[{"citation":{"mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023."},"day":"06","supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.15479/at:ista:12809","page":"115","file_date_updated":"2024-04-08T22:30:03Z","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","has_accepted_license":"1","ddc":["570"],"type":"dissertation","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"RySh"}],"alternative_title":["ISTA Thesis"],"file":[{"file_id":"12814","file_size":9881969,"content_type":"application/pdf","date_created":"2023-04-07T06:16:06Z","relation":"main_file","embargo":"2024-04-07","checksum":"35b5997d2b0acb461f9d33d073da0df5","creator":"cchlebak","access_level":"open_access","date_updated":"2024-04-08T22:30:03Z","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf"},{"date_created":"2023-04-07T06:17:11Z","relation":"source_file","access_level":"closed","checksum":"81198f63c294890f6d58e8b29782efdc","creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","date_updated":"2024-04-08T22:30:03Z","embargo_to":"open_access","file_id":"12815","content_type":"application/pdf","file_size":44201583},{"relation":"source_file","date_created":"2023-04-07T06:18:05Z","file_name":"Thesis_CatarinaAlcarva_final.docx","date_updated":"2024-04-08T22:30:03Z","creator":"cchlebak","checksum":"0317bf7f457bb585f99d453ffa69eb53","access_level":"closed","embargo_to":"open_access","file_id":"12816","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":84731244}],"corr_author":"1","degree_awarded":"PhD","_id":"12809","year":"2023","date_published":"2023-04-06T00:00:00Z","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","month":"04","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"oa_version":"Published Version","project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Alcarva","first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","full_name":"Alcarva, Catarina"}],"date_created":"2023-04-06T07:54:09Z","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-07T13:53:28Z"},{"file_date_updated":"2024-11-30T23:30:03Z","page":"142","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"doi":"10.15479/at:ista:14622","supervisor":[{"last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"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>.","ista":"Sack S. 2023. Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","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>","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>","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>.","short":"S. Sack, Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ieee":"S. Sack, “Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023."},"day":"30","alternative_title":["ISTA Thesis"],"corr_author":"1","file":[{"file_id":"14635","file_size":11947523,"content_type":"application/pdf","relation":"main_file","date_created":"2023-11-30T15:53:10Z","embargo":"2024-11-30","file_name":"PhD_Thesis.pdf","date_updated":"2024-11-30T23:30:03Z","access_level":"open_access","creator":"ssack","checksum":"068fd3570506ec42b2faa390de784bc4"},{"file_name":"PhD Thesis (1).zip","date_updated":"2024-11-30T23:30:03Z","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","creator":"ssack","access_level":"closed","relation":"source_file","date_created":"2023-11-30T15:54:11Z","content_type":"application/zip","file_size":18422964,"embargo_to":"open_access","file_id":"14636"}],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"type":"dissertation","publication_status":"published","ddc":["530"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"13125","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11471"},{"id":"9760","status":"public","relation":"part_of_dissertation"}]},"has_accepted_license":"1","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","title":"Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems","month":"11","date_published":"2023-11-30T00:00:00Z","year":"2023","_id":"14622","degree_awarded":"PhD","date_updated":"2026-04-07T13:53:47Z","publication_identifier":{"issn":["2663-337X"]},"author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","first_name":"Stefan","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508"}],"date_created":"2023-11-28T10:58:13Z","project":[{"name":"IMB PhD Nomination Fellowship - Stefan Sack","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"file":[{"checksum":"0d71423888eeccaa60d8f41197f26306","creator":"dernst","access_level":"open_access","date_updated":"2023-06-13T07:28:36Z","file_name":"2023_PhysRevA_Sack.pdf","date_created":"2023-06-13T07:28:36Z","relation":"main_file","file_size":2524611,"content_type":"application/pdf","success":1,"file_id":"13131"}],"corr_author":"1","department":[{"_id":"MaSe"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","ddc":["530"],"publication":"Physical Review A","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"17208","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"14622"}]},"publisher":"American Physical Society","file_date_updated":"2023-06-13T07:28:36Z","doi":"10.1103/physreva.107.062404","issue":"6","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"062404","license":"https://creativecommons.org/licenses/by/4.0/","isi":1,"day":"02","citation":{"ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>.","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., &#38; Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>."},"date_updated":"2026-05-05T22:30:21Z","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"date_created":"2023-06-07T06:57:32Z","author":[{"orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","last_name":"Sack"},{"last_name":"Medina Ramos","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869"},{"first_name":"Richard","last_name":"Kueng","full_name":"Kueng, Richard"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"oa_version":"Published Version","arxiv":1,"abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"oa":1,"volume":107,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]},"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"scopus_import":"1","month":"06","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","date_published":"2023-06-02T00:00:00Z","_id":"13125","year":"2023","intvolume":"       107"},{"page":"1630-1635","keyword":["General Physics and Astronomy"],"file_date_updated":"2024-01-29T11:25:38Z","isi":1,"day":"01","citation":{"short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","ieee":"S. Mukhopadhyay <i>et al.</i>, “Superconductivity from a melted insulator in Josephson junction arrays,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1630–1635, 2023.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>.","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. 2023;19:1630-1635. doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., &#38; Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41567-023-02161-w","acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","publication_status":"published","type":"journal_article","corr_author":"1","file":[{"file_size":1977706,"content_type":"application/pdf","file_id":"14899","success":1,"creator":"dernst","access_level":"open_access","checksum":"1fc86d71bfbf836e221c1e925343adc5","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","date_updated":"2024-01-29T11:25:38Z","date_created":"2024-01-29T11:25:38Z","relation":"main_file"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"17881","status":"public"}]},"publisher":"Springer Nature","ddc":["530"],"publication":"Nature Physics","status":"public","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","article_type":"original","language":[{"iso":"eng"}],"_id":"14032","year":"2023","intvolume":"        19","month":"11","scopus_import":"1","title":"Superconductivity from a melted insulator in Josephson junction arrays","date_published":"2023-11-01T00:00:00Z","date_created":"2023-08-11T07:41:17Z","author":[{"first_name":"Soham","last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham"},{"orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L","first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714"},{"last_name":"Puglia","first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","orcid":"0000-0003-1144-2763"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin","full_name":"Zemlicka, Martin","orcid":"0009-0005-0878-3032"},{"last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"project":[{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"date_updated":"2026-05-05T22:30:23Z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"volume":19,"oa":1,"external_id":{"isi":["001054563800006"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator."}]},{"ec_funded":1,"status":"public","article_type":"original","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"year":"2023","_id":"12521","intvolume":"         7","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","scopus_import":"1","month":"02","date_published":"2023-02-01T00:00:00Z","author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"last_name":"Khudiakova","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"date_created":"2023-02-06T13:59:12Z","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"date_updated":"2026-05-05T22:30:25Z","publication_identifier":{"issn":["2056-3744"]},"volume":7,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"file_date_updated":"2023-08-16T11:43:33Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"citation":{"ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023."},"day":"01","isi":1,"acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"1","doi":"10.1093/evlett/qrac004","article_number":"qrac004","quality_controlled":"1","type":"journal_article","publication_status":"published","file":[{"date_created":"2023-08-16T11:43:33Z","relation":"main_file","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","access_level":"open_access","creator":"dernst","file_name":"2023_EvLetters_Mrnjavac.pdf","date_updated":"2023-08-16T11:43:33Z","file_id":"14068","success":1,"content_type":"application/pdf","file_size":2592189}],"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"18531","relation":"dissertation_contains"}]},"publisher":"Oxford University Press","ddc":["570"],"publication":"Evolution Letters"},{"publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663-337X"]},"date_updated":"2026-04-07T13:57:40Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"date_created":"2023-12-18T19:14:28Z","author":[{"full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1,"date_published":"2023-12-20T00:00:00Z","month":"12","title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","degree_awarded":"PhD","year":"2023","_id":"14697","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"alternative_title":["ISTA Thesis"],"file":[{"file_id":"14699","file_size":51585778,"content_type":"application/pdf","date_created":"2023-12-20T09:35:34Z","relation":"main_file","embargo":"2024-12-20","creator":"jstopp","checksum":"457927165d5d556305d3086f6b83e5c7","access_level":"open_access","date_updated":"2024-12-20T23:30:04Z","file_name":"Thesis.pdf"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":69625950,"embargo_to":"open_access","file_id":"14700","date_updated":"2024-12-20T23:30:04Z","file_name":"Thesis.docx","creator":"jstopp","access_level":"closed","checksum":"e8d26449ac461f5e8478a62c9507506f","relation":"source_file","date_created":"2023-12-20T09:35:35Z"}],"corr_author":"1","publication_status":"published","type":"dissertation","ddc":["570"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"14360","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"12272"},{"relation":"part_of_dissertation","id":"14274","status":"public"},{"status":"public","id":"6328","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7885"}]},"file_date_updated":"2024-12-20T23:30:04Z","page":"226","supervisor":[{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"doi":"10.15479/at:ista:14697","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"day":"20","citation":{"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>.","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>","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>","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>.","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.","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."}},{"type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"corr_author":"1","publisher":"American Association for the Advancement of Science","related_material":{"record":[{"relation":"research_data","status":"public","id":"14279"},{"relation":"dissertation_contains","status":"public","id":"19745"},{"id":"14697","status":"public","relation":"dissertation_contains"}]},"publication":"Science Immunology","keyword":["General Medicine","Immunology"],"citation":{"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.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>","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>","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>.","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.","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>."},"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"day":"01","isi":1,"article_number":"adc9584","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.","doi":"10.1126/sciimmunol.adc9584","issue":"87","project":[{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","last_name":"Alanko","first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","last_name":"Ucar"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola","last_name":"Canigova","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola"},{"full_name":"Stopp, Julian A","last_name":"Stopp","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan","full_name":"Schwarz, Jan"},{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-09-06T08:07:51Z","publication_identifier":{"issn":["2470-9468"]},"date_updated":"2026-05-05T22:30:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"pmid":1,"volume":8,"oa":1,"abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","intvolume":"         8","year":"2023","_id":"14274","date_published":"2023-09-01T00:00:00Z","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","scopus_import":"1","month":"09"},{"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","article_type":"original","status":"public","date_published":"2023-09-13T00:00:00Z","month":"09","scopus_import":"1","title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","intvolume":"        14","year":"2023","_id":"14360","publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2026-05-05T22:30:26Z","date_created":"2023-09-24T22:01:10Z","author":[{"full_name":"Sitarska, Ewa","first_name":"Ewa","last_name":"Sitarska"},{"first_name":"Silvia Dias","last_name":"Almeida","full_name":"Almeida, Silvia Dias"},{"first_name":"Marianne Sandvold","last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold"},{"full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Czuchnowski, Jakub","first_name":"Jakub","last_name":"Czuchnowski"},{"full_name":"Siggel, Marc","first_name":"Marc","last_name":"Siggel"},{"full_name":"Roessner, Rita","last_name":"Roessner","first_name":"Rita"},{"last_name":"Tschanz","first_name":"Aline","full_name":"Tschanz, Aline"},{"full_name":"Ejsing, Christer","last_name":"Ejsing","first_name":"Christer"},{"full_name":"Schwab, Yannick","last_name":"Schwab","first_name":"Yannick"},{"last_name":"Kosinski","first_name":"Jan","full_name":"Kosinski, Jan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Kreshuk","first_name":"Anna","full_name":"Kreshuk, Anna"},{"full_name":"Erzberger, Anna","first_name":"Anna","last_name":"Erzberger"},{"first_name":"Alba","last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba"}],"abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"oa_version":"Published Version","external_id":{"isi":["001087583700008"],"pmid":["37704612"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"volume":14,"oa":1,"file_date_updated":"2023-09-25T08:22:58Z","article_number":"5644","doi":"10.1038/s41467-023-41173-1","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.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"day":"13","citation":{"mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","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>.","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.","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>","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>","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).","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."},"department":[{"_id":"MiSi"}],"file":[{"creator":"dernst","access_level":"open_access","checksum":"ad670e3b3c64fc585675948370f6b149","file_name":"2023_NatureComm_Sitarska.pdf","date_updated":"2023-09-25T08:22:58Z","date_created":"2023-09-25T08:22:58Z","relation":"main_file","file_size":2725421,"content_type":"application/pdf","success":1,"file_id":"14365"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","ddc":["570"],"publication":"Nature Communications","publisher":"Springer Nature","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14697"}]},"has_accepted_license":"1"},{"publication_status":"published","type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_id":"14390","embargo_to":"open_access","file_size":114932847,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_created":"2023-10-04T10:11:53Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_updated":"2024-10-05T22:30:03Z","creator":"pradler","checksum":"87eef11fbc5c7df0826f12a3a629b444","access_level":"closed"},{"checksum":"3253e099b7126469d941fd9419d68b4f","creator":"pradler","access_level":"open_access","date_updated":"2024-10-05T22:30:03Z","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","embargo":"2024-10-04","date_created":"2023-10-04T10:11:21Z","relation":"main_file","content_type":"application/pdf","file_size":37838778,"file_id":"14391"}],"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"has_accepted_license":"1","OA_place":"publisher","related_material":{"record":[{"relation":"research_data","status":"public","id":"10934"},{"relation":"part_of_dissertation","status":"public","id":"11373"},{"id":"7387","status":"public","relation":"part_of_dissertation"}]},"publisher":"Institute of Science and Technology Austria","ddc":["572"],"page":"156","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"file_date_updated":"2024-10-05T22:30:03Z","day":"25","citation":{"mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/at:ista:14280","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"supervisor":[{"last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"date_created":"2023-09-06T10:58:25Z","author":[{"orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Radler"}],"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis"}],"date_updated":"2026-04-07T14:06:05Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"status":"public","ec_funded":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2023","_id":"14280","degree_awarded":"PhD","month":"09","title":"Spatiotemporal signaling during assembly of the bacterial divisome","date_published":"2023-09-25T00:00:00Z"},{"publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"corr_author":"1","file":[{"success":1,"file_id":"14395","content_type":"application/pdf","file_size":6144866,"date_created":"2023-10-04T11:40:51Z","relation":"main_file","creator":"dernst","checksum":"a33d91e398e548f34003170e10988368","access_level":"open_access","file_name":"2023_NatureNeuroscience_Gupta.pdf","date_updated":"2023-10-04T11:40:51Z"}],"publisher":"Springer Nature","related_material":{"record":[{"id":"12370","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"18574"}]},"has_accepted_license":"1","publication":"Nature Neuroscience","ddc":["570"],"page":"606-614","file_date_updated":"2023-10-04T11:40:51Z","isi":1,"day":"01","citation":{"short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” <i>Nature Neuroscience</i>, vol. 26. Springer Nature, pp. 606–614, 2023.","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>.","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. 2023;26:606-614. doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &#38; Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>, vol. 26, Springer Nature, 2023, pp. 606–14, doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>."},"doi":"10.1038/s41593-023-01280-0","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"date_created":"2023-01-23T14:14:19Z","author":[{"first_name":"Divyansh","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","full_name":"Gupta, Divyansh"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser","first_name":"Anton L","full_name":"Sumser, Anton L","orcid":"0000-0002-4792-1881"},{"full_name":"Symonova, Olga","orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","first_name":"Olga"},{"last_name":"Svaton","first_name":"Jan","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","full_name":"Svaton, Jan","orcid":"0000-0002-6198-2939"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"date_updated":"2026-05-05T22:30:31Z","external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":26,"abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.","lang":"eng"}],"oa_version":"Published Version","status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","intvolume":"        26","_id":"12349","year":"2023","date_published":"2023-04-01T00:00:00Z","month":"04","scopus_import":"1","title":"Panoramic visual statistics shape retina-wide organization of receptive fields"},{"has_accepted_license":"1","related_material":{"record":[{"relation":"used_in_publication","id":"12349","status":"public"},{"status":"public","id":"18574","relation":"used_in_publication"}]},"publisher":"Institute of Science and Technology Austria","ddc":["571"],"type":"research_data","corr_author":"1","contributor":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Symonova","first_name":"Olga"},{"contributor_type":"researcher","last_name":"Mlynarski","first_name":"Wiktor 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D., Sumser, A. L., &#38; Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>.","mla":"Gupta, Divyansh, et al. <i>Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023)."},"day":"26","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"doi":"10.15479/AT:ISTA:12370","file_date_updated":"2023-01-26T10:51:34Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. "}],"author":[{"orcid":"0000-0001-7400-6665","full_name":"Gupta, Divyansh","first_name":"Divyansh","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","first_name":"Anton L","last_name":"Sumser"},{"first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"date_created":"2023-01-25T12:45:18Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"}],"date_updated":"2026-05-05T22:30:31Z","_id":"12370","year":"2023","title":"Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields","month":"01","date_published":"2023-01-26T00:00:00Z","ec_funded":1,"status":"public","article_processing_charge":"No"},{"date_created":"2023-04-04T18:57:11Z","author":[{"first_name":"Mara","last_name":"Julseth","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","full_name":"Julseth, Mara"}],"publication_identifier":{"issn":["2791-4585"]},"date_updated":"2026-04-07T14:01:51Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"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_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","degree_awarded":"MS","year":"2023","_id":"12800","date_published":"2023-04-05T00:00:00Z","month":"04","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","publication_status":"published","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file":[{"date_created":"2023-04-06T06:09:40Z","relation":"supplementary_material","access_level":"closed","creator":"mjulseth","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","date_updated":"2023-06-02T22:30:04Z","file_name":"Dispersaldata.xlsx","embargo_to":"open_access","file_id":"12805","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_size":52795},{"date_created":"2023-04-06T06:11:27Z","relation":"supplementary_material","embargo":"2023-06-01","access_level":"open_access","checksum":"5a13b6d204371572e249f03795bc0d04","creator":"mjulseth","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_updated":"2023-06-02T22:30:04Z","file_id":"12806","file_size":787239,"content_type":"application/vnd.wolfram.nb"},{"date_created":"2023-04-06T08:26:12Z","relation":"source_file","access_level":"closed","checksum":"c3ec842839ed1e66bf2618ae33047df8","creator":"mjulseth","file_name":"ThesisMaraJulseth_04_23.docx","date_updated":"2023-06-02T22:30:04Z","file_id":"12812","embargo_to":"open_access","file_size":1061763,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_size":1741364,"content_type":"application/pdf","file_id":"12813","creator":"mjulseth","access_level":"open_access","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.pdf","date_created":"2023-04-06T08:26:37Z","relation":"main_file","embargo":"2023-06-01"}],"corr_author":"1","alternative_title":["ISTA Master's Thesis"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","OA_place":"publisher","ddc":["576"],"page":"21","file_date_updated":"2023-06-02T22:30:04Z","day":"05","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.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","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.","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>","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>."},"supervisor":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"doi":"10.15479/at:ista:12800"},{"supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.15479/at:ista:12781","day":"23","citation":{"short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>"},"file_date_updated":"2024-04-22T22:30:06Z","page":"127","ddc":["570","572"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","OA_place":"publisher","related_material":{"record":[{"id":"12138","status":"public","relation":"part_of_dissertation"}]},"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"alternative_title":["ISTA Thesis"],"file":[{"creator":"vkravchu","checksum":"5ebb6345cb4119f93460c81310265a6d","access_level":"open_access","date_updated":"2024-04-22T22:30:06Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","embargo":"2024-04-20","date_created":"2023-04-19T14:33:41Z","relation":"main_file","content_type":"application/pdf","file_size":6071553,"file_id":"12852"},{"file_id":"12853","file_size":19468766,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_created":"2023-04-19T14:33:52Z","embargo":"2024-04-20","date_updated":"2024-04-22T22:30:06Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","access_level":"open_access","creator":"vkravchu","checksum":"c12055c48411d030d2afa51de2166221"}],"corr_author":"1","publication_status":"published","type":"dissertation","date_published":"2023-03-23T00:00:00Z","month":"03","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","degree_awarded":"PhD","_id":"12781","year":"2023","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1,"abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"date_updated":"2026-04-07T14:10:40Z","project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541"},{"grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"date_created":"2023-03-31T12:24:42Z","author":[{"full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","first_name":"Vladyslav"}]},{"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"month":"10","doi":"10.1101/2023.10.09.561523","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","date_published":"2023-10-10T00:00:00Z","day":"10","_id":"14591","year":"2023","citation":{"ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” <i>bioRxiv</i>. .","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","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>","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>","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>.","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>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.09.561523"}],"corr_author":"1","date_updated":"2026-05-05T22:30:33Z","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"date_created":"2023-11-22T10:17:49Z","author":[{"last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nagel","first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","last_name":"Hlavata","full_name":"Hlavata, Annamaria"},{"first_name":"Erika","last_name":"Isono","full_name":"Isono, Erika"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"publication_status":"draft","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"type":"preprint","oa_version":"Preprint","publication":"bioRxiv","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"id":"15330","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"14510","status":"public"}]},"oa":1,"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ddc":["570"],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"14591","relation":"part_of_dissertation"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8139","status":"public"}]},"OA_place":"publisher","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"file":[{"embargo_to":"open_access","file_id":"14567","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20824903,"relation":"source_file","date_created":"2023-11-20T09:18:51Z","date_updated":"2024-11-23T23:30:38Z","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","access_level":"closed","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","creator":"ngnyliuk"},{"content_type":"application/pdf","file_size":24871844,"file_id":"14568","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_updated":"2024-11-23T23:30:38Z","access_level":"open_access","creator":"ngnyliuk","checksum":"bfc96d47fc4e7e857dd71656097214a4","embargo":"2024-11-23","relation":"main_file","date_created":"2023-11-20T09:23:11Z"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"publication_status":"published","type":"dissertation","supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/at:ista:14510","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"10","citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","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>.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","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>","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>","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>."},"keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"file_date_updated":"2024-11-23T23:30:38Z","page":"180","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. ","lang":"eng"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"date_updated":"2026-05-05T22:30:34Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"date_created":"2023-11-10T09:10:06Z","author":[{"full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-11-10T00:00:00Z","month":"11","title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","degree_awarded":"PhD","year":"2023","_id":"14510","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1},{"ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","degree_awarded":"PhD","year":"2023","_id":"12470","date_published":"2023-01-09T00:00:00Z","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","month":"01","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235"}],"date_created":"2023-01-31T15:10:53Z","publication_identifier":{"isbn":["978-3-99078-026-8"],"issn":["2663-337X"]},"date_updated":"2026-04-07T14:11:10Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"oa_version":"Published Version","page":"201","file_date_updated":"2023-07-27T22:30:54Z","citation":{"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>.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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>.","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>","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>","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.","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."},"day":"09","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/at:ista:12470","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"type":"dissertation","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"file":[{"file_id":"12471","content_type":"application/pdf","file_size":41771714,"embargo":"2023-07-09","date_created":"2023-01-31T15:11:42Z","relation":"main_file","checksum":"1a2306e5f59f52df598e7ecfadf921ac","access_level":"open_access","creator":"cchlebak","date_updated":"2023-07-27T22:30:54Z","file_name":"20230109_PhD_thesis_JM_final.pdf"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":66983464,"embargo_to":"open_access","file_id":"12472","date_updated":"2023-07-10T22:30:04Z","file_name":"20230109_PhD_thesis_JM_final.docx","checksum":"0bebbdee0773443959e1f6ab8caf281f","creator":"cchlebak","access_level":"closed","relation":"source_file","date_created":"2023-01-31T15:11:51Z"}],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","has_accepted_license":"1","related_material":{"record":[{"id":"11943","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"11950","relation":"part_of_dissertation"}]},"ddc":["610"]},{"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","date_published":"2023-08-24T00:00:00Z","title":"Generalizing medial axes with homology switches","month":"08","degree_awarded":"MS","year":"2023","_id":"14226","publication_identifier":{"issn":["2791-4585"]},"date_updated":"2026-04-07T14:02:30Z","author":[{"first_name":"Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R"}],"date_created":"2023-08-24T13:01:18Z","abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"file_date_updated":"2024-02-26T23:30:03Z","page":"43","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"doi":"10.15479/at:ista:14226","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>","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>","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>.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","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>.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023."},"day":"24","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"corr_author":"1","alternative_title":["ISTA Master's Thesis"],"file":[{"date_created":"2023-08-24T13:02:49Z","relation":"source_file","creator":"cchlebak","checksum":"453caf851d75c3478c10ed09bd242a91","access_level":"closed","file_name":"documents-export-2023-08-24.zip","date_updated":"2024-02-26T23:30:03Z","file_id":"14227","embargo_to":"open_access","file_size":15501411,"content_type":"application/x-zip-compressed"},{"file_size":6854783,"content_type":"application/pdf","file_id":"14228","access_level":"open_access","creator":"cchlebak","checksum":"7349d29963d6695e555e171748648d9a","date_updated":"2024-02-26T23:30:03Z","file_name":"thesis_pdf_a.pdf","date_created":"2023-08-24T13:03:42Z","relation":"main_file","embargo":"2024-02-25"}],"type":"dissertation","publication_status":"published","ddc":["500"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","has_accepted_license":"1"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"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"}],"oa_version":"Published Version","author":[{"full_name":"Kirillova, Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","last_name":"Kirillova","first_name":"Kseniia"}],"date_created":"2023-02-09T07:45:05Z","publication_identifier":{"issn":["2791-4585"]},"date_updated":"2026-04-07T14:06:26Z","degree_awarded":"MS","_id":"12531","year":"2023","date_published":"2023-02-08T00:00:00Z","title":"Panoramic functional gradients across the mouse retina","month":"02","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","OA_place":"publisher","ddc":["570"],"type":"dissertation","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"file":[{"file_id":"12532","content_type":"application/pdf","file_size":8369317,"embargo":"2024-02-08","date_created":"2023-02-09T08:03:32Z","relation":"main_file","creator":"cchlebak","access_level":"open_access","checksum":"57d8da3a6c749eb1556b7435fe266a5f","date_updated":"2024-02-09T23:30:03Z","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf"},{"file_id":"12535","embargo_to":"open_access","file_size":11204408,"content_type":"application/x-zip-compressed","date_created":"2023-02-10T09:32:06Z","relation":"source_file","access_level":"closed","creator":"cchlebak","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","date_updated":"2024-02-09T23:30:03Z","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip"}],"corr_author":"1","alternative_title":["ISTA Master's Thesis"],"citation":{"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>.","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>","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>","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>.","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.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023."},"day":"08","supervisor":[{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"doi":"10.15479/at:ista:12531","page":"46","file_date_updated":"2024-02-09T23:30:03Z"},{"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"date_created":"2023-09-13T10:07:18Z","author":[{"last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna"}],"project":[{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"}],"date_updated":"2026-04-14T09:50:54Z","publication_identifier":{"issn":["2663-337X"]},"year":"2023","_id":"14323","degree_awarded":"PhD","month":"09","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","date_published":"2023-09-13T00:00:00Z","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7883"}]},"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","ddc":["570"],"publication_status":"published","type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2023-09-13T09:52:52Z","relation":"main_file","embargo":"2025-03-13","creator":"kkuzmicz","checksum":"bd83596869c814b24aeff7077d031c0e","access_level":"open_access","date_updated":"2025-03-13T23:30:05Z","file_name":"PhDThesis_KK_final_pdfA.pdf","file_id":"14324","file_size":10147911,"content_type":"application/pdf"},{"checksum":"aa2757ae4c3478041fd7e62c587d3e4d","creator":"kkuzmicz","access_level":"closed","file_name":"thesis_KK_final_corrections_092023.docx","date_updated":"2025-03-13T23:30:05Z","date_created":"2023-09-13T09:53:29Z","relation":"source_file","file_size":103980668,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14325","embargo_to":"open_access"}],"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"day":"13","citation":{"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>","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>","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>.","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","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."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.15479/at:ista:14323","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","supervisor":[{"first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"page":"151","file_date_updated":"2025-03-13T23:30:05Z"},{"department":[{"_id":"AnKi"}],"file":[{"file_name":"2023_CurrOpSystBioloy_Minchington.pdf","date_updated":"2024-01-29T11:06:45Z","checksum":"8a75c4e29fd9b62e3c50663c2265b173","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2024-01-29T11:06:45Z","content_type":"application/pdf","file_size":598842,"file_id":"14896","success":1}],"corr_author":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"Current Opinion in Systems Biology","ddc":["570"],"publisher":"Elsevier","has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19763"}]},"file_date_updated":"2024-01-29T11:06:45Z","article_number":"100459","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","doi":"10.1016/j.coisb.2023.100459","citation":{"mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>, vol. 35, 100459, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>.","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>.","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. 2023;35. doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>","apa":"Minchington, T., Rus, S., &#38; Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” <i>Current Opinion in Systems Biology</i>, vol. 35. Elsevier, 2023."},"day":"01","publication_identifier":{"eissn":["2452-3100"]},"date_updated":"2026-05-05T22:31:01Z","project":[{"_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"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"author":[{"full_name":"Minchington, Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas","last_name":"Minchington"},{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","first_name":"Stefanie","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-06-18T22:00:46Z","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":35,"oa":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","status":"public","date_published":"2023-09-01T00:00:00Z","title":"Control of tissue dimensions in the developing neural tube and somites","scopus_import":"1","month":"09","intvolume":"        35","year":"2023","_id":"13136"}]