[{"article_number":"e2221313120","isi":1,"acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the  National  Natural  Science  Foundation  of  China  (32170265  and  32022007),  Hainan  Provincial  Natural  Science  Foundation  of  China  (323CXTD379),  Chinese  Universities  Scientific  Fund  (2023TC019),  Beijing  Municipal  Natural  Science  Foundation  (5192011),  Beijing  Outstanding  University  Discipline  Program,  and  China Postdoctoral Science Foundation (BH2020259460).","intvolume":"       120","file_date_updated":"2023-12-13T23:30:03Z","date_created":"2023-07-09T22:01:12Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2023","publication_status":"published","citation":{"ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","ieee":"Y. Wang <i>et al.</i>, “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25. National Academy of Sciences, 2023.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(25). doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>.","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023)."},"oa_version":"Published Version","ddc":["570"],"month":"06","publisher":"National Academy of Sciences","pmid":1,"date_published":"2023-06-12T00:00:00Z","type":"journal_article","abstract":[{"text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","date_updated":"2023-12-13T23:30:04Z","scopus_import":"1","author":[{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"first_name":"Zhi","last_name":"Yuan","full_name":"Yuan, Zhi"},{"full_name":"Wang, Jinyi","first_name":"Jinyi","last_name":"Wang"},{"last_name":"Xiao","first_name":"Huixin","full_name":"Xiao, Huixin"},{"full_name":"Wan, Lu","last_name":"Wan","first_name":"Lu"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"}],"issue":"25","file":[{"relation":"main_file","date_updated":"2023-12-13T23:30:03Z","embargo":"2023-12-12","access_level":"open_access","file_name":"2023_PNAS_Wang.pdf","file_size":5244581,"creator":"alisjak","checksum":"d800e06252eaefba28531fa9440f23f0","content_type":"application/pdf","date_created":"2023-07-10T08:48:40Z","file_id":"13204"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa":1,"doi":"10.1073/pnas.2221313120","has_accepted_license":"1","volume":120,"external_id":{"isi":["001030689600003"],"pmid":["37307446"]},"article_type":"original","article_processing_charge":"No","_id":"13201","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"fulldoi":"https://doi.org/10.1073/pnas.2221313120","day":"12","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]}},{"publication_identifier":{"issn":["0092-8674"]},"page":"1950-1967.e25","day":"27","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"fulldoi":"https://doi.org/10.1016/j.cell.2023.02.037","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"_id":"12802","title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","article_type":"original","external_id":{"pmid":["36996814"],"isi":["000991468700001"]},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","volume":186,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","success":1,"relation":"main_file","date_updated":"2023-05-02T09:26:21Z","content_type":"application/pdf","file_id":"12889","date_created":"2023-05-02T09:26:21Z","file_size":15712841,"file_name":"2023_Cell_Knaus.pdf","creator":"dernst","checksum":"47e94fbe19e86505b429cb7a5b503ce6"}],"project":[{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020"}],"doi":"10.1016/j.cell.2023.02.037","oa":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"issue":"9","corr_author":"1","author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","first_name":"Lisa","last_name":"Knaus"},{"first_name":"Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173"},{"full_name":"Malzl, Daniel","first_name":"Daniel","last_name":"Malzl"},{"full_name":"Gerykova Bujalkova, Maria","first_name":"Maria","last_name":"Gerykova Bujalkova"},{"last_name":"Smogavec","first_name":"Mateja","full_name":"Smogavec, Mateja"},{"full_name":"Schwarz, Lena A.","last_name":"Schwarz","first_name":"Lena A."},{"first_name":"Sarah","last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","full_name":"Gorkiewicz, Sarah"},{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian"},{"full_name":"Knittl-Frank, Christian","first_name":"Christian","last_name":"Knittl-Frank"},{"full_name":"Tassinari, Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","last_name":"Tassinari","first_name":"Marianna"},{"full_name":"Maulide, Nuno","first_name":"Nuno","last_name":"Maulide"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"scopus_import":"1","date_updated":"2026-11-09T23:30:13Z","quality_controlled":"1","status":"public","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction."}],"related_material":{"record":[{"id":"13107","relation":"dissertation_contains","status":"public"},{"id":"19557","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","relation":"press_release","description":"News on ISTA Website"}]},"publisher":"Elsevier","month":"04","ddc":["570"],"date_published":"2023-04-27T00:00:00Z","pmid":1,"oa_version":"Published Version","citation":{"chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>","short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>"},"publication_status":"published","date_created":"2023-04-05T08:15:40Z","year":"2023","publication":"Cell","intvolume":"       186","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","isi":1,"file_date_updated":"2023-05-02T09:26:21Z"},{"ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","_id":"14697","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"page":"226","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-038-1"]},"day":"20","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"fulldoi":"https://doi.org/10.15479/at:ista:14697","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"doi":"10.15479/at:ista:14697","oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file":[{"access_level":"open_access","embargo":"2024-12-20","relation":"main_file","date_updated":"2024-12-20T23:30:04Z","file_id":"14699","date_created":"2023-12-20T09:35:34Z","content_type":"application/pdf","creator":"jstopp","checksum":"457927165d5d556305d3086f6b83e5c7","file_name":"Thesis.pdf","file_size":51585778},{"embargo_to":"open_access","relation":"source_file","date_updated":"2024-12-20T23:30:04Z","access_level":"closed","file_name":"Thesis.docx","file_size":69625950,"checksum":"e8d26449ac461f5e8478a62c9507506f","creator":"jstopp","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14700","date_created":"2023-12-20T09:35:35Z"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","status":"public","abstract":[{"text":"During my Ph.D. research, I managed a series of projects, each focused on the\r\nmechanisms underlying cell migration. My work involved an in-depth examination of\r\nthe complex strategies employed by neutrophils, with a specific focus on their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient perception. However, it\r\nis essential to acknowledge that not all projects yielded successful results, as some\r\nideas were discontinued and are archived for future reference within this thesis.\r\nMy main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source\r\ntype – linear or point-like. By combining single-cell tracking in 3D environments with\r\nproxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential gradients from point sources. In addition, neutrophils\r\nexhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over\r\ntime and employed a \"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic \"tumbles\" for efficient navigation.\r\nThe project extended to the possibility of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings, pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences\r\nin migratory efficacy were detected across pore sizes and device heights, quantifying\r\ngradient manipulation effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\" (LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through extensive experimentation with multiple\r\nparameters, we attempted to trigger responses from neutrophils. Despite these efforts\r\nand collaboration, the project failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line. Despite their existence, their migratory behavior was largely\r\nunexplored due to potential limitations. Through differentiation protocol refinements we\r\nenhanced their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils. Despite this, the improved migration potential of these cells pointed toward\r\ntheir utility for in vitro murine neutrophil migration studies.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14360"},{"id":"12272","relation":"part_of_dissertation","status":"public"},{"id":"6328","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"7885","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14274"}]},"language":[{"iso":"eng"}],"type":"dissertation","OA_place":"publisher","author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp"}],"date_updated":"2026-06-18T17:34:48Z","year":"2023","date_created":"2023-12-18T19:14:28Z","publication_status":"published","file_date_updated":"2024-12-20T23:30:04Z","date_published":"2023-12-20T00:00:00Z","ddc":["570"],"month":"12","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","citation":{"ista":"Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","ieee":"J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","ama":"Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","short":"J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","mla":"Stopp, Julian A. <i>Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>.","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>"}},{"file_date_updated":"2023-09-25T08:22:58Z","intvolume":"        14","isi":1,"acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","article_number":"5644","publication_status":"published","year":"2023","date_created":"2023-09-24T22:01:10Z","publication":"Nature Communications","oa_version":"Published Version","citation":{"short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>.","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"date_published":"2023-09-13T00:00:00Z","pmid":1,"publisher":"Springer Nature","ddc":["570"],"month":"09","language":[{"iso":"eng"}],"abstract":[{"text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14697"}]},"type":"journal_article","status":"public","quality_controlled":"1","scopus_import":"1","date_updated":"2026-11-09T23:30:14Z","author":[{"full_name":"Sitarska, Ewa","last_name":"Sitarska","first_name":"Ewa"},{"last_name":"Almeida","first_name":"Silvia Dias","full_name":"Almeida, Silvia Dias"},{"first_name":"Marianne Sandvold","last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold"},{"first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A"},{"full_name":"Czuchnowski, Jakub","last_name":"Czuchnowski","first_name":"Jakub"},{"first_name":"Marc","last_name":"Siggel","full_name":"Siggel, Marc"},{"full_name":"Roessner, Rita","first_name":"Rita","last_name":"Roessner"},{"full_name":"Tschanz, Aline","last_name":"Tschanz","first_name":"Aline"},{"first_name":"Christer","last_name":"Ejsing","full_name":"Ejsing, Christer"},{"first_name":"Yannick","last_name":"Schwab","full_name":"Schwab, Yannick"},{"full_name":"Kosinski, Jan","first_name":"Jan","last_name":"Kosinski"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"full_name":"Kreshuk, Anna","last_name":"Kreshuk","first_name":"Anna"},{"first_name":"Anna","last_name":"Erzberger","full_name":"Erzberger, Anna"},{"full_name":"Diz-Muñoz, Alba","last_name":"Diz-Muñoz","first_name":"Alba"}],"oa":1,"doi":"10.1038/s41467-023-41173-1","file":[{"access_level":"open_access","success":1,"date_updated":"2023-09-25T08:22:58Z","relation":"main_file","content_type":"application/pdf","date_created":"2023-09-25T08:22:58Z","file_id":"14365","file_name":"2023_NatureComm_Sitarska.pdf","file_size":2725421,"creator":"dernst","checksum":"ad670e3b3c64fc585675948370f6b149"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"has_accepted_license":"1","volume":14,"article_processing_charge":"Yes (via OA deal)","article_type":"original","external_id":{"pmid":["37704612"],"isi":["001087583700008"]},"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","_id":"14360","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1038/s41467-023-41173-1","department":[{"_id":"MiSi"}],"day":"13","publication_identifier":{"eissn":["2041-1723"]}},{"status":"public","type":"dissertation","OA_place":"publisher","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"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Kirillova, Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","last_name":"Kirillova","first_name":"Kseniia"}],"date_updated":"2026-04-07T14:06:26Z","year":"2023","date_created":"2023-02-09T07:45:05Z","publication_status":"published","file_date_updated":"2024-02-09T23:30:03Z","ddc":["570"],"month":"02","publisher":"Institute of Science and Technology Austria","date_published":"2023-02-08T00:00:00Z","oa_version":"Published Version","citation":{"apa":"Kirillova, K. (2023). <i>Panoramic functional gradients across the mouse retina</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>","mla":"Kirillova, Kseniia. <i>Panoramic Functional Gradients across the Mouse Retina</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"12531","title":"Panoramic functional gradients across the mouse retina","page":"46","publication_identifier":{"issn":["2791-4585"]},"day":"08","supervisor":[{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"degree_awarded":"MS","fulldoi":"https://doi.org/10.15479/at:ista:12531","file":[{"file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","file_size":8369317,"creator":"cchlebak","checksum":"57d8da3a6c749eb1556b7435fe266a5f","content_type":"application/pdf","file_id":"12532","date_created":"2023-02-09T08:03:32Z","date_updated":"2024-02-09T23:30:03Z","relation":"main_file","embargo":"2024-02-08","access_level":"open_access"},{"creator":"cchlebak","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","file_size":11204408,"file_id":"12535","date_created":"2023-02-10T09:32:06Z","content_type":"application/x-zip-compressed","relation":"source_file","date_updated":"2024-02-09T23:30:03Z","embargo_to":"open_access","access_level":"closed"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"oa":1,"doi":"10.15479/at:ista:12531","corr_author":"1","alternative_title":["ISTA Master's Thesis"],"article_processing_charge":"No","has_accepted_license":"1"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","_id":"14323","supervisor":[{"orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"}],"publication_identifier":{"issn":["2663-337X"]},"page":"151","day":"13","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"fulldoi":"https://doi.org/10.15479/at:ista:14323","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"doi":"10.15479/at:ista:14323","oa":1,"project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"checksum":"bd83596869c814b24aeff7077d031c0e","creator":"kkuzmicz","file_name":"PhDThesis_KK_final_pdfA.pdf","file_size":10147911,"date_created":"2023-09-13T09:52:52Z","file_id":"14324","content_type":"application/pdf","relation":"main_file","date_updated":"2025-03-13T23:30:05Z","access_level":"open_access","embargo":"2025-03-13"},{"access_level":"closed","relation":"source_file","date_updated":"2025-03-13T23:30:05Z","embargo_to":"open_access","file_id":"14325","date_created":"2023-09-13T09:53:29Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"kkuzmicz","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","file_size":103980668,"file_name":"thesis_KK_final_corrections_092023.docx"}],"corr_author":"1","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"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"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7883"}]},"OA_place":"publisher","type":"dissertation","author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna"}],"date_updated":"2026-04-14T09:50:54Z","publication_status":"published","date_created":"2023-09-13T10:07:18Z","year":"2023","file_date_updated":"2025-03-13T23:30:05Z","date_published":"2023-09-13T00:00:00Z","publisher":"Institute of Science and Technology Austria","month":"09","ddc":["570"],"citation":{"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.","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.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","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.","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>"},"oa_version":"Published Version"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]},"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"}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","quality_controlled":"1","date_updated":"2026-11-09T23:30:18Z","scopus_import":"1","author":[{"full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","last_name":"Bocanegra","first_name":"Laura"},{"last_name":"Singh","first_name":"Amrita","full_name":"Singh, Amrita","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Zagórski","first_name":"Marcin P","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998"}],"file_date_updated":"2023-10-04T11:13:28Z","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.).","isi":1,"intvolume":"        19","year":"2023","date_created":"2023-04-16T22:01:09Z","publication":"Nature Physics","publication_status":"published","citation":{"apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., &#38; Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>","mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>.","chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>.","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058.","ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. 2023;19:1050-1058. doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>","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,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1050–1058, 2023."},"oa_version":"Published Version","pmid":1,"date_published":"2023-07-01T00:00:00Z","month":"07","ddc":["570"],"publisher":"Springer Nature","title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","_id":"12837","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1038/s41567-023-01977-w","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"day":"01","page":"1050-1058","corr_author":"1","oa":1,"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41567-023-01977-w","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"dernst","checksum":"858225a4205b74406e5045006cdd853f","file_size":5532285,"file_name":"2023_NaturePhysics_Boncanegra.pdf","date_created":"2023-10-04T11:13:28Z","file_id":"14392","content_type":"application/pdf","date_updated":"2023-10-04T11:13:28Z","relation":"main_file","success":1,"access_level":"open_access"}],"has_accepted_license":"1","volume":19,"article_processing_charge":"No","article_type":"original","external_id":{"isi":["000964029300003"],"pmid":["37456593"]}},{"date_updated":"2026-04-14T09:50:54Z","author":[{"last_name":"Bocanegra","first_name":"Laura","full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","type":"dissertation","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9349","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12837"}]},"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"}],"status":"public","citation":{"ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","apa":"Bocanegra, L. (2023). <i>Epithelial dynamics during mouse neural tube development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>","mla":"Bocanegra, Laura. <i>Epithelial Dynamics during Mouse Neural Tube Development</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>.","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023."},"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","ddc":["570"],"month":"05","date_published":"2023-05-23T00:00:00Z","file_date_updated":"2024-06-01T22:30:04Z","publication_status":"published","date_created":"2023-05-23T19:10:42Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"fulldoi":"https://doi.org/10.15479/at:ista:13081","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"page":"93","day":"23","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"}],"_id":"13081","title":"Epithelial dynamics during mouse neural tube development","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"corr_author":"1","file":[{"creator":"lbocaneg","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","file_name":"Thesis_final_LauraBocanegra.docx","file_size":25615534,"date_created":"2023-05-25T06:32:12Z","file_id":"13089","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_updated":"2024-06-01T22:30:04Z","embargo_to":"open_access","access_level":"closed"},{"relation":"main_file","date_updated":"2024-06-01T22:30:04Z","embargo":"2024-05-31","access_level":"open_access","file_size":12386046,"file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","creator":"lbocaneg","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","content_type":"application/pdf","date_created":"2023-05-25T06:32:16Z","file_id":"13090"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa":1,"doi":"10.15479/at:ista:13081"},{"date_updated":"2026-04-07T14:01:51Z","author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","full_name":"Julseth, Mara","first_name":"Mara","last_name":"Julseth"}],"language":[{"iso":"eng"}],"abstract":[{"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. ","lang":"eng"}],"OA_place":"publisher","type":"dissertation","status":"public","citation":{"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.","apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","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.","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."},"oa_version":"Published Version","date_published":"2023-04-05T00:00:00Z","publisher":"Institute of Science and Technology Austria","month":"04","ddc":["576"],"file_date_updated":"2023-06-02T22:30:04Z","publication_status":"published","date_created":"2023-04-04T18:57:11Z","year":"2023","fulldoi":"https://doi.org/10.15479/at:ista:12800","degree_awarded":"MS","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"supervisor":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"day":"05","page":"21","publication_identifier":{"issn":["2791-4585"]},"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","_id":"12800","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","article_processing_charge":"No","alternative_title":["ISTA Master's Thesis"],"corr_author":"1","oa":1,"doi":"10.15479/at:ista:12800","file":[{"file_name":"Dispersaldata.xlsx","file_size":52795,"checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","creator":"mjulseth","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"12805","date_created":"2023-04-06T06:09:40Z","embargo_to":"open_access","date_updated":"2023-06-02T22:30:04Z","relation":"supplementary_material","access_level":"closed"},{"file_id":"12806","date_created":"2023-04-06T06:11:27Z","content_type":"application/vnd.wolfram.nb","checksum":"5a13b6d204371572e249f03795bc0d04","creator":"mjulseth","file_size":787239,"file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","embargo":"2023-06-01","access_level":"open_access","relation":"supplementary_material","date_updated":"2023-06-02T22:30:04Z"},{"checksum":"c3ec842839ed1e66bf2618ae33047df8","creator":"mjulseth","file_name":"ThesisMaraJulseth_04_23.docx","file_size":1061763,"date_created":"2023-04-06T08:26:12Z","file_id":"12812","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_updated":"2023-06-02T22:30:04Z","embargo_to":"open_access","access_level":"closed"},{"date_updated":"2023-06-02T22:30:04Z","relation":"main_file","access_level":"open_access","embargo":"2023-06-01","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","creator":"mjulseth","file_name":"ThesisMaraJulseth_04_23.pdf","file_size":1741364,"date_created":"2023-04-06T08:26:37Z","file_id":"12813","content_type":"application/pdf"}]},{"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","doi":"10.15479/at:ista:14422","project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"}],"oa":1,"file":[{"access_level":"open_access","embargo":"2024-10-12","relation":"main_file","date_updated":"2024-10-13T22:30:04Z","file_id":"14424","date_created":"2023-10-12T14:53:50Z","content_type":"application/pdf","creator":"cchlebak","checksum":"7f636555eae7803323df287672fd13ed","file_name":"Confavreux_Thesis_2A.pdf","file_size":30599717},{"access_level":"closed","embargo_to":"open_access","relation":"source_file","date_updated":"2024-10-13T22:30:04Z","content_type":"application/x-zip-compressed","date_created":"2023-10-18T07:38:34Z","file_id":"14440","file_name":"Confavreux Thesis.zip","file_size":68406739,"checksum":"725e85946db92290a4583a0de9779e1b","creator":"cchlebak"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"corr_author":"1","supervisor":[{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"}],"publication_identifier":{"issn":["2663-337X"]},"day":"12","page":"148","fulldoi":"https://doi.org/10.15479/at:ista:14422","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"TiVo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ec_funded":1,"title":"Synapseek: Meta-learning synaptic plasticity rules","_id":"14422","date_published":"2023-10-12T00:00:00Z","publisher":"Institute of Science and Technology Austria","month":"10","ddc":["610"],"oa_version":"Published Version","citation":{"apa":"Confavreux, B. J. (2023). <i>Synapseek: Meta-learning synaptic plasticity rules</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>","mla":"Confavreux, Basile J. <i>Synapseek: Meta-Learning Synaptic Plasticity Rules</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria."},"publication_status":"published","date_created":"2023-10-12T14:13:25Z","year":"2023","file_date_updated":"2024-10-13T22:30:04Z","author":[{"id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J","first_name":"Basile J","last_name":"Confavreux"}],"date_updated":"2026-07-07T06:53:33Z","status":"public","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9633","relation":"part_of_dissertation","status":"public"}]},"abstract":[{"lang":"eng","text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n"}],"OA_place":"publisher","type":"dissertation"},{"doi":"10.1523/JNEUROSCI.0194-23.2023","project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"file":[{"checksum":"e2503c8f84be1050e28f64320f1d5bd2","creator":"dernst","file_name":"2023_JourNeuroscience_Nardin.pdf","file_size":2280632,"file_id":"14674","date_created":"2023-12-11T11:30:37Z","content_type":"application/pdf","relation":"main_file","date_updated":"2024-06-02T22:30:03Z","access_level":"open_access","embargo":"2024-06-01"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"issue":"48","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37758476"],"isi":["001148071000005"]},"article_type":"original","has_accepted_license":"1","volume":43,"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","_id":"14656","page":"8140-8156","day":"29","publication_identifier":{"eissn":["1529-2401"]},"fulldoi":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"publication_status":"published","date_created":"2023-12-10T23:00:58Z","publication":"The Journal of Neuroscience","year":"2023","file_date_updated":"2024-06-02T22:30:03Z","intvolume":"        43","isi":1,"acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","date_published":"2023-11-29T00:00:00Z","pmid":1,"publisher":"Society for Neuroscience","ddc":["570"],"month":"11","oa_version":"Published Version","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156."},"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"related_material":{"record":[{"id":"10077","relation":"earlier_version","status":"public"}]},"type":"journal_article","author":[{"full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570"},{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina","first_name":"Cristina","last_name":"Savin"}],"scopus_import":"1","date_updated":"2026-07-06T12:47:25Z"},{"volume":62,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.11591"}],"article_processing_charge":"No","das_tickbox":"1","external_id":{"arxiv":["2208.11591"],"isi":["000906607900001"]},"article_type":"original","corr_author":"1","issue":"1","oa":1,"doi":"10.1364/ao.474118","keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"researchdata_availability":"upon request","fulldoi":"https://doi.org/10.1364/ao.474118","supplementarymaterial":"yes","department":[{"_id":"OnHo"}],"publication_identifier":{"issn":["1559-128X"],"eissn":["2155-3165"]},"arxiv":1,"day":"01","page":"1-7","title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","_id":"14759","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","oa_version":"Preprint","citation":{"ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. 2023;62(1):1-7. doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7.","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” <i>Applied Optics</i>, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023.","short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","apa":"Wald, S., Diorico, F. R., &#38; Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>","chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>. Optica Publishing Group, 2023. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>.","mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>."},"date_published":"2023-01-01T00:00:00Z","publisher":"Optica Publishing Group","month":"01","intvolume":"        62","acknowledgement":"We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript.","isi":1,"publication_status":"published","publication":"Applied Optics","date_created":"2024-01-08T13:19:14Z","year":"2023","dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","scopus_import":"1","date_updated":"2026-11-09T23:30:26Z","author":[{"orcid":"0000-0002-5869-1604","first_name":"Sebastian","last_name":"Wald","id":"133F200A-B015-11E9-AD41-0EDAE5697425","full_name":"Wald, Sebastian"},{"orcid":"0000-0002-4947-8924","last_name":"Diorico","first_name":"Fritz R","full_name":"Diorico, Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"20798","relation":"dissertation_contains","status":"public"}]},"abstract":[{"lang":"eng","text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method."}],"type":"journal_article","quality_controlled":"1","status":"public"},{"article_type":"original","external_id":{"isi":["001018100800002"],"arxiv":["2210.12443"],"pmid":["37355691"]},"article_processing_charge":"Yes","volume":14,"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","success":1,"relation":"main_file","date_updated":"2023-07-10T10:10:54Z","content_type":"application/pdf","file_id":"13206","date_created":"2023-07-10T10:10:54Z","file_name":"2023_NatureComms_Qiu.pdf","file_size":1349134,"creator":"alisjak","checksum":"ec7ccd2c08f90d59cab302fd0d7776a4"}],"doi":"10.1038/s41467-023-39493-3","oa":1,"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"corr_author":"1","day":"24","arxiv":1,"publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"JoFi"}],"fulldoi":"https://doi.org/10.1038/s41467-023-39493-3","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13200","title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","month":"06","ddc":["000"],"publisher":"Nature Research","pmid":1,"date_published":"2023-06-24T00:00:00Z","citation":{"ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>","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.","ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” <i>Nature Communications</i>, vol. 14. Nature Research, 2023.","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., &#38; Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>, vol. 14, 3784, Nature Research, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>.","chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>. Nature Research, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>."},"oa_version":"Published Version","publication":"Nature Communications","year":"2023","date_created":"2023-07-09T22:01:11Z","publication_status":"published","article_number":"3784","isi":1,"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.","intvolume":"        14","file_date_updated":"2023-07-10T10:10:54Z","author":[{"orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","first_name":"Liu"},{"orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","first_name":"Rishabh","last_name":"Sahu"},{"orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J"},{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876"},{"last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"APC_amount":"6228 EUR","DOAJ_listed":"1","date_updated":"2026-11-09T23:30:28Z","OA_type":"gold","scopus_import":"1","status":"public","quality_controlled":"1","type":"journal_article","OA_place":"publisher","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."}],"related_material":{"record":[{"relation":"dissertation_contains","id":"18871","status":"public"}]},"language":[{"iso":"eng"}]},{"status":"public","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."}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"19073"},{"relation":"dissertation_contains","id":"18871","status":"public"}]},"language":[{"iso":"eng"}],"type":"preprint","OA_place":"repository","author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","first_name":"Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876"},{"orcid":"0009-0001-2346-5236","full_name":"Werner, Thomas","id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7","last_name":"Werner","first_name":"Thomas"},{"last_name":"Sahu","first_name":"Rishabh","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162"},{"orcid":"0000-0001-8319-2148","last_name":"Kapoor","first_name":"Lucky","full_name":"Kapoor, Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"orcid":"0000-0003-4345-4267","first_name":"Liu","last_name":"Qiu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"date_updated":"2026-11-09T23:30:28Z","publication":"arXiv","date_created":"2025-01-29T11:11:34Z","year":"2023","publication_status":"draft","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.","date_published":"2023-10-25T00:00:00Z","month":"10","citation":{"short":"G.M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, J.M. Fink, ArXiv (n.d.).","chicago":"Arnold, Georg M, Thomas Werner, Rishabh Sahu, Lucky Kapoor, Liu Qiu, and Johannes M Fink. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>.","mla":"Arnold, Georg M., et al. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","apa":"Arnold, G. M., Werner, T., Sahu, R., Kapoor, L., Qiu, L., &#38; Fink, J. M. (n.d.). All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>","ista":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","ieee":"G. M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, and J. M. Fink, “All-optical single-shot readout of a superconducting qubit,” <i>arXiv</i>. .","ama":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>"},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"title":"All-optical single-shot readout of a superconducting qubit","_id":"18953","arxiv":1,"day":"25","fulldoi":"https://doi.org/10.48550/ARXIV.2310.16817","department":[{"_id":"JoFi"}],"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a","grant_number":"101089099","name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"doi":"10.48550/ARXIV.2310.16817","oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"corr_author":"1","article_processing_charge":"No","external_id":{"arxiv":["2310.16817"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.16817"}]},{"type":"journal_article","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"14279","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"14697","status":"public"},{"id":"19745","relation":"dissertation_contains","status":"public"}]},"abstract":[{"lang":"eng","text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization."}],"quality_controlled":"1","status":"public","scopus_import":"1","date_updated":"2026-11-09T23:30:30Z","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H","first_name":"Jonna H","last_name":"Alanko","orcid":"0000-0002-7698-3061"},{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217"},{"full_name":"Canigova, Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","first_name":"Nikola","orcid":"0000-0002-8518-5926"},{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A"},{"first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan"},{"last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt"}],"intvolume":"         8","isi":1,"acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","article_number":"adc9584","publication_status":"published","year":"2023","date_created":"2023-09-06T08:07:51Z","publication":"Science Immunology","citation":{"chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>"},"oa_version":"Published Version","publisher":"American Association for the Advancement of Science","month":"09","ddc":["570"],"date_published":"2023-09-01T00:00:00Z","pmid":1,"_id":"14274","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"fulldoi":"https://doi.org/10.1126/sciimmunol.adc9584","publication_identifier":{"issn":["2470-9468"]},"day":"01","issue":"87","corr_author":"1","doi":"10.1126/sciimmunol.adc9584","project":[{"call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"oa":1,"keyword":["General Medicine","Immunology"],"volume":8,"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"article_type":"original","article_processing_charge":"No"},{"status":"public","OA_place":"publisher","type":"dissertation","language":[{"iso":"eng"}],"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"}],"author":[{"first_name":"Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X"}],"date_updated":"2026-04-07T14:02:30Z","publication_status":"published","year":"2023","date_created":"2023-08-24T13:01:18Z","file_date_updated":"2024-02-26T23:30:03Z","publisher":"Institute of Science and Technology Austria","ddc":["500"],"month":"08","date_published":"2023-08-24T00:00:00Z","citation":{"apa":"Stephenson, E. R. (2023). <i>Generalizing medial axes with homology switches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>","mla":"Stephenson, Elizabeth R. <i>Generalizing Medial Axes with Homology Switches</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>.","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>","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."},"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"14226","title":"Generalizing medial axes with homology switches","publication_identifier":{"issn":["2791-4585"]},"day":"24","page":"43","supervisor":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"fulldoi":"https://doi.org/10.15479/at:ista:14226","degree_awarded":"MS","file":[{"file_size":15501411,"file_name":"documents-export-2023-08-24.zip","checksum":"453caf851d75c3478c10ed09bd242a91","creator":"cchlebak","content_type":"application/x-zip-compressed","file_id":"14227","date_created":"2023-08-24T13:02:49Z","embargo_to":"open_access","date_updated":"2024-02-26T23:30:03Z","relation":"source_file","access_level":"closed"},{"content_type":"application/pdf","date_created":"2023-08-24T13:03:42Z","file_id":"14228","file_size":6854783,"file_name":"thesis_pdf_a.pdf","creator":"cchlebak","checksum":"7349d29963d6695e555e171748648d9a","embargo":"2024-02-25","access_level":"open_access","relation":"main_file","date_updated":"2024-02-26T23:30:03Z"}],"oa":1,"doi":"10.15479/at:ista:14226","corr_author":"1","alternative_title":["ISTA Master's Thesis"],"article_processing_charge":"No","has_accepted_license":"1"},{"date_published":"2023-11-10T00:00:00Z","ddc":["570"],"month":"11","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). <i>Mechanism of clathrin-coated vesicle  formation during endocytosis in plants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>.","mla":"Gnyliukh, Nataliia. <i>Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>","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."},"date_created":"2023-11-10T09:10:06Z","year":"2023","publication_status":"published","file_date_updated":"2024-11-23T23:30:38Z","author":[{"orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-11-09T23:30:41Z","status":"public","abstract":[{"lang":"eng","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. "}],"related_material":{"record":[{"id":"14591","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9887"},{"id":"8139","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"type":"dissertation","OA_place":"publisher","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:14510","oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_updated":"2024-11-23T23:30:38Z","relation":"source_file","embargo_to":"open_access","access_level":"closed","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","creator":"ngnyliuk","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","file_size":20824903,"date_created":"2023-11-20T09:18:51Z","file_id":"14567","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"embargo":"2024-11-23","access_level":"open_access","relation":"main_file","date_updated":"2024-11-23T23:30:38Z","content_type":"application/pdf","date_created":"2023-11-20T09:23:11Z","file_id":"14568","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","file_size":24871844,"creator":"ngnyliuk","checksum":"bfc96d47fc4e7e857dd71656097214a4"}],"corr_author":"1","supervisor":[{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"day":"10","page":"180","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"fulldoi":"https://doi.org/10.15479/at:ista:14510","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","_id":"14510"},{"month":"10","article_processing_charge":"No","date_published":"2023-10-10T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.09.561523","open_access":"1"}],"oa_version":"Preprint","citation":{"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.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","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. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” <i>bioRxiv</i>. .","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, <a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>"},"publication_status":"draft","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.1101/2023.10.09.561523","oa":1,"date_created":"2023-11-22T10:17:49Z","year":"2023","publication":"bioRxiv","corr_author":"1","author":[{"last_name":"Gnyliukh","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843"},{"first_name":"Marie-Kristin","last_name":"Nagel","full_name":"Nagel, Marie-Kristin"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria"},{"full_name":"Isono, Erika","first_name":"Erika","last_name":"Isono"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"day":"10","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"fulldoi":"https://doi.org/10.1101/2023.10.09.561523","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_updated":"2026-11-09T23:30:41Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"_id":"14591","OA_place":"repository","type":"preprint","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","language":[{"iso":"eng"}],"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."}],"related_material":{"record":[{"id":"15330","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14510"}]}},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"12471","date_created":"2023-01-31T15:11:42Z","content_type":"application/pdf","creator":"cchlebak","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_size":41771714,"file_name":"20230109_PhD_thesis_JM_final.pdf","embargo":"2023-07-09","access_level":"open_access","date_updated":"2023-07-27T22:30:54Z","relation":"main_file"},{"date_created":"2023-01-31T15:11:51Z","file_id":"12472","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_name":"20230109_PhD_thesis_JM_final.docx","file_size":66983464,"access_level":"closed","relation":"source_file","date_updated":"2023-07-10T22:30:04Z","embargo_to":"open_access"}],"doi":"10.15479/at:ista:12470","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"oa":1,"corr_author":"1","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"12470","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","publication_identifier":{"isbn":["978-3-99078-026-8"],"issn":["2663-337X"]},"day":"09","page":"201","supervisor":[{"orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"fulldoi":"https://doi.org/10.15479/at:ista:12470","degree_awarded":"PhD","year":"2023","date_created":"2023-01-31T15:10:53Z","publication_status":"published","file_date_updated":"2023-07-27T22:30:54Z","ddc":["610"],"month":"01","publisher":"Institute of Science and Technology Austria","date_published":"2023-01-09T00:00:00Z","oa_version":"Published Version","citation":{"apa":"Michalska, J. M. (2023). <i>A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>","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. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>.","mla":"Michalska, Julia M. <i>A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>.","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:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>","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."},"status":"public","type":"dissertation","OA_place":"publisher","related_material":{"record":[{"relation":"part_of_dissertation","id":"11943","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11950"}]},"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"}],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-3862-1235","first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M"}],"date_updated":"2026-07-06T12:50:45Z"},{"publication_status":"published","year":"2023","date_created":"2023-11-28T10:58:13Z","file_date_updated":"2024-11-30T23:30:03Z","publisher":"Institute of Science and Technology Austria","month":"11","ddc":["530"],"date_published":"2023-11-30T00:00:00Z","doi_confirm":"1","citation":{"ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","apa":"Sack, S. (2023). <i>Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>.","mla":"Sack, Stefan. <i>Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>."},"oa_version":"Published Version","status":"public","OA_place":"publisher","type":"dissertation","language":[{"iso":"eng"}],"abstract":[{"text":"This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum\r\ncomputation due to their moderate hardware requirements and resilience to noise. Our\r\nprimary focus lies on two particular types of VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE), utilized for finding ground states of quantum many-body systems.\r\nIn the first part of the thesis, we examine the issue of effective parameter initialization for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA often leads to\r\nconvergence in local minima with sub-optimal performance. To mitigate this issue, we propose\r\nan initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization leads to the same performance as the best of an exponentially\r\nscaling number of random initializations.\r\nThe second study introduces Transition States (TS), stationary points with a single direction\r\nof descent, as a tool for systematically exploring the QAOA optimization landscape. This\r\nleads us to propose a novel greedy parameter initialization strategy that guarantees for the\r\nenergy to decrease with increasing number of circuit layers.\r\nIn the third section, we extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations of qubits. This chapter provides theoretical insights and practical strategies for\r\nleveraging the increased computational power of qudits in the context of quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients that obstruct efficient parameter optimization. This novel approach relies\r\non defining a notion of weak barren plateaus based on the entropies of local reduced density\r\nmatrices and showcases how these can be efficiently quantified using shadow tomography.\r\nTo illustrate the approach we employ the strategy in the VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization and throughout the optimization.\r\nTaken together, this thesis greatly enhances our understanding of parameter initialization and\r\noptimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method to address the challenge of barren plateaus using the VQE. These\r\ninsights are instrumental in advancing the field of near-term quantum computation.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"13125","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"11471","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9760"}]},"author":[{"orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"}],"date_updated":"2026-09-14T08:36:32Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"file":[{"checksum":"068fd3570506ec42b2faa390de784bc4","creator":"ssack","file_size":11947523,"file_name":"PhD_Thesis.pdf","date_created":"2023-11-30T15:53:10Z","file_id":"14635","content_type":"application/pdf","relation":"main_file","date_updated":"2024-11-30T23:30:03Z","embargo":"2024-11-30","access_level":"open_access"},{"embargo_to":"open_access","relation":"source_file","date_updated":"2024-11-30T23:30:03Z","access_level":"closed","file_name":"PhD Thesis (1).zip","file_size":18422964,"checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","creator":"ssack","content_type":"application/zip","date_created":"2023-11-30T15:54:11Z","file_id":"14636"}],"oa":1,"project":[{"name":"IBM PhD Nomination Fellowship - Stefan Sack","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"doi":"10.15479/at:ista:14622","corr_author":"1","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ec_funded":1,"_id":"14622","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","day":"30","page":"142","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"fulldoi":"https://doi.org/10.15479/at:ista:14622","degree_awarded":"PhD"}]