Ruetten, Virginia Marie Sophie;
(2024)
Whole body-brain functional imaging and interrogation platform: technology development, analysis methods and applications.
Doctoral thesis (Ph.D), UCL (University College London).
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Abstract
Organisms evolved to overcome physiological challenges and exploit their environments. Many solutions are not localized to a specific cell type or a specific organ; instead, they are implemented in distributed networks of cells across different organ systems. Traditionally, physiological subsystems of organisms have been studied in isolation, making it challenging to connect different subfields of biology. Here we introduce a system for imaging cellular dynamics of virtually all cells in a vertebrate, read out via calcium fluctuations. Larval zebrafish expressing calcium indicators under a ubiquitous promoter were imaged in spontaneous conditions and under physiological stressors (e.g.: cold). We imaged calcium dynamics across brain and body, and developed a registration pipeline for computationally stabilizing the tissue across the entire animal. We observed a plethora of spatio-temporal footprints of multicellular processes, including pulsatile traveling waves along the kidney and ultraslow fluctuations in ependymal cell activity locked to whole-brain dynamics and motor activity. We adapted clustering and dimensionality reduction methods to better capture the types of multiscale dynamics prevalent in the data, proposing coherence and non-time reversibility as two informative metrics, as compared to correlation- or variance-based approaches. To assist in data interpretation and to be able to follow up such observations at cellular and sub-cellular scale, we developed two whole fish ExM protocols compatible with animals as old as 21dpf for immunostaining and RNA probing. Together, these tools provide a powerful platform to study whole-body physiology and physiology-driven decision making.
| Type: | Thesis (Doctoral) |
|---|---|
| Qualification: | Ph.D |
| Title: | Whole body-brain functional imaging and interrogation platform: technology development, analysis methods and applications |
| Open access status: | An open access version is available from UCL Discovery |
| Language: | English |
| Additional information: | Copyright © The Author 2024. Original content in this thesis is licensed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) Licence (https://creativecommons.org/licenses/by/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request. |
| Keywords: | calcium imaging, gaussian processes, whole body physiology, zebrafish |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Gatsby Computational Neurosci Unit |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10191610 |
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