[{"alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:14280","language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","date_created":"2023-09-06T10:58:25Z","_id":"14280","doi":"10.15479/at:ista:14280","article_processing_charge":"No","ec_funded":1,"date_updated":"2026-04-07T14:06:05Z","page":"156","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"OA_place":"publisher","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","month":"09","date_published":"2023-09-25T00:00:00Z","file":[{"embargo_to":"open_access","file_size":114932847,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"87eef11fbc5c7df0826f12a3a629b444","file_name":"PhD Thesis_Philipp Radler_20231004.docx","file_id":"14390","date_updated":"2024-10-05T22:30:03Z","relation":"source_file","date_created":"2023-10-04T10:11:53Z","access_level":"closed","creator":"pradler"},{"relation":"main_file","access_level":"open_access","creator":"pradler","date_created":"2023-10-04T10:11:21Z","content_type":"application/pdf","file_size":37838778,"file_id":"14391","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","checksum":"3253e099b7126469d941fd9419d68b4f","embargo":"2024-10-04","date_updated":"2024-10-05T22:30:03Z"}],"year":"2023","supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"}],"type":"dissertation","ddc":["572"],"day":"25","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division"},{"grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall"},{"name":"Reconstitution of bacterial cell wall synthesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"oa":1,"publication_status":"published","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"author":[{"full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "}],"file_date_updated":"2024-10-05T22:30:03Z","related_material":{"record":[{"id":"10934","status":"public","relation":"research_data"},{"relation":"part_of_dissertation","status":"public","id":"11373"},{"relation":"part_of_dissertation","id":"7387","status":"public"}]},"citation":{"apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria."}},{"fulldoi":"https://doi.org/10.15479/at:ista:12809","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-04-06T07:54:09Z","has_accepted_license":"1","article_processing_charge":"No","_id":"12809","doi":"10.15479/at:ista:12809","page":"115","date_updated":"2026-04-07T13:53:28Z","status":"public","OA_place":"publisher","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"file":[{"relation":"main_file","date_created":"2023-04-07T06:16:06Z","creator":"cchlebak","access_level":"open_access","file_size":9881969,"content_type":"application/pdf","date_updated":"2024-04-08T22:30:03Z","embargo":"2024-04-07","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","checksum":"35b5997d2b0acb461f9d33d073da0df5","file_id":"12814"},{"file_id":"12815","checksum":"81198f63c294890f6d58e8b29782efdc","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","date_updated":"2024-04-08T22:30:03Z","embargo_to":"open_access","content_type":"application/pdf","file_size":44201583,"creator":"cchlebak","access_level":"closed","date_created":"2023-04-07T06:17:11Z","relation":"source_file"},{"date_created":"2023-04-07T06:18:05Z","access_level":"closed","creator":"cchlebak","relation":"source_file","date_updated":"2024-04-08T22:30:03Z","checksum":"0317bf7f457bb585f99d453ffa69eb53","file_name":"Thesis_CatarinaAlcarva_final.docx","file_id":"12816","file_size":84731244,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"}],"date_published":"2023-04-06T00:00:00Z","month":"04","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"}],"year":"2023","type":"dissertation","day":"06","ddc":["570"],"oa":1,"project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Alcarva, Catarina","last_name":"Alcarva","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","first_name":"Catarina"}],"file_date_updated":"2024-04-08T22:30:03Z","citation":{"apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria."},"corr_author":"1","abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}]},{"department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-10-01T22:30:11Z","doi":"10.15479/AT:ISTA:13116","_id":"13116","ec_funded":1,"article_processing_charge":"No","has_accepted_license":"1","date_created":"2023-06-02T12:30:40Z","oa_version":"Published Version","fulldoi":"https://doi.org/10.15479/AT:ISTA:13116","corr_author":"1","abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. "}],"author":[{"first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova","full_name":"Dunajova, Zuzana"},{"full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze"},{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler"},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"first_name":"Dörte","full_name":"Brandis, Dörte","last_name":"Brandis"},{"full_name":"Velicky, Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","first_name":"Philipp"},{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Richard W.","full_name":"Wong, Richard W.","last_name":"Wong"},{"last_name":"Elgeti","full_name":"Elgeti, Jens","first_name":"Jens"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","last_name":"Loose"}],"citation":{"chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>.","mla":"Dunajova, Zuzana, et al. <i>Chiral and Nematic Phases of Flexible Active Filaments</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023)."},"file_date_updated":"2023-08-08T11:17:28Z","related_material":{"record":[{"status":"public","id":"13314","relation":"used_in_publication"},{"id":"21423","status":"public","relation":"used_in_publication"}]},"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell"},{"name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"oa":1,"ddc":["539"],"day":"26","type":"research_data","year":"2023","month":"07","title":"Chiral and nematic phases of flexible active 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work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M.  was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). "},{"quality_controlled":"1","publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"project":[{"name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020"},{"name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"oa":1,"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"pmid":1,"corr_author":"1","file_date_updated":"2024-01-30T14:28:30Z","citation":{"short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. <i>Nature Physics</i>. 2023;19:1916-1926. doi:<a href=\"https://doi.org/10.1038/s41567-023-02218-w\">10.1038/s41567-023-02218-w</a>","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02218-w\">https://doi.org/10.1038/s41567-023-02218-w</a>","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02218-w\">https://doi.org/10.1038/s41567-023-02218-w</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1916–1926, 2023.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:<a href=\"https://doi.org/10.1038/s41567-023-02218-w\">10.1038/s41567-023-02218-w</a>."},"related_material":{"record":[{"status":"public","id":"13116","relation":"research_data"},{"id":"21439","status":"public","relation":"research_data"},{"id":"21423","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","full_name":"Dunajova, Zuzana","last_name":"Dunajova"},{"last_name":"Prats Mateu","full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze"},{"first_name":"Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","full_name":"Radler, Philipp"},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"last_name":"Brandis","full_name":"Brandis, Dörte","first_name":"Dörte","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd"},{"orcid":"0000-0002-2340-7431","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","full_name":"Velicky, Philipp"},{"full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"},{"first_name":"Richard W.","full_name":"Wong, Richard W.","last_name":"Wong"},{"first_name":"Jens","full_name":"Elgeti, Jens","last_name":"Elgeti"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin"}],"publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","month":"12","title":"Chiral and nematic phases of flexible active filaments","date_published":"2023-12-01T00:00:00Z","file":[{"date_updated":"2024-01-30T14:28:30Z","file_id":"14916","file_name":"2023_NaturePhysics_Dunajova.pdf","checksum":"bc7673ca07d37309013a86166577b2f7","content_type":"application/pdf","file_size":22471673,"creator":"dernst","access_level":"open_access","date_created":"2024-01-30T14:28:30Z","relation":"main_file","success":1}],"acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","ddc":["530"],"publication":"Nature Physics","day":"01","type":"journal_article","article_type":"original","intvolume":"        19","scopus_import":"1","date_updated":"2026-10-01T22:30:11Z","page":"1916-1926","doi":"10.1038/s41567-023-02218-w","_id":"13314","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":19,"external_id":{"pmid":["38075437"],"isi":["001178645300041"]},"fulldoi":"https://doi.org/10.1038/s41567-023-02218-w","has_accepted_license":"1","isi":1,"date_created":"2023-07-27T14:44:45Z","oa_version":"Published Version","language":[{"iso":"eng"}]},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"OA_place":"publisher","status":"public","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"_id":"12781","doi":"10.15479/at:ista:12781","article_processing_charge":"No","ec_funded":1,"date_updated":"2026-04-07T14:10:40Z","page":"127","oa_version":"Published Version","language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2023-03-31T12:24:42Z","alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:12781","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"corr_author":"1","file_date_updated":"2024-04-22T22:30:06Z","citation":{"short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>."},"related_material":{"record":[{"id":"12138","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","orcid":"0000-0001-9523-9089"}],"project":[{"grant_number":"25541","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"call_identifier":"H2020","grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines"}],"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"oa":1,"publication_status":"published","type":"dissertation","ddc":["570","572"],"day":"23","month":"03","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","date_published":"2023-03-23T00:00:00Z","file":[{"content_type":"application/pdf","file_size":6071553,"embargo":"2024-04-20","date_updated":"2024-04-22T22:30:06Z","file_id":"12852","checksum":"5ebb6345cb4119f93460c81310265a6d","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","relation":"main_file","access_level":"open_access","creator":"vkravchu","date_created":"2023-04-19T14:33:41Z"},{"access_level":"open_access","creator":"vkravchu","date_created":"2023-04-19T14:33:52Z","relation":"source_file","embargo":"2024-04-20","date_updated":"2024-04-22T22:30:06Z","file_id":"12853","checksum":"c12055c48411d030d2afa51de2166221","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19468766}],"supervisor":[{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"year":"2023"},{"supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"year":"2023","month":"05","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","date_published":"2023-05-05T00:00:00Z","file":[{"date_created":"2023-05-05T13:01:14Z","creator":"aschauer","access_level":"open_access","relation":"main_file","checksum":"59b0303dc483f40a96a610a90aab7ee9","file_name":"Thesis_Schauer_final.pdf","file_id":"12907","date_updated":"2024-05-06T22:30:03Z","embargo":"2024-05-05","file_size":31434230,"content_type":"application/pdf"},{"relation":"source_file","date_created":"2023-05-05T13:04:15Z","creator":"aschauer","access_level":"closed","file_size":43809109,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2024-05-06T22:30:03Z","file_name":"Thesis_Schauer_final.docx","checksum":"25f54e12479b6adaabd129a20568e6c1","file_id":"12908"}],"ddc":["570"],"day":"05","type":"dissertation","publication_status":"published","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239"}],"publication_identifier":{"issn":["2663-337X"]},"oa":1,"corr_author":"1","abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","last_name":"Schauer"}],"related_material":{"record":[{"id":"7888","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8966","status":"public"}]},"citation":{"ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>"},"file_date_updated":"2024-05-06T22:30:03Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:12891","has_accepted_license":"1","date_created":"2023-05-05T08:48:20Z","language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2025-06-12T06:56:58Z","page":"190","doi":"10.15479/at:ista:12891","_id":"12891","article_processing_charge":"No","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"quality_controlled":"1","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa":1,"pmid":1,"abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"author":[{"last_name":"Wang","full_name":"Wang, Yalu","first_name":"Yalu"},{"first_name":"Zhi","full_name":"Yuan, Zhi","last_name":"Yuan"},{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"full_name":"Xiao, Huixin","last_name":"Xiao","first_name":"Huixin"},{"first_name":"Lu","last_name":"Wan","full_name":"Wan, Lu"},{"full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"}],"file_date_updated":"2023-12-13T23:30:03Z","citation":{"short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(25). doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>.","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>.","ieee":"Y. Wang <i>et al.</i>, “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25. National Academy of Sciences, 2023."},"publisher":"National Academy of Sciences","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2023","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","month":"06","file":[{"date_updated":"2023-12-13T23:30:03Z","embargo":"2023-12-12","file_name":"2023_PNAS_Wang.pdf","checksum":"d800e06252eaefba28531fa9440f23f0","file_id":"13204","file_size":5244581,"content_type":"application/pdf","date_created":"2023-07-10T08:48:40Z","access_level":"open_access","creator":"alisjak","relation":"main_file"}],"acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the  National  Natural  Science  Foundation  of  China  (32170265  and  32022007),  Hainan  Provincial  Natural  Science  Foundation  of  China  (323CXTD379),  Chinese  Universities  Scientific  Fund  (2023TC019),  Beijing  Municipal  Natural  Science  Foundation  (5192011),  Beijing  Outstanding  University  Discipline  Program,  and  China Postdoctoral Science Foundation (BH2020259460).","date_published":"2023-06-12T00:00:00Z","ddc":["570"],"issue":"25","day":"12","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","intvolume":"       120","type":"journal_article","date_updated":"2023-12-13T23:30:04Z","scopus_import":"1","_id":"13201","doi":"10.1073/pnas.2221313120","article_processing_charge":"No","department":[{"_id":"JiFr"}],"article_number":"e2221313120","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"volume":120,"fulldoi":"https://doi.org/10.1073/pnas.2221313120","external_id":{"isi":["001030689600003"],"pmid":["37307446"]},"isi":1,"has_accepted_license":"1","date_created":"2023-07-09T22:01:12Z","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"status":"public","OA_place":"publisher","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"doi":"10.15479/at:ista:12531","_id":"12531","article_processing_charge":"No","date_updated":"2026-04-07T14:06:26Z","page":"46","language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","date_created":"2023-02-09T07:45:05Z","alternative_title":["ISTA Master's Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:12531","degree_awarded":"MS","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","abstract":[{"lang":"eng","text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics."}],"author":[{"id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","first_name":"Kseniia","last_name":"Kirillova","full_name":"Kirillova, Kseniia"}],"file_date_updated":"2024-02-09T23:30:03Z","citation":{"apa":"Kirillova, K. (2023). <i>Panoramic functional gradients across the mouse retina</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","mla":"Kirillova, Kseniia. <i>Panoramic Functional Gradients across the Mouse Retina</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria."},"publication_identifier":{"issn":["2791-4585"]},"oa":1,"publication_status":"published","type":"dissertation","ddc":["570"],"day":"08","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"02","title":"Panoramic functional gradients across the mouse retina","file":[{"file_size":8369317,"content_type":"application/pdf","date_updated":"2024-02-09T23:30:03Z","embargo":"2024-02-08","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","checksum":"57d8da3a6c749eb1556b7435fe266a5f","file_id":"12532","relation":"main_file","date_created":"2023-02-09T08:03:32Z","creator":"cchlebak","access_level":"open_access"},{"date_updated":"2024-02-09T23:30:03Z","file_id":"12535","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","content_type":"application/x-zip-compressed","file_size":11204408,"embargo_to":"open_access","creator":"cchlebak","access_level":"closed","date_created":"2023-02-10T09:32:06Z","relation":"source_file"}],"date_published":"2023-02-08T00:00:00Z","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"year":"2023"},{"oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-038-1"]},"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Stopp","full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","short":"J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","ama":"Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","chicago":"Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","mla":"Stopp, Julian A. <i>Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>.","ieee":"J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>"},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14360"},{"status":"public","id":"12272","relation":"part_of_dissertation"},{"status":"public","id":"6328","relation":"part_of_dissertation"},{"status":"public","id":"7885","relation":"part_of_dissertation"},{"id":"14274","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2024-12-20T23:30:04Z","corr_author":"1","abstract":[{"text":"During my Ph.D. research, I managed a series of projects, each focused on the\r\nmechanisms underlying cell migration. My work involved an in-depth examination of\r\nthe complex strategies employed by neutrophils, with a specific focus on their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient perception. However, it\r\nis essential to acknowledge that not all projects yielded successful results, as some\r\nideas were discontinued and are archived for future reference within this thesis.\r\nMy main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source\r\ntype – linear or point-like. By combining single-cell tracking in 3D environments with\r\nproxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential gradients from point sources. In addition, neutrophils\r\nexhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over\r\ntime and employed a \"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic \"tumbles\" for efficient navigation.\r\nThe project extended to the possibility of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings, pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences\r\nin migratory efficacy were detected across pore sizes and device heights, quantifying\r\ngradient manipulation effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\" (LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through extensive experimentation with multiple\r\nparameters, we attempted to trigger responses from neutrophils. Despite these efforts\r\nand collaboration, the project failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line. Despite their existence, their migratory behavior was largely\r\nunexplored due to potential limitations. Through differentiation protocol refinements we\r\nenhanced their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils. Despite this, the improved migration potential of these cells pointed toward\r\ntheir utility for in vitro murine neutrophil migration studies.","lang":"eng"}],"file":[{"file_size":51585778,"content_type":"application/pdf","date_updated":"2024-12-20T23:30:04Z","embargo":"2024-12-20","checksum":"457927165d5d556305d3086f6b83e5c7","file_name":"Thesis.pdf","file_id":"14699","relation":"main_file","date_created":"2023-12-20T09:35:34Z","creator":"jstopp","access_level":"open_access"},{"relation":"source_file","creator":"jstopp","access_level":"closed","date_created":"2023-12-20T09:35:35Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":69625950,"file_id":"14700","checksum":"e8d26449ac461f5e8478a62c9507506f","file_name":"Thesis.docx","date_updated":"2024-12-20T23:30:04Z"}],"date_published":"2023-12-20T00:00:00Z","month":"12","title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","supervisor":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"year":"2023","type":"dissertation","day":"20","ddc":["570"],"ec_funded":1,"article_processing_charge":"No","_id":"14697","doi":"10.15479/at:ista:14697","page":"226","date_updated":"2026-06-18T17:34:48Z","status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"fulldoi":"https://doi.org/10.15479/at:ista:14697","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-12-18T19:14:28Z","has_accepted_license":"1"},{"type":"journal_article","intvolume":"        14","article_type":"original","ddc":["570"],"publication":"Nature Communications","day":"13","title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","month":"09","date_published":"2023-09-13T00:00:00Z","file":[{"date_created":"2023-09-25T08:22:58Z","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2023-09-25T08:22:58Z","checksum":"ad670e3b3c64fc585675948370f6b149","file_name":"2023_NatureComm_Sitarska.pdf","file_id":"14365","file_size":2725421,"content_type":"application/pdf"}],"acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","year":"2023","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"pmid":1,"citation":{"mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>.","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>"},"file_date_updated":"2023-09-25T08:22:58Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14697"}]},"author":[{"first_name":"Ewa","full_name":"Sitarska, Ewa","last_name":"Sitarska"},{"last_name":"Almeida","full_name":"Almeida, Silvia Dias","first_name":"Silvia Dias"},{"full_name":"Beckwith, Marianne Sandvold","last_name":"Beckwith","first_name":"Marianne Sandvold"},{"last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"first_name":"Jakub","full_name":"Czuchnowski, Jakub","last_name":"Czuchnowski"},{"first_name":"Marc","last_name":"Siggel","full_name":"Siggel, Marc"},{"last_name":"Roessner","full_name":"Roessner, Rita","first_name":"Rita"},{"last_name":"Tschanz","full_name":"Tschanz, Aline","first_name":"Aline"},{"last_name":"Ejsing","full_name":"Ejsing, Christer","first_name":"Christer"},{"first_name":"Yannick","last_name":"Schwab","full_name":"Schwab, Yannick"},{"last_name":"Kosinski","full_name":"Kosinski, Jan","first_name":"Jan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"full_name":"Erzberger, Anna","last_name":"Erzberger","first_name":"Anna"},{"full_name":"Diz-Muñoz, Alba","last_name":"Diz-Muñoz","first_name":"Alba"}],"publication_identifier":{"eissn":["2041-1723"]},"oa":1,"quality_controlled":"1","publication_status":"published","oa_version":"Published Version","language":[{"iso":"eng"}],"has_accepted_license":"1","isi":1,"date_created":"2023-09-24T22:01:10Z","volume":14,"external_id":{"isi":["001087583700008"],"pmid":["37704612"]},"fulldoi":"https://doi.org/10.1038/s41467-023-41173-1","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"5644","department":[{"_id":"MiSi"}],"_id":"14360","doi":"10.1038/s41467-023-41173-1","article_processing_charge":"Yes (via OA deal)","date_updated":"2026-10-01T22:30:17Z","scopus_import":"1"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska"}],"related_material":{"record":[{"id":"7883","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2025-03-13T23:30:05Z","citation":{"short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023."},"corr_author":"1","abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"}],"publication_status":"published","type":"dissertation","day":"13","ddc":["570"],"date_published":"2023-09-13T00:00:00Z","file":[{"relation":"main_file","date_created":"2023-09-13T09:52:52Z","creator":"kkuzmicz","access_level":"open_access","file_size":10147911,"content_type":"application/pdf","date_updated":"2025-03-13T23:30:05Z","embargo":"2025-03-13","file_name":"PhDThesis_KK_final_pdfA.pdf","checksum":"bd83596869c814b24aeff7077d031c0e","file_id":"14324"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":103980668,"embargo_to":"open_access","date_updated":"2025-03-13T23:30:05Z","file_id":"14325","file_name":"thesis_KK_final_corrections_092023.docx","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","relation":"source_file","creator":"kkuzmicz","access_level":"closed","date_created":"2023-09-13T09:53:29Z"}],"month":"09","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","supervisor":[{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"year":"2023","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"article_processing_charge":"No","doi":"10.15479/at:ista:14323","_id":"14323","page":"151","date_updated":"2026-04-14T09:50:54Z","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-09-13T10:07:18Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/at:ista:14323","alternative_title":["ISTA Thesis"]},{"author":[{"first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","full_name":"Bocanegra, Laura","last_name":"Bocanegra"},{"first_name":"Amrita","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958","last_name":"Singh","full_name":"Singh, Amrita"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"first_name":"Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","last_name":"Zagórski"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-10-04T11:13:28Z","related_material":{"record":[{"id":"13081","status":"public","relation":"dissertation_contains"}]},"citation":{"ista":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 19, 1050–1058.","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058.","ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. 2023;19:1050-1058. doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1050–1058, 2023.","mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>.","chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>.","apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., &#38; Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>"},"pmid":1,"corr_author":"1","abstract":[{"text":"As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","oa":1,"project":[{"grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"day":"01","publication":"Nature Physics","ddc":["570"],"article_type":"original","intvolume":"        19","type":"journal_article","year":"2023","date_published":"2023-07-01T00:00:00Z","file":[{"access_level":"open_access","creator":"dernst","date_created":"2023-10-04T11:13:28Z","success":1,"relation":"main_file","date_updated":"2023-10-04T11:13:28Z","file_id":"14392","file_name":"2023_NaturePhysics_Boncanegra.pdf","checksum":"858225a4205b74406e5045006cdd853f","content_type":"application/pdf","file_size":5532285}],"acknowledgement":"We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).","month":"07","title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","page":"1050-1058","scopus_import":"1","date_updated":"2026-10-01T22:30:18Z","ec_funded":1,"article_processing_charge":"No","_id":"12837","doi":"10.1038/s41567-023-01977-w","date_created":"2023-04-16T22:01:09Z","isi":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1038/s41567-023-01977-w","external_id":{"pmid":["37456593"],"isi":["000964029300003"]},"volume":19},{"publication_status":"published","oa":1,"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"9349","status":"public"},{"id":"12837","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2024-06-01T22:30:04Z","citation":{"mla":"Bocanegra, Laura. <i>Epithelial Dynamics during Mouse Neural Tube Development</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>.","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>.","apa":"Bocanegra, L. (2023). <i>Epithelial dynamics during mouse neural tube development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023."},"author":[{"last_name":"Bocanegra","full_name":"Bocanegra, Laura","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling.  Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis."}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","year":"2023","supervisor":[{"last_name":"Kicheva","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998"}],"date_published":"2023-05-23T00:00:00Z","file":[{"date_created":"2023-05-25T06:32:12Z","access_level":"closed","creator":"lbocaneg","relation":"source_file","file_name":"Thesis_final_LauraBocanegra.docx","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","file_id":"13089","date_updated":"2024-06-01T22:30:04Z","embargo_to":"open_access","file_size":25615534,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_created":"2023-05-25T06:32:16Z","access_level":"open_access","creator":"lbocaneg","relation":"main_file","date_updated":"2024-06-01T22:30:04Z","embargo":"2024-05-31","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","file_id":"13090","file_size":12386046,"content_type":"application/pdf"}],"title":"Epithelial dynamics during mouse neural tube development","month":"05","day":"23","ddc":["570"],"type":"dissertation","page":"93","date_updated":"2026-04-14T09:50:54Z","article_processing_charge":"No","_id":"13081","doi":"10.15479/at:ista:13081","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"OA_place":"publisher","status":"public","fulldoi":"https://doi.org/10.15479/at:ista:13081","alternative_title":["ISTA Thesis"],"date_created":"2023-05-23T19:10:42Z","has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}]},{"doi":"10.15479/at:ista:12800","_id":"12800","article_processing_charge":"No","date_updated":"2026-04-07T14:01:51Z","page":"21","status":"public","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"alternative_title":["ISTA Master's Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:12800","language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","date_created":"2023-04-04T18:57:11Z","publication_identifier":{"issn":["2791-4585"]},"oa":1,"publication_status":"published","degree_awarded":"MS","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara","full_name":"Julseth, Mara","last_name":"Julseth"}],"citation":{"mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>"},"file_date_updated":"2023-06-02T22:30:04Z","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","month":"04","file":[{"date_updated":"2023-06-02T22:30:04Z","file_name":"Dispersaldata.xlsx","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","file_id":"12805","file_size":52795,"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","embargo_to":"open_access","date_created":"2023-04-06T06:09:40Z","access_level":"closed","creator":"mjulseth","relation":"supplementary_material"},{"content_type":"application/vnd.wolfram.nb","file_size":787239,"embargo":"2023-06-01","date_updated":"2023-06-02T22:30:04Z","file_id":"12806","checksum":"5a13b6d204371572e249f03795bc0d04","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","relation":"supplementary_material","access_level":"open_access","creator":"mjulseth","date_created":"2023-04-06T06:11:27Z"},{"file_size":1061763,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2023-06-02T22:30:04Z","checksum":"c3ec842839ed1e66bf2618ae33047df8","file_name":"ThesisMaraJulseth_04_23.docx","file_id":"12812","relation":"source_file","date_created":"2023-04-06T08:26:12Z","access_level":"closed","creator":"mjulseth"},{"date_updated":"2023-06-02T22:30:04Z","embargo":"2023-06-01","file_name":"ThesisMaraJulseth_04_23.pdf","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","file_id":"12813","file_size":1741364,"content_type":"application/pdf","date_created":"2023-04-06T08:26:37Z","access_level":"open_access","creator":"mjulseth","relation":"main_file"}],"date_published":"2023-04-05T00:00:00Z","supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"year":"2023","type":"dissertation","ddc":["576"],"day":"05"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","citation":{"ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","apa":"Confavreux, B. J. (2023). <i>Synapseek: Meta-learning synaptic plasticity rules</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>.","mla":"Confavreux, Basile J. <i>Synapseek: Meta-Learning Synaptic Plasticity Rules</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>."},"file_date_updated":"2024-10-13T22:30:04Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9633"}]},"author":[{"last_name":"Confavreux","full_name":"Confavreux, Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J"}],"abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"corr_author":"1","oa":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","call_identifier":"H2020"}],"publication_status":"published","type":"dissertation","day":"12","ddc":["610"],"date_published":"2023-10-12T00:00:00Z","file":[{"creator":"cchlebak","access_level":"open_access","date_created":"2023-10-12T14:53:50Z","relation":"main_file","file_id":"14424","checksum":"7f636555eae7803323df287672fd13ed","file_name":"Confavreux_Thesis_2A.pdf","embargo":"2024-10-12","date_updated":"2024-10-13T22:30:04Z","content_type":"application/pdf","file_size":30599717},{"file_size":68406739,"content_type":"application/x-zip-compressed","embargo_to":"open_access","date_updated":"2024-10-13T22:30:04Z","checksum":"725e85946db92290a4583a0de9779e1b","file_name":"Confavreux Thesis.zip","file_id":"14440","relation":"source_file","date_created":"2023-10-18T07:38:34Z","access_level":"closed","creator":"cchlebak"}],"title":"Synapseek: Meta-learning synaptic plasticity rules","month":"10","supervisor":[{"full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"year":"2023","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"OA_place":"publisher","status":"public","department":[{"_id":"GradSch"},{"_id":"TiVo"}],"ec_funded":1,"article_processing_charge":"No","doi":"10.15479/at:ista:14422","_id":"14422","page":"148","date_updated":"2026-07-07T06:53:33Z","oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2023-10-12T14:13:25Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/at:ista:14422","alternative_title":["ISTA Thesis"]},{"page":"8140-8156","scopus_import":"1","date_updated":"2026-07-06T12:47:25Z","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","_id":"14656","doi":"10.1523/JNEUROSCI.0194-23.2023","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","external_id":{"isi":["001148071000005"],"pmid":["37758476"]},"fulldoi":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","volume":43,"date_created":"2023-12-10T23:00:58Z","has_accepted_license":"1","isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","oa":1,"project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","call_identifier":"FP7"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1529-2401"]},"file_date_updated":"2024-06-02T22:30:03Z","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>."},"related_material":{"record":[{"status":"public","id":"10077","relation":"earlier_version"}]},"author":[{"orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","full_name":"Nardin, Michele","last_name":"Nardin"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina"}],"abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Society for Neuroscience","year":"2023","acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","date_published":"2023-11-29T00:00:00Z","file":[{"relation":"main_file","date_created":"2023-12-11T11:30:37Z","access_level":"open_access","creator":"dernst","file_size":2280632,"content_type":"application/pdf","date_updated":"2024-06-02T22:30:03Z","embargo":"2024-06-01","checksum":"e2503c8f84be1050e28f64320f1d5bd2","file_name":"2023_JourNeuroscience_Nardin.pdf","file_id":"14674"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","month":"11","publication":"The Journal of Neuroscience","day":"29","issue":"48","ddc":["570"],"type":"journal_article","intvolume":"        43","article_type":"original"},{"intvolume":"        62","article_type":"original","type":"journal_article","day":"01","publication":"Applied Optics","issue":"1","date_published":"2023-01-01T00:00:00Z","acknowledgement":"We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript.","title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","month":"01","year":"2023","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","publisher":"Optica Publishing Group","author":[{"first_name":"Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","orcid":"0000-0002-5869-1604","full_name":"Wald, Sebastian","last_name":"Wald"},{"last_name":"Diorico","full_name":"Diorico, Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","first_name":"Fritz R","orcid":"0000-0002-4947-8924"},{"first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","full_name":"Hosten, Onur"}],"supplementarymaterial":"yes","citation":{"apa":"Wald, S., Diorico, F. R., &#38; Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” <i>Applied Optics</i>, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023.","mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>.","chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>. Optica Publishing Group, 2023. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>.","ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. 2023;62(1):1-7. doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>","short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7."},"related_material":{"record":[{"id":"20798","status":"public","relation":"dissertation_contains"}]},"corr_author":"1","researchdata_availability":"upon request","abstract":[{"text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method.","lang":"eng"}],"oa":1,"arxiv":1,"publication_identifier":{"issn":["1559-128X"],"eissn":["2155-3165"]},"publication_status":"published","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.11591","open_access":"1"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","date_created":"2024-01-08T13:19:14Z","isi":1,"das_tickbox":"1","fulldoi":"https://doi.org/10.1364/ao.474118","external_id":{"arxiv":["2208.11591"],"isi":["000906607900001"]},"volume":62,"dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","status":"public","department":[{"_id":"OnHo"}],"article_processing_charge":"No","doi":"10.1364/ao.474118","_id":"14759","page":"1-7","keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"date_updated":"2026-10-01T22:30:31Z","scopus_import":"1"},{"external_id":{"pmid":["37355691"],"isi":["001018100800002"],"arxiv":["2210.12443"]},"fulldoi":"https://doi.org/10.1038/s41467-023-39493-3","volume":14,"date_created":"2023-07-09T22:01:11Z","has_accepted_license":"1","isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2026-10-01T22:30:33Z","scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes","_id":"13200","doi":"10.1038/s41467-023-39493-3","article_number":"3784","department":[{"_id":"JoFi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","status":"public","year":"2023","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","file":[{"checksum":"ec7ccd2c08f90d59cab302fd0d7776a4","file_name":"2023_NatureComms_Qiu.pdf","file_id":"13206","date_updated":"2023-07-10T10:10:54Z","file_size":1349134,"content_type":"application/pdf","date_created":"2023-07-10T10:10:54Z","access_level":"open_access","creator":"alisjak","relation":"main_file","success":1}],"date_published":"2023-06-24T00:00:00Z","month":"06","title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","publication":"Nature Communications","day":"24","ddc":["000"],"OA_type":"gold","type":"journal_article","APC_amount":"6228 EUR","intvolume":"        14","article_type":"original","publication_status":"published","quality_controlled":"1","arxiv":1,"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"citation":{"chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>. Nature Research, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>.","ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” <i>Nature Communications</i>, vol. 14. Nature Research, 2023.","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>, vol. 14, 3784, Nature Research, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>.","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., &#38; Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>","ista":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784.","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>"},"related_material":{"record":[{"id":"18871","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2023-07-10T10:10:54Z","DOAJ_listed":"1","author":[{"first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu","last_name":"Qiu"},{"full_name":"Sahu, Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","orcid":"0000-0001-6264-2162"},{"last_name":"Hease","full_name":"Hease, William J","first_name":"William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold","full_name":"Arnold, Georg M"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"abstract":[{"text":"Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks.","lang":"eng"}],"corr_author":"1","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Research"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Arnold","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","orcid":"0000-0003-1397-7876"},{"id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7","orcid":"0009-0001-2346-5236","first_name":"Thomas","full_name":"Werner, Thomas","last_name":"Werner"},{"last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","orcid":"0000-0001-6264-2162"},{"id":"84b9700b-15b2-11ec-abd3-831089e67615","first_name":"Lucky","orcid":"0000-0001-8319-2148","last_name":"Kapoor","full_name":"Kapoor, Lucky"},{"full_name":"Qiu, Liu","last_name":"Qiu","first_name":"Liu","orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac"},{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"citation":{"ista":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","short":"G.M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, J.M. Fink, ArXiv (n.d.).","ama":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>","chicago":"Arnold, Georg M, Thomas Werner, Rishabh Sahu, Lucky Kapoor, Liu Qiu, and Johannes M Fink. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>.","mla":"Arnold, Georg M., et al. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","ieee":"G. M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, and J. M. Fink, “All-optical single-shot readout of a superconducting qubit,” <i>arXiv</i>. .","apa":"Arnold, G. M., Werner, T., Sahu, R., Kapoor, L., Qiu, L., &#38; Fink, J. M. (n.d.). All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>"},"related_material":{"record":[{"id":"19073","status":"public","relation":"later_version"},{"status":"public","id":"18871","relation":"dissertation_contains"}]},"corr_author":"1","abstract":[{"text":"The rapid development of superconducting quantum hardware is expected to run into significant I/O restrictions due to the need for large-scale error correction in a cryogenic environment. Classical data centers rely on fiber-optic interconnects to remove similar networking bottlenecks and to allow for reconfigurable, software-defined infrastructures. In the same spirit, ultra-cold electro-optic links have been proposed and used to generate qubit control signals, or to replace cryogenic readout electronics. So far, the latter suffered from either low efficiency, low bandwidth and the need for additional microwave drives, or breaking of Cooper pairs and qubit states. In this work we realize electro-optic microwave photonics at millikelvin temperatures to implement a radio-over-fiber qubit readout that does not require any active or passive cryogenic microwave equipment. We demonstrate all-optical single-shot-readout by means of the Jaynes-Cummings nonlinearity in a circulator-free readout scheme. Importantly, we do not observe any direct radiation impact on the qubit state as verified with high-fidelity quantum-non-demolition measurements despite the absence of shielding elements. This compatibility between superconducting circuits and telecom wavelength light is not only a prerequisite to establish modular quantum networks, it is also relevant for multiplexed readout of superconducting photon detectors and classical superconducting logic. Moreover, this experiment showcases the potential of electro-optic radiometry in harsh environments - an electronics-free sensing principle that extends into the THz regime with applications in radio astronomy, planetary missions and earth observation.","lang":"eng"}],"oa":1,"arxiv":1,"project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states","grant_number":"101089099","_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"publication_status":"draft","type":"preprint","day":"25","publication":"arXiv","date_published":"2023-10-25T00:00:00Z","acknowledgement":"We thank F. Hassani and M. Zemlicka for assistance\r\nwith qubit design and high power readout respectively,\r\nand P. Winkel and I. Pop at KIT for providing the JPA.\r\nThis work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG\r\nQUNNECT) and no. 101089099 (ERC CoG cQEO), the\r\nEuropean Union’s Horizon 2020 research and innovation\r\nprogram under grant agreement no. 899354 (FETopen\r\nSuperQuLAN) and the Austrian Science Fund (FWF)\r\nthrough BeyondC (grant no. F7105). L.Q. acknowledges\r\ngenerous support from the ISTFELLOW programme\r\nand G.A. is the recipient of a DOC fellowship of the\r\nAustrian Academy of Sciences at IST Austria.","month":"10","title":"All-optical single-shot readout of a superconducting qubit","year":"2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","OA_place":"repository","department":[{"_id":"JoFi"}],"article_processing_charge":"No","ec_funded":1,"_id":"18953","doi":"10.48550/ARXIV.2310.16817","date_updated":"2026-10-01T22:30:33Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.16817"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","date_created":"2025-01-29T11:11:34Z","fulldoi":"https://doi.org/10.48550/ARXIV.2310.16817","external_id":{"arxiv":["2310.16817"]}},{"volume":8,"fulldoi":"https://doi.org/10.1126/sciimmunol.adc9584","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"isi":1,"date_created":"2023-09-06T08:07:51Z","language":[{"iso":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"date_updated":"2026-10-01T22:30:35Z","scopus_import":"1","keyword":["General Medicine","Immunology"],"_id":"14274","doi":"10.1126/sciimmunol.adc9584","article_processing_charge":"No","ec_funded":1,"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"article_number":"adc9584","status":"public","year":"2023","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","month":"09","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","date_published":"2023-09-01T00:00:00Z","issue":"87","ddc":["570"],"day":"01","publication":"Science Immunology","intvolume":"         8","article_type":"original","type":"journal_article","quality_controlled":"1","publication_status":"published","publication_identifier":{"issn":["2470-9468"]},"project":[{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"oa":1,"corr_author":"1","pmid":1,"abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"author":[{"last_name":"Alanko","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","first_name":"Jonna H"},{"first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","last_name":"Ucar"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola","orcid":"0000-0002-8518-5926","last_name":"Canigova","full_name":"Canigova, Nikola"},{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"last_name":"Schwarz","full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"}],"related_material":{"record":[{"status":"public","id":"14279","relation":"research_data"},{"status":"public","id":"14697","relation":"dissertation_contains"},{"id":"19745","status":"public","relation":"dissertation_contains"}]},"citation":{"mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>"},"publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]