Flows and forces in the early development of an averaged zebrafish embryo. A novel analysis pipeline for the dynamics of embryogenesis.

by Alejandro Jurado Jiménez
Doctoral thesis
Date of Examination:2025-06-02
Date of issue:2025-06-26
Advisor:Prof. Dr. Timo Betz
Referee:Prof. Dr. Jan Huisken
Referee:Prof. Dr. Ramin Golestanian
Referee:Dr. Robert Mettin
Referee:Prof. Dr. Stefan Klumpp
Referee:Dr. Thomas Frank
Persistent Address: http://dx.doi.org/10.53846/goediss-11336

 

 

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Abstract

English

Our current knowledge on collective cell phenomena such as wound healing, cancer invasion and embryogenesis heavily relies on biochemistry. However, new advances in the field of cell dynamics have shown how mechanosensing plays a crucial role in such processes. Tackling the still open questions from the new, fresh perspective of biophysics has proven to be an excellent complement to the up-to-date studies, shining light into complex phenomena which can not be fully understood relying only on genetics and chemical signaling. Embryogenesis is a particularly intricate phenomenon, where an orchestration of many interconnected mechanisms can transform a zygote into a complex, living structure in a matter of hours. The initial collective motion leading to the differentiation of the primordial germ layers in an embryo, named gastrulation, are usually studied in fast developing organisms, such as Xenopus, Drosophila melanogaster and Zebrafish (Danio rerio). Despite the vast literature covering the first hours of gastrulation in several species, some of the details about those collective motions in Zebrafish in particular are still to be fully understood, such as the exact mechanics of doming and epiboly. One such open question is the mechanism leading to the early embryonic symmetry breaking, where the left-right asymmetry of the body plan is established for the first time. In this work we present a new approach to investigate that particular phenomenon from a mechanical point of view. Our aim is to understand the mechanical state of the embryonic tissue leading to its first symmetry breaking during epiboly: the shield formation. We present a working pipeline built for the construction of average embryonic datasets based solely on the registration of cellular velocity fields, without the necessity for additional fluorescent labels or hand-curated alignments. Along with it, we developed a user-friendly analysis tool for the calculation of surface stresses as felt by in vivo force sensors, versatile enough to be used in several biophysical contexts, such as for the analysis of nuclear geometry. Together, these two tools enable a novel insight into the mechanical evolution of the embryo prior and during symmetry breaking. Our findings reveal the existence of a ventral-dorsal mechanical polarity, representing a novel report, as evidenced by an in-depth analysis of velocity fields and stress maps.
Keywords: embryogenesis; biophysics; lightsheet microscopy; in-vivo force inference; cell dynamics
 
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