QUANTIFICATION AND ANALYSIS OF SPATIO-TEMPORAL WAVES IN DYNAMIC CELLULAR SYSTEMS

Abstract

Rhythms are signatures of life. From the nanoscopic flicker of molecular switches to the metronomic beating of the heart, internally generated clocks regulate virtually every aspect of physiology, thereby shaping the very essence of living systems. This dissertation addresses two interrelated questions: How can such biological rhythms be captured and quantified with sufficient resolution, and do common design principles underlie their organization across different biological scales? This work follows a cohesive narrative that investigates rhythmic phenomena across progressively smaller spatial and temporal domains, while concurrently developing novel analytical tools to advance their characterization. We begin with a survey of oscillatory phenomena spanning multiple orders of magnitude, introducing multiscale modeling as a unifying framework for integrating diverse biological rhythms. With this broad context established, we turn to specific experimental systems, starting with gut motility in an ex vivo crayfish model. By isolating central, myogenic, and serotonergic inputs, we find that chemical cues can restore contraction strength but reduce spatial synchrony in the absence of central control. These results suggest that local sensing mechanisms may be essential for coordinating large-scale motor patterns. The focus then shifts to a finer spatial scale: actin dynamics in astrocytes, a type of glial cell. Using a custom optical-flow analysis pipeline, we identify recurrent actin "hotspots" whose activity is suppressed by engineered nanotopographies but enhanced in the presence of neighboring neurons. These findings suggest that the cytoskeleton itself functions as a dynamic sensor of mechanical and biochemical cues. Building on this insight into cellular sensing, we next examine how cells interact with their environment during development. In growing cortical neurons, actin wave tracks and growth-cone trajectories initially align with nanotopographic cues; however, this influence diminishes as axons mature. The observed decline points to age-dependent cytoskeletal plasticity as a potential factor limiting regenerative capacity in adult neurons. In the final part of this work, we extend our analysis from two-dimensional imaging to the three-dimensional microenvironments in which cells naturally reside. As most, if not all tissues function in three dimensions, spatial depth fundamentally alters how motion is encoded and perceived. To address this complexity, we adapt the optical-flow framework to volumetric datasets. Applications to actin dynamics in Dictyostelium and axonal growth in Drosophila pupal wings reveal spatial patterns obscured in two-dimensional projections. Complementary experiments involving calcium imaging and electrophysiological recordings in the gut further link local intracellular activity with large-scale contractions, thereby reinforcing the broader theme of wave propagation across scales. Overall, this work aims to bridge wave phenomena across diverse spatial and temporal domains, unifying them under the central theme of local versus global control in the coordination of biological rhythms.