Geometry and transport in development

Abstract

Shape changes are some of the most visually striking features of biological development at all scales of living matter. With recent advances in high-resolution microscopy, it becomes possible to track the morphology and motion of systems ranging from organelles to every single cell within specific tissues or even whole organisms. This enables quantitative physical modeling to understand the phenomena driving and controlling the emergence of spatial patterns and organization in development.

In the first half of this thesis, we consider two problems arising in fruit fly oogenesis. In a small organ known as the egg chamber, we apply ideas from continuum and statistical mechanics to explain the nonlinear dynamics and regulation of nuclear envelope shape and of a cytoplasmic transport event known as `nurse cell dumping'. In particular, these results show how biological and physical mechanisms can cooperate to enable or regulate developmental processes.

In the second half of this thesis, we consider zebrafish embryogenesis, during which thousands of cells collectively migrate to lay out the organism's body plan. Here, a direct physical modeling approach is hampered by the exploding complexity of a three-dimensional many-body dynamic which obfuscates the identification of relevant degrees of freedom. In this context, we investigate ways to translate cell trajectories into lower-dimensional representations and to capture the essential ordering principles of collective cell organization. By leveraging model inference techniques, the resulting representation of the collective cell dynamics enables a compact characterization of developmental symmetry breaking.