{"article_processing_charge":"No","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"month":"09","date_updated":"2023-09-27T14:16:45Z","type":"dissertation","file":[{"relation":"source_file","checksum":"6e47871c74f85008b9876112eb3fcfa1","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Shayan-Thesis-Final.docx","access_level":"closed","embargo_to":"open_access","creator":"sshamip","date_updated":"2021-09-11T22:30:05Z","file_id":"8351","date_created":"2020-09-09T11:06:27Z","file_size":65194814},{"file_id":"8352","date_created":"2020-09-09T11:06:13Z","file_size":23729605,"date_updated":"2021-09-11T22:30:05Z","content_type":"application/pdf","creator":"sshamip","access_level":"open_access","embargo":"2021-09-10","file_name":"Shayan-Thesis-Final.pdf","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","relation":"main_file"}],"day":"09","degree_awarded":"PhD","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."}],"date_published":"2020-09-09T00:00:00Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","oa_version":"None","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2020-09-09T11:12:10Z","alternative_title":["ISTA Thesis"],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"661"},{"id":"6508","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7001"},{"status":"public","relation":"part_of_dissertation","id":"735"}]},"publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"}],"has_accepted_license":"1","page":"107","doi":"10.15479/AT:ISTA:8350","_id":"8350","language":[{"iso":"eng"}],"citation":{"ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","mla":"Shamipour, Shayan. <i>Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes </i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","apa":"Shamipour, S. (2020). <i>Bulk actin dynamics drive phase segregation in zebrafish oocytes </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>."},"year":"2020","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"ddc":["570"],"file_date_updated":"2021-09-11T22:30:05Z","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts."}