[{"status":"public","oa_version":"Published Version","type":"dissertation","doi":"10.15479/at:ista:14280","publication_status":"published","author":[{"full_name":"Radler, Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","first_name":"Philipp"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"date_updated":"2026-04-07T14:06:05Z","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023."},"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","grant_number":"679239"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","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"},{"grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425","name":"Reconstitution of bacterial cell wall synthesis"}],"file_date_updated":"2024-10-05T22:30:03Z","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"page":"156","file":[{"creator":"pradler","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14390","date_created":"2023-10-04T10:11:53Z","access_level":"closed","embargo_to":"open_access","checksum":"87eef11fbc5c7df0826f12a3a629b444","relation":"source_file","file_size":114932847,"file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_updated":"2024-10-05T22:30:03Z"},{"checksum":"3253e099b7126469d941fd9419d68b4f","embargo":"2024-10-04","relation":"main_file","file_size":37838778,"file_name":"PhD Thesis_Philipp Radler_20231004.pdf","date_updated":"2024-10-05T22:30:03Z","creator":"pradler","content_type":"application/pdf","file_id":"14391","date_created":"2023-10-04T10:11:21Z","access_level":"open_access"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"10934"},{"relation":"part_of_dissertation","status":"public","id":"11373"},{"relation":"part_of_dissertation","status":"public","id":"7387"}]},"degree_awarded":"PhD","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."}],"date_created":"2023-09-06T10:58:25Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"alternative_title":["ISTA Thesis"],"year":"2023","date_published":"2023-09-25T00:00:00Z","ddc":["572"],"day":"25","supervisor":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose"}],"publisher":"Institute of Science and Technology Austria","_id":"14280","title":"Spatiotemporal signaling during assembly of the bacterial divisome","ec_funded":1,"OA_place":"publisher","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"]},{"author":[{"full_name":"Gupta, Divyansh","last_name":"Gupta","first_name":"Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665"},{"last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sumser, Anton L","last_name":"Sumser","first_name":"Anton L","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","full_name":"Symonova, Olga","last_name":"Symonova"},{"id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","orcid":"0000-0002-6198-2939","first_name":"Jan","full_name":"Svaton, Jan","last_name":"Svaton"},{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"date_updated":"2026-05-13T22:30:35Z","status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41593-023-01280-0","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"page":"606-614","acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","related_material":{"record":[{"relation":"research_data","status":"public","id":"12370"},{"id":"18574","status":"public","relation":"dissertation_contains"}]},"file":[{"date_updated":"2023-10-04T11:40:51Z","file_name":"2023_NatureNeuroscience_Gupta.pdf","relation":"main_file","checksum":"a33d91e398e548f34003170e10988368","file_size":6144866,"file_id":"14395","access_level":"open_access","success":1,"date_created":"2023-10-04T11:40:51Z","content_type":"application/pdf","creator":"dernst"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"language":[{"iso":"eng"}],"citation":{"mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023, pp. 606–14, doi:10.1038/s41593-023-01280-0.","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience. Springer Nature, 2023. https://doi.org/10.1038/s41593-023-01280-0.","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., & Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0"},"has_accepted_license":"1","corr_author":"1","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017"}],"file_date_updated":"2023-10-04T11:40:51Z","scopus_import":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2023","date_published":"2023-04-01T00:00:00Z","quality_controlled":"1","date_created":"2023-01-23T14:14:19Z","intvolume":" 26","abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.","lang":"eng"}],"ec_funded":1,"article_type":"original","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","volume":26,"publication":"Nature Neuroscience","pmid":1,"ddc":["570"],"publisher":"Springer Nature","day":"01","_id":"12349"},{"has_accepted_license":"1","citation":{"mla":"Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","ista":"Gupta D, Sumser AL, Jösch MA. 2023. 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It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. ","lang":"eng"}],"date_created":"2023-01-25T12:45:18Z","oa":1,"tmp":{"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","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"year":"2023","date_published":"2023-01-26T00:00:00Z"},{"month":"04","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2791-4585"]},"file":[{"file_name":"Dispersaldata.xlsx","date_updated":"2023-06-02T22:30:04Z","embargo_to":"open_access","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","relation":"supplementary_material","file_size":52795,"file_id":"12805","date_created":"2023-04-06T06:09:40Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","creator":"mjulseth"},{"date_updated":"2023-06-02T22:30:04Z","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","embargo":"2023-06-01","relation":"supplementary_material","checksum":"5a13b6d204371572e249f03795bc0d04","file_size":787239,"file_id":"12806","access_level":"open_access","date_created":"2023-04-06T06:11:27Z","content_type":"application/vnd.wolfram.nb","creator":"mjulseth"},{"creator":"mjulseth","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12812","date_created":"2023-04-06T08:26:12Z","access_level":"closed","checksum":"c3ec842839ed1e66bf2618ae33047df8","embargo_to":"open_access","relation":"source_file","file_size":1061763,"date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.docx"},{"access_level":"open_access","date_created":"2023-04-06T08:26:37Z","file_id":"12813","creator":"mjulseth","content_type":"application/pdf","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.pdf","file_size":1741364,"embargo":"2023-06-01","relation":"main_file","checksum":"3132cc998fbe3ae2a3a83c2a69367f37"}],"page":"21","language":[{"iso":"eng"}],"citation":{"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.","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.","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.","mla":"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, doi:10.15479/at:ista:12800.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","apa":"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. https://doi.org/10.15479/at:ista:12800","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. https://doi.org/10.15479/at:ista:12800."},"has_accepted_license":"1","corr_author":"1","file_date_updated":"2023-06-02T22:30:04Z","author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara","full_name":"Julseth, Mara","last_name":"Julseth"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_updated":"2026-04-07T14:01:51Z","status":"public","type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:12800","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","OA_place":"publisher","ddc":["576"],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publisher":"Institute of Science and Technology Austria","day":"05","_id":"12800","oa":1,"year":"2023","alternative_title":["ISTA Master's Thesis"],"date_published":"2023-04-05T00:00:00Z","degree_awarded":"MS","date_created":"2023-04-04T18:57:11Z","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. "}]},{"month":"03","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"EM-Fac"}],"related_material":{"record":[{"id":"12138","status":"public","relation":"part_of_dissertation"}]},"page":"127","file":[{"file_id":"12852","date_created":"2023-04-19T14:33:41Z","access_level":"open_access","creator":"vkravchu","content_type":"application/pdf","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","date_updated":"2024-04-22T22:30:06Z","checksum":"5ebb6345cb4119f93460c81310265a6d","embargo":"2024-04-20","relation":"main_file","file_size":6071553},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"vkravchu","file_id":"12853","date_created":"2023-04-19T14:33:52Z","access_level":"open_access","checksum":"c12055c48411d030d2afa51de2166221","embargo":"2024-04-20","relation":"source_file","file_size":19468766,"file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","date_updated":"2024-04-22T22:30:06Z"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"has_accepted_license":"1","citation":{"mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","ieee":"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:10.15479/at:ista:12781","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781"},"language":[{"iso":"eng"}],"file_date_updated":"2024-04-22T22:30:06Z","project":[{"grant_number":"25541","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020"}],"corr_author":"1","article_processing_charge":"No","author":[{"first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089","full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk"}],"date_updated":"2026-04-07T14:10:40Z","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"status":"public","doi":"10.15479/at:ista:12781","publication_status":"published","oa_version":"Published Version","type":"dissertation","OA_place":"publisher","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","ec_funded":1,"ddc":["570","572"],"_id":"12781","day":"23","supervisor":[{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2023-03-23T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2023","degree_awarded":"PhD","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"}],"date_created":"2023-03-31T12:24:42Z"},{"citation":{"apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523."},"language":[{"iso":"eng"}],"_id":"14591","corr_author":"1","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"day":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","OA_place":"repository","ec_funded":1,"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","publication":"bioRxiv","related_material":{"record":[{"status":"public","relation":"later_version","id":"15330"},{"status":"public","relation":"dissertation_contains","id":"14510"}]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"status":"public","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"date_created":"2023-11-22T10:17:49Z","publication_status":"draft","doi":"10.1101/2023.10.09.561523","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.09.561523"}],"type":"preprint","oa_version":"Preprint","author":[{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"},{"full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"last_name":"Nagel","full_name":"Nagel, Marie-Kristin","first_name":"Marie-Kristin"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","last_name":"Hlavata","full_name":"Hlavata, Annamaria"},{"last_name":"Isono","full_name":"Isono, Erika","first_name":"Erika"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"article_processing_charge":"No","oa":1,"date_published":"2023-10-10T00:00:00Z","date_updated":"2026-05-13T22:30:37Z","year":"2023","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}]},{"type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:14510","status":"public","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"date_updated":"2026-05-13T22:30:39Z","article_processing_charge":"No","author":[{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"}],"corr_author":"1","file_date_updated":"2024-11-23T23:30:38Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"language":[{"iso":"eng"}],"citation":{"ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510."},"has_accepted_license":"1","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"file":[{"file_size":20824903,"relation":"source_file","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","embargo_to":"open_access","date_updated":"2024-11-23T23:30:38Z","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","creator":"ngnyliuk","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2023-11-20T09:18:51Z","file_id":"14567"},{"file_id":"14568","date_created":"2023-11-20T09:23:11Z","access_level":"open_access","content_type":"application/pdf","creator":"ngnyliuk","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_updated":"2024-11-23T23:30:38Z","checksum":"bfc96d47fc4e7e857dd71656097214a4","embargo":"2024-11-23","relation":"main_file","file_size":24871844}],"page":"180","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14591"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8139"}]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"11","date_created":"2023-11-10T09:10:06Z","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. ","lang":"eng"}],"degree_awarded":"PhD","year":"2023","alternative_title":["ISTA Thesis"],"date_published":"2023-11-10T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin"}],"publisher":"Institute of Science and Technology Austria","day":"10","_id":"14510","ddc":["570"],"keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"ec_funded":1,"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","OA_place":"publisher"},{"degree_awarded":"PhD","date_created":"2023-01-31T15:10:53Z","abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"alternative_title":["ISTA Thesis"],"year":"2023","date_published":"2023-01-09T00:00:00Z","ddc":["610"],"day":"09","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G"}],"_id":"12470","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","ec_funded":1,"OA_place":"publisher","status":"public","oa_version":"Published Version","type":"dissertation","doi":"10.15479/at:ista:12470","publication_status":"published","article_processing_charge":"No","author":[{"first_name":"Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","last_name":"Michalska"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"date_updated":"2026-04-07T14:11:10Z","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470"},"file_date_updated":"2023-07-27T22:30:54Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-026-8"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"page":"201","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11943"},{"relation":"part_of_dissertation","status":"public","id":"11950"}]},"file":[{"content_type":"application/pdf","creator":"cchlebak","file_id":"12471","access_level":"open_access","date_created":"2023-01-31T15:11:42Z","embargo":"2023-07-09","relation":"main_file","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_size":41771714,"file_name":"20230109_PhD_thesis_JM_final.pdf","date_updated":"2023-07-27T22:30:54Z"},{"access_level":"closed","date_created":"2023-01-31T15:11:51Z","file_id":"12472","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-07-10T22:30:04Z","file_name":"20230109_PhD_thesis_JM_final.docx","file_size":66983464,"relation":"source_file","embargo_to":"open_access","checksum":"0bebbdee0773443959e1f6ab8caf281f"}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"08","file":[{"date_updated":"2024-02-26T23:30:03Z","file_name":"documents-export-2023-08-24.zip","file_size":15501411,"checksum":"453caf851d75c3478c10ed09bd242a91","embargo_to":"open_access","relation":"source_file","date_created":"2023-08-24T13:02:49Z","access_level":"closed","file_id":"14227","creator":"cchlebak","content_type":"application/x-zip-compressed"},{"file_name":"thesis_pdf_a.pdf","date_updated":"2024-02-26T23:30:03Z","embargo":"2024-02-25","relation":"main_file","checksum":"7349d29963d6695e555e171748648d9a","file_size":6854783,"file_id":"14228","access_level":"open_access","date_created":"2023-08-24T13:03:42Z","creator":"cchlebak","content_type":"application/pdf"}],"page":"43","publication_identifier":{"issn":["2791-4585"]},"citation":{"chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023."},"has_accepted_license":"1","language":[{"iso":"eng"}],"corr_author":"1","file_date_updated":"2024-02-26T23:30:03Z","author":[{"first_name":"Elizabeth R","orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","full_name":"Stephenson, Elizabeth R"}],"article_processing_charge":"No","date_updated":"2026-04-07T14:02:30Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"status":"public","publication_status":"published","doi":"10.15479/at:ista:14226","type":"dissertation","oa_version":"Published Version","OA_place":"publisher","title":"Generalizing medial axes with homology switches","ddc":["500"],"_id":"14226","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"day":"24","oa":1,"date_published":"2023-08-24T00:00:00Z","year":"2023","alternative_title":["ISTA Master's Thesis"],"degree_awarded":"MS","date_created":"2023-08-24T13:01:18Z","abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}]},{"title":"Panoramic functional gradients across the mouse retina","OA_place":"publisher","ddc":["570"],"day":"08","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Jösch, Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A"}],"_id":"12531","oa":1,"tmp":{"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","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"alternative_title":["ISTA Master's Thesis"],"year":"2023","date_published":"2023-02-08T00:00:00Z","degree_awarded":"MS","date_created":"2023-02-09T07:45:05Z","abstract":[{"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.","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"02","publication_identifier":{"issn":["2791-4585"]},"page":"46","file":[{"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","date_created":"2023-02-09T08:03:32Z","file_id":"12532","file_size":8369317,"embargo":"2024-02-08","relation":"main_file","checksum":"57d8da3a6c749eb1556b7435fe266a5f","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","date_updated":"2024-02-09T23:30:03Z"},{"file_size":11204408,"embargo_to":"open_access","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","relation":"source_file","date_updated":"2024-02-09T23:30:03Z","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","content_type":"application/x-zip-compressed","creator":"cchlebak","date_created":"2023-02-10T09:32:06Z","access_level":"closed","file_id":"12535"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531.","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria."},"file_date_updated":"2024-02-09T23:30:03Z","corr_author":"1","author":[{"full_name":"Kirillova, Kseniia","last_name":"Kirillova","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","first_name":"Kseniia"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"date_updated":"2026-04-07T14:06:26Z","status":"public","oa_version":"Published Version","type":"dissertation","doi":"10.15479/at:ista:12531","publication_status":"published"},{"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.","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.","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.","mla":"Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14323.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:10.15479/at:ista:14323","apa":"Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14323","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. https://doi.org/10.15479/at:ista:14323."},"has_accepted_license":"1","language":[{"iso":"eng"}],"corr_author":"1","file_date_updated":"2025-03-13T23:30:05Z","project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","file":[{"file_id":"14324","access_level":"open_access","date_created":"2023-09-13T09:52:52Z","creator":"kkuzmicz","content_type":"application/pdf","date_updated":"2025-03-13T23:30:05Z","file_name":"PhDThesis_KK_final_pdfA.pdf","relation":"main_file","embargo":"2025-03-13","checksum":"bd83596869c814b24aeff7077d031c0e","file_size":10147911},{"creator":"kkuzmicz","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2023-09-13T09:53:29Z","file_id":"14325","file_size":103980668,"relation":"source_file","embargo_to":"open_access","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","date_updated":"2025-03-13T23:30:05Z","file_name":"thesis_KK_final_corrections_092023.docx"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7883"}]},"page":"151","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published","doi":"10.15479/at:ista:14323","type":"dissertation","oa_version":"Published Version","author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna"}],"article_processing_charge":"No","date_updated":"2026-04-14T09:50:54Z","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"ddc":["570"],"_id":"14323","supervisor":[{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"publisher":"Institute of Science and Technology Austria","day":"13","OA_place":"publisher","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","degree_awarded":"PhD","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"}],"date_created":"2023-09-13T10:07:18Z","tmp":{"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","image":"/images/cc_by_nc_nd.png"},"oa":1,"date_published":"2023-09-13T00:00:00Z","year":"2023","alternative_title":["ISTA Thesis"]},{"date_updated":"2026-05-13T22:31:10Z","department":[{"_id":"AnKi"}],"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Minchington, Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas"},{"orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","full_name":"Rus, Stefanie","last_name":"Rus"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"publication_status":"published","doi":"10.1016/j.coisb.2023.100459","type":"journal_article","oa_version":"Published Version","status":"public","file":[{"date_updated":"2024-01-29T11:06:45Z","file_name":"2023_CurrOpSystBioloy_Minchington.pdf","relation":"main_file","checksum":"8a75c4e29fd9b62e3c50663c2265b173","file_size":598842,"file_id":"14896","success":1,"access_level":"open_access","date_created":"2024-01-29T11:06:45Z","creator":"dernst","content_type":"application/pdf"}],"related_material":{"record":[{"id":"19763","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","publication_identifier":{"eissn":["2452-3100"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","scopus_import":"1","corr_author":"1","file_date_updated":"2024-01-29T11:06:45Z","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_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","grant_number":"F7802"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"citation":{"mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35, 100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” Current Opinion in Systems Biology, vol. 35. Elsevier, 2023.","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.","apa":"Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2023.100459","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459"},"has_accepted_license":"1","article_number":"100459","language":[{"iso":"eng"}],"date_published":"2023-09-01T00:00:00Z","year":"2023","tmp":{"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","image":"/images/cc_by_nc_nd.png"},"oa":1,"intvolume":" 35","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"date_created":"2023-06-18T22:00:46Z","quality_controlled":"1","publication":"Current Opinion in Systems Biology","volume":35,"article_type":"original","title":"Control of tissue dimensions in the developing neural tube and somites","_id":"13136","publisher":"Elsevier","day":"01","ddc":["570"]},{"scopus_import":"1","corr_author":"1","project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2023-10-04T11:13:28Z","citation":{"ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 2023;19:1050-1058. doi:10.1038/s41567-023-01977-w","chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w.","apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., & Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w","mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:10.1038/s41567-023-01977-w.","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.","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature Physics, vol. 19. Springer Nature, pp. 1050–1058, 2023.","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058."},"has_accepted_license":"1","language":[{"iso":"eng"}],"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.).","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13081"}]},"file":[{"file_name":"2023_NaturePhysics_Boncanegra.pdf","date_updated":"2023-10-04T11:13:28Z","file_size":5532285,"relation":"main_file","checksum":"858225a4205b74406e5045006cdd853f","success":1,"access_level":"open_access","date_created":"2023-10-04T11:13:28Z","file_id":"14392","content_type":"application/pdf","creator":"dernst"}],"page":"1050-1058","external_id":{"pmid":["37456593"],"isi":["000964029300003"]},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_status":"published","doi":"10.1038/s41567-023-01977-w","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","date_updated":"2026-05-13T22:31:13Z","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"article_processing_charge":"No","author":[{"last_name":"Bocanegra","full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"full_name":"Singh, Amrita","last_name":"Singh","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958","first_name":"Amrita"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","last_name":"Zagórski"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"_id":"12837","publisher":"Springer Nature","day":"01","ddc":["570"],"pmid":1,"publication":"Nature Physics","volume":19,"ec_funded":1,"title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","article_type":"original","date_created":"2023-04-16T22:01:09Z","intvolume":" 19","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"}],"quality_controlled":"1","date_published":"2023-07-01T00:00:00Z","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1},{"language":[{"iso":"eng"}],"citation":{"ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081","apa":"Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081.","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","mla":"Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081."},"has_accepted_license":"1","corr_author":"1","file_date_updated":"2024-06-01T22:30:04Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"05","publication_identifier":{"issn":["2663-337X"]},"page":"93","file":[{"date_updated":"2024-06-01T22:30:04Z","file_name":"Thesis_final_LauraBocanegra.docx","file_size":25615534,"relation":"source_file","embargo_to":"open_access","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","access_level":"closed","date_created":"2023-05-25T06:32:12Z","file_id":"13089","creator":"lbocaneg","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"creator":"lbocaneg","content_type":"application/pdf","file_id":"13090","access_level":"open_access","date_created":"2023-05-25T06:32:16Z","relation":"main_file","embargo":"2024-05-31","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","file_size":12386046,"file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","date_updated":"2024-06-01T22:30:04Z"}],"related_material":{"record":[{"id":"9349","status":"public","relation":"part_of_dissertation"},{"id":"12837","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:13081","article_processing_charge":"No","author":[{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"date_updated":"2026-04-14T09:50:54Z","ddc":["570"],"supervisor":[{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"publisher":"Institute of Science and Technology Austria","day":"23","_id":"13081","title":"Epithelial dynamics during mouse neural tube development","OA_place":"publisher","degree_awarded":"PhD","date_created":"2023-05-23T19:10:42Z","abstract":[{"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.","lang":"eng"}],"oa":1,"tmp":{"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","image":"/images/cc_by_nc_nd.png"},"year":"2023","alternative_title":["ISTA Thesis"],"date_published":"2023-05-23T00:00:00Z"},{"corr_author":"1","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"},{"grant_number":"ESP39 49461","name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3"}],"file_date_updated":"2024-01-02T11:39:38Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution, vol. 40, no. 12. Oxford University Press, 2023.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:10.1093/molbev/msad245.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., & Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245.","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245"},"article_number":"msad245","has_accepted_license":"1","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage"}],"record":[{"relation":"research_data","status":"public","id":"14614"},{"id":"19386","relation":"dissertation_contains","status":"public"}]},"file":[{"file_name":"2023_MolecularBioEvo_Lasne.pdf","date_updated":"2024-01-02T11:39:38Z","file_size":8623505,"checksum":"47c1c72fb499f26ea52d216b242208c8","relation":"main_file","date_created":"2024-01-02T11:39:38Z","success":1,"access_level":"open_access","file_id":"14727","creator":"dernst","content_type":"application/pdf"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["001122489000003"],"pmid":["37988296"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"12","type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1093/molbev/msad245","status":"public","isi":1,"department":[{"_id":"BeVi"}],"date_updated":"2026-05-13T22:31:20Z","article_processing_charge":"Yes","author":[{"orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine","full_name":"Lasne, Clementine","last_name":"Lasne"},{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380"},{"full_name":"Layana Franco, Lorena Alexandra","last_name":"Layana Franco","first_name":"Lorena Alexandra","orcid":"0000-0002-1253-6297","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"publisher":"Oxford University Press","day":"01","_id":"14613","pmid":1,"ddc":["570"],"publication":"Molecular Biology and Evolution","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","article_type":"original","volume":40,"quality_controlled":"1","intvolume":" 40","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"date_created":"2023-11-27T16:14:37Z","year":"2023","issue":"12","date_published":"2023-12-01T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"volume":14,"OA_place":"publisher","article_type":"original","title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","ec_funded":1,"publication":"Nature Communications","ddc":["000"],"pmid":1,"_id":"13200","day":"24","arxiv":1,"publisher":"Nature Research","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"APC_amount":"6228 EUR","oa":1,"date_published":"2023-06-24T00:00:00Z","year":"2023","abstract":[{"lang":"eng","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."}],"date_created":"2023-07-09T22:01:11Z","intvolume":" 14","quality_controlled":"1","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","DOAJ_listed":"1","external_id":{"isi":["001018100800002"],"pmid":["37355691"],"arxiv":["2210.12443"]},"OA_type":"gold","file":[{"creator":"alisjak","content_type":"application/pdf","file_id":"13206","date_created":"2023-07-10T10:10:54Z","access_level":"open_access","success":1,"checksum":"ec7ccd2c08f90d59cab302fd0d7776a4","relation":"main_file","file_size":1349134,"date_updated":"2023-07-10T10:10:54Z","file_name":"2023_NatureComms_Qiu.pdf"}],"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.","related_material":{"record":[{"id":"18871","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"eissn":["2041-1723"]},"article_number":"3784","has_accepted_license":"1","citation":{"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,” Nature Communications, vol. 14. Nature Research, 2023.","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","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.","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications, vol. 14, 3784, Nature Research, 2023, doi:10.1038/s41467-023-39493-3.","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. Nature Communications. 2023;14. doi:10.1038/s41467-023-39493-3","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., & Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-023-39493-3","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.” Nature Communications. Nature Research, 2023. https://doi.org/10.1038/s41467-023-39493-3."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2023-07-10T10:10:54Z","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","grant_number":"899354"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"corr_author":"1","article_processing_charge":"Yes","author":[{"id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","orcid":"0000-0003-4345-4267","first_name":"Liu","full_name":"Qiu, Liu","last_name":"Qiu"},{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","first_name":"Rishabh","full_name":"Sahu, Rishabh","last_name":"Sahu"},{"full_name":"Hease, William J","last_name":"Hease","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166"},{"last_name":"Arnold","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","first_name":"Georg M"},{"last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"date_updated":"2026-05-13T22:31:21Z","department":[{"_id":"JoFi"}],"isi":1,"status":"public","doi":"10.1038/s41467-023-39493-3","publication_status":"published","oa_version":"Published Version","type":"journal_article"},{"publication":"arXiv","OA_place":"repository","title":"All-optical single-shot readout of a superconducting qubit","ec_funded":1,"_id":"18953","day":"25","arxiv":1,"date_published":"2023-10-25T00:00:00Z","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.16817"}],"abstract":[{"lang":"eng","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."}],"date_created":"2025-01-29T11:11:34Z","external_id":{"arxiv":["2310.16817"]},"related_material":{"record":[{"id":"19073","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18871"}]},"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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states","_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a","grant_number":"101089099"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"corr_author":"1","citation":{"mla":"Arnold, Georg M., et al. “All-Optical Single-Shot Readout of a Superconducting Qubit.” ArXiv, doi:10.48550/ARXIV.2310.16817.","short":"G.M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, J.M. Fink, ArXiv (n.d.).","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,” arXiv. .","ista":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv, 10.48550/ARXIV.2310.16817.","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.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2310.16817.","apa":"Arnold, G. M., Werner, T., Sahu, R., Kapoor, L., Qiu, L., & Fink, J. M. (n.d.). All-optical single-shot readout of a superconducting qubit. arXiv. https://doi.org/10.48550/ARXIV.2310.16817","ama":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv. doi:10.48550/ARXIV.2310.16817"},"language":[{"iso":"eng"}],"date_updated":"2026-05-13T22:31:21Z","department":[{"_id":"JoFi"}],"author":[{"last_name":"Arnold","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","first_name":"Georg M"},{"last_name":"Werner","full_name":"Werner, Thomas","id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7","orcid":"0009-0001-2346-5236","first_name":"Thomas"},{"full_name":"Sahu, Rishabh","last_name":"Sahu","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162"},{"first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky","last_name":"Kapoor"},{"first_name":"Liu","orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu","last_name":"Qiu"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"article_processing_charge":"No","doi":"10.48550/ARXIV.2310.16817","publication_status":"draft","oa_version":"Preprint","type":"preprint","status":"public"},{"scopus_import":"1","corr_author":"1","file_date_updated":"2023-06-06T07:31:20Z","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"citation":{"chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6.","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023)."},"has_accepted_license":"1","article_number":"2998","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"13124","status":"public","relation":"research_data"},{"id":"19533","relation":"dissertation_contains","status":"public"}]},"file":[{"date_created":"2023-06-06T07:31:20Z","access_level":"open_access","success":1,"file_id":"13123","creator":"dernst","content_type":"application/pdf","date_updated":"2023-06-06T07:31:20Z","file_name":"2023_NaturePhysics_Redchenko.pdf","file_size":1654389,"checksum":"a857df40f0882859c48a1ff1e2001ec2","relation":"main_file"}],"acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","external_id":{"arxiv":["2205.03293"],"isi":["001001099700002"],"pmid":["37225689"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"eissn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publication_status":"published","doi":"10.1038/s41467-023-38761-6","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","date_updated":"2026-05-13T22:31:23Z","department":[{"_id":"JoFi"}],"article_processing_charge":"No","author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander V.","first_name":"Alexander V."},{"first_name":"Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","last_name":"Sett"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin","orcid":"0009-0005-0878-3032","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander N.","last_name":"Poddubny","full_name":"Poddubny, Alexander N."},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink"}],"_id":"13117","arxiv":1,"publisher":"Springer Nature","day":"24","ddc":["530"],"pmid":1,"publication":"Nature Communications","volume":14,"ec_funded":1,"article_type":"original","title":"Tunable directional photon scattering from a pair of superconducting qubits","date_created":"2023-06-04T22:01:02Z","abstract":[{"text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality.","lang":"eng"}],"intvolume":" 14","quality_controlled":"1","date_published":"2023-05-24T00:00:00Z","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1},{"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"6","year":"2023","date_published":"2023-03-01T00:00:00Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"intvolume":" 32","date_created":"2023-01-12T12:09:17Z","title":"On the origin and structure of haplotype blocks","article_type":"original","volume":32,"publication":"Molecular Ecology","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"pmid":1,"ddc":["570"],"day":"01","publisher":"Wiley","_id":"12159","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","full_name":"Shipilina, Daria","last_name":"Shipilina"},{"first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","last_name":"Pal"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"date_updated":"2026-05-13T22:31:22Z","status":"public","isi":1,"oa_version":"Published Version","type":"journal_article","doi":"10.1111/mec.16793","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"page":"1441-1457","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"14062","access_level":"open_access","success":1,"date_created":"2023-08-16T08:15:41Z","relation":"main_file","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_size":7144607,"file_name":"2023_MolecularEcology_Shipilina.pdf","date_updated":"2023-08-16T08:15:41Z"}],"acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","related_material":{"record":[{"id":"20694","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793"},"project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"file_date_updated":"2023-08-16T08:15:41Z","corr_author":"1","scopus_import":"1"},{"ddc":["000"],"_id":"11442","arxiv":1,"publisher":"Association for Computing Machinery","day":"01","volume":41,"OA_place":"publisher","ec_funded":1,"article_type":"original","title":"Closed-loop control of direct ink writing via reinforcement learning","PlanS_conform":"1","publication":"ACM Transactions on Graphics","intvolume":" 41","abstract":[{"text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. ","lang":"eng"}],"date_created":"2022-06-10T06:41:47Z","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2022-06-01T00:00:00Z","year":"2022","issue":"4","citation":{"mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” ACM Transactions on Graphics, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:10.1145/3528223.3530144.","ieee":"M. Piovarci et al., “Closed-loop control of direct ink writing via reinforcement learning,” ACM Transactions on Graphics, vol. 41, no. 4. Association for Computing Machinery, 2022.","ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).","ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 2022;41(4). doi:10.1145/3528223.3530144","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” ACM Transactions on Graphics. Association for Computing Machinery, 2022. https://doi.org/10.1145/3528223.3530144.","apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3528223.3530144"},"has_accepted_license":"1","article_number":"112","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2022-06-28T08:32:58Z","project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication","grant_number":"M03319"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"06","acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/"}]},"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"11467","success":1,"access_level":"open_access","date_created":"2022-06-28T08:32:58Z","relation":"main_file","checksum":"27f6fe41c6ff84d50445cc9b0176d45b","file_size":33994829,"file_name":"2022_ACM_acceptedversion_Piovarci.pdf","date_updated":"2022-06-28T08:32:58Z"}],"OA_type":"hybrid","external_id":{"isi":["000830989200091"],"arxiv":["2201.11819"]},"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"isi":1,"status":"public","publication_status":"published","doi":"10.1145/3528223.3530144","type":"journal_article","oa_version":"Submitted Version","article_processing_charge":"No","author":[{"full_name":"Piovarci, Michael","last_name":"Piovarci","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","orcid":"0000-0002-5062-4474","first_name":"Michael"},{"full_name":"Foshey, Michael","last_name":"Foshey","first_name":"Michael"},{"last_name":"Xu","full_name":"Xu, Jie","first_name":"Jie"},{"last_name":"Erps","full_name":"Erps, Timothy","first_name":"Timothy"},{"first_name":"Vahid","full_name":"Babaei, Vahid","last_name":"Babaei"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"first_name":"Szymon","full_name":"Rusinkiewicz, Szymon","last_name":"Rusinkiewicz"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"date_updated":"2025-09-10T09:36:45Z","department":[{"_id":"BeBi"}]}]