergänzen können. In dieser Dissertation untersuchen wir, wie großskalige Eigenschaften von Geweben aus dem kollektiven Verhalten einzelner Zellen hervorgehen. Dazu konzentrieren wir uns auf Epitheliengewebe, welches eine der Grundgewebearten in Tieren darstellt. Wir stellen theoretische Untersuchungen zu rheologischen Eigenschaften und zu zellulärer Polarität von Epithelien an. Diese theoretischen Untersuchungen vergleichen wir mit experimentellen Beobachtungen am sich entwickelnden Flügel der schwarzbäuchigen Taufliege (Drosophila melanogaster). Um die Mechanik von Epithelien zu untersuchen, entwickeln wir zunächst eine geometrische Beschreibung für die Verformung von zweidimensionalen zellulären Netzwerken. Unsere Beschreibung zerlegt die mittlere Verformung des gesamten Netzwerks in zelluläre Beitrage. Zum Beispiel wird eine Scherverformung des gesamten Netzwerks auf der zellulären Ebene exakt repräsentiert: einerseits durch die Verformung einzelner Zellen und andererseits durch topologische Veränderungen des zellulären Netzwerks. Mit Hilfe dieser Beschreibung quantifizieren wir die Verformung des Fliegenflügels während des Puppenstadiums. Des Weiteren führen wir die Verformung des Flügels auf ihre zellulären Beiträge zurück. Wir nutzen diese Beschreibung auch als Ausgangspunkt, um effektive rheologische Eigenschaften von Epithelien in Abhängigkeit von zellulären Fluktuationen zu untersuchen. Dazu simulieren wir Epithelgewebe mittels eines Vertex Modells, welches einzelne Zellen als elastische Polygone abstrahiert. Wir erweitern dieses Vertex Modell um zelluläre Fluktuationen und um die Möglichkeit, Schersimulationen beliebiger Dauer durchzuführen. Die Analyse des stationären Zustands dieser Simulationen ergibt plastisches Verhalten bei kleiner Fluktuationsamplitude und visko-elastisches Verhalten bei großer Fluktuationsamplitude. Neben mechanischen Eigenschaften untersuchen wir auch die Umorientierung einer Zellpolarität in Epithelien. Dazu entwickeln wir eine einfache hydrodynamische Beschreibung für die Umorientierung eines Polaritätsfeldes. Wir berücksichtigen dabei insbesondere Effekte durch Scherung, durch ein anderes Polaritätsfeld und durch einen lokalen Gleichrichtungseffekt. Um unsere theoretische Beschreibung mit experimentellen Daten zu vergleichen, entwickeln wir Methoden um Polaritätsmuster im Fliegenflügel zu quantifizieren. Schließlich stellen wir fest, dass unsere hydrodynamische Beschreibung in der Tat beobachtete Polaritätsmuster reproduziert. Das gilt nicht nur im Wildtypen, sondern auch in genetisch veränderten Tieren.:1 Introduction 1.1 The development of multi-cellular organisms 1.2 Biology of epithelial tissues 1.3 The model system Drosophila melanogaster 1.4 Planar cell polarity 1.5 Physical description of biological tissues 1.6 Overview over this thesis 2 Tissue shear in cellular networks 2.1 Geometry of tissue deformation on the cellular scale 2.2 Decomposition of the large-scale flow field into cellular contributions 2.3 Cellular contributions to the flow field in the fruit fly wing 2.4 Discussion 3 Rheological behavior of vertex model tissue under external shear 3.1 A vertex model to describe epithelial mechanics 3.2 Fluctuation-induced fluidization of tissue 3.3 Discussion 4 Quantitative study of polarity reorientation in the fruit fly wing 4.1 Experimentally quantified polarity patterns 4.2 Effective hydrodynamic theory for polarity reorientation 4.3 Comparison of theory and experiment 4.4 Discussion 5 Conclusions and outlook Appendices: A Algebra of real 2 × 2 matrices B Deformation of triangle networks C Simple shear simulations using the vertex model D Coarse-graining of a cellular Core PCP model E Quantification of polarity patterns in the fruit fly wing F Theory for polarity reorientation in the fruit fly wing G Boundary conditions for the polarity field in the fruit fly wing Table of symbols Bibliograph

Understanding Mechanics and Polarity in Two-Dimensional Tissues

During development, cells consume energy, divide, rearrange, and die. Bulk properties such as viscosity and elasticity emerge from cell-scale mechanics and dynamics. Order appears, for example in patterns of hair outgrowth, or in the predominately hexagonal pattern of cell boundaries in the wing of a fruit fly. In the past fifty years, much progress has been made in understanding tissues as living materials. However, the physical mechanisms underlying tissue-scale behaviour are not completely understood. Here we apply theories from statistical physics and fluid dynamics to understand mechanics and order in two-dimensional tissues. We restrict our attention to the mechanics and dynamics of cell boundaries and vertices, and to planar polarity, a type of long-ranged order visible in anisotropic patterns of proteins and hair outgrowth. Our principle tool for understanding mechanics and dynamics is a vertex model where cell shapes are represented using polygons. We analytically derive the ground-state diagram of this vertex model, finding it to be dominated by the geometric requirement that cells be polygons, and the topological requirement that those polygons tile the plane. We present a simplified algorithm for cell division and growth, and furthermore derive a dynamic equation for the vertex model, which we use to demonstrate the emergence of quasistatic behaviour in the limit of slow growth. All our results relating to the vertex model are consistent with and build off past calculations and experiments. To investigate the emergence of planar polarity, we develop quantification methods for cell flow and planar polarity based on confocal microscope images of developing fly wings. We analyze cell flow using a velocity gradient tensor, which is uniquely decomposed into terms corresponding to local compression, shear, and rotations. We argue that a pattern in an inhomogeneously flowing tissue will necessarily be reorganized, motivating a hydrodynamic theory of polarity reorientation. Using such a coarse-grained theory of polarity reorientation, we show that the quantified patterns of shear and rotation in the wing are consistent with the observed polarity reorganization, and conclude that cell flow reorients planar polarity in the wing of the fruit fly. Finally, we present a cell-scale model of planar polarity based on the vertex model, unifying the themes of this thesis

Modelling cell motility and chemotaxis with evolving surface finite elements

We present a mathematical and a computational framework for the modelling of cell motility. The cell membrane is represented by an evolving surface, with the movement of the cell determined by the interaction of various forces that act normal to the surface. We consider external forces such as those that may arise owing to inhomogeneities in the medium and a pressure that constrains the enclosed volume, as well as internal forces that arise from the reaction of the cells' surface to stretching and bending. We also consider a protrusive force associated with a reaction-diffusion system (RDS) posed on the cell membrane, with cell polarization modelled by this surface RDS. The computational method is based on an evolving surface finite-element method. The general method can account for the large deformations that arise in cell motility and allows the simulation of cell migration in three dimensions. We illustrate applications of the proposed modelling framework and numerical method by reporting on numerical simulations of a model for eukaryotic chemotaxis and a model for the persistent movement of keratocytes in two and three space dimensions. Movies of the simulated cells can be obtained from http://homepages.warwick.ac.uk/maskae/CV_Warwick/Chemotaxis.html

Topologically Trivial Closed Walks in Directed Surface Graphs

Let G be a directed graph with n vertices and m edges, embedded on a surface S, possibly with boundary, with first Betti number beta. We consider the complexity of finding closed directed walks in G that are either contractible (trivial in homotopy) or bounding (trivial in integer homology) in S. Specifically, we describe algorithms to determine whether G contains a simple contractible cycle in O(n+m) time, or a contractible closed walk in O(n+m) time, or a bounding closed walk in O(beta (n+m)) time. Our algorithms rely on subtle relationships between strong connectivity in G and in the dual graph G^*; our contractible-closed-walk algorithm also relies on a seminal topological result of Hass and Scott. We also prove that detecting simple bounding cycles is NP-hard. We also describe three polynomial-time algorithms to compute shortest contractible closed walks, depending on whether the fundamental group of the surface is free, abelian, or hyperbolic. A key step in our algorithm for hyperbolic surfaces is the construction of a context-free grammar with O(g^2L^2) non-terminals that generates all contractible closed walks of length at most L, and only contractible closed walks, in a system of quads of genus g >= 2. Finally, we show that computing shortest simple contractible cycles, shortest simple bounding cycles, and shortest bounding closed walks are all NP-hard

Development of High Angular Resolution Diffusion Imaging Analysis Paradigms for the Investigation of Neuropathology

Diffusion weighted magnetic resonance imaging (DW-MRI), provides unique insight into the microstructure of neural white matter tissue, allowing researchers to more fully investigate white matter disorders. The abundance of clinical research projects incorporating DW-MRI into their acquisition protocols speaks to the value this information lends to the study of neurological disease. However, the most widespread DW-MRI technique, diffusion tensor imaging (DTI), possesses serious limitations which restrict its utility in regions of complex white matter. Fueled by advances in DW-MRI acquisition protocols and technologies, a group of exciting new DW-MRI models, developed to address these concerns, are now becoming available to clinical researchers. The emergence of these new imaging techniques, categorized as high angular resolution diffusion imaging (HARDI), has generated the need for sophisticated computational neuroanatomic techniques able to account for the high dimensionality and structure of HARDI data. The goal of this thesis is the development of such techniques utilizing prominent HARDI data models. Specifically, methodologies for spatial normalization, population atlas building and structural connectivity have been developed and validated. These methods form the core of a comprehensive analysis paradigm allowing the investigation of local white matter microarcitecture, as well as, systemic properties of neuronal connectivity. The application of this framework to the study of schizophrenia and the autism spectrum disorders demonstrate its sensitivity sublte differences in white matter organization, as well as, its applicability to large population DW-MRI studies

Approaches to studying smectic layer elasticity and field induced deformations

The initial aim of the work presented in this thesis was to examine smectic layer compressibility with a view to improving our understanding of the stability of intermediate phases. A natural starting point was to investigate the smectic-A phase, as it is the most basic of the smectic phases. The response of the layered structure to external fields is also a focus of this thesis as electric and magnetic fields enable the layer properties to be probed. Investigations into the reorientation dynamics of smectic-A layers in magnetic fields were performed using geometries and cell thicknesses (>50 μm) that are not feasible using electric fields. Data presented in this thesis show that three distinct reorientation mechanisms can occur, one of which is previously unreported and bridges the gap between the previously known mechanisms. The new mechanism observed in 270 μm and 340 μm thickness cells exhibits multiple stage reorientation on a timescale between tens and hundreds of seconds. Using conventional electro-optic techniques combined with a theoretical approach developed by others, this thesis presents a new technique to provide measurement of relative smectic layer compressibility of eight smectic-A liquid crystalline materials. The method presented here combines data on cell thickness, dielectric anisotropy and the measurement of the voltage threshold of the toroidal to stripe domain transition. As expected, the experimental data indicated that materials with shorter molecular lengths had the largest relative layer compressibility. Finally, direct measurement of smectic layer compressibility was investigated and the design of an apparatus capable of such measurements was undertaken. Preliminary results from such an apparatus are presented along with a discussion on the steps taken to develop the design.EThOS - Electronic Theses Online ServiceEPSRCGBUnited Kingdo