--- OA_place: publisher _id: '20357' acknowledged_ssus: - _id: ScienComp - _id: E-Lib acknowledgement: "I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova citation: ama: Ruzickova N. Effect propagation in biological networks. 2025. doi:10.15479/AT-ISTA-20357 apa: Ruzickova, N. (2025). Effect propagation in biological networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20357 chicago: Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20357. ieee: N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025. ista: Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria. mla: Ruzickova, Natalia. Effect Propagation in Biological Networks. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20357. short: N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-15T17:04:48Z date_published: 2025-09-15T00:00:00Z date_updated: 2026-10-02T10:15:31Z day: '15' ddc: - '570' - '530' degree_awarded: PhD department: - _id: GradSch - _id: GaTk doi: 10.15479/AT-ISTA-20357 doi_confirm: '1' file: - access_level: closed checksum: 0582508d439b233497384f83a8307398 content_type: application/x-zip-compressed creator: cchlebak date_created: 2026-08-07T10:57:05Z date_updated: 2026-09-15T22:30:02Z embargo_to: open_access file_id: '22661' file_name: 2025_Ruzickova_Natalia_Thesis.zip file_size: 56464803 relation: source_file - access_level: open_access checksum: b722289fd550abede63adc27b9c61784 content_type: application/pdf creator: cchlebak date_created: 2026-08-07T10:57:34Z date_updated: 2026-09-15T22:30:02Z embargo: 2026-09-15 file_id: '22662' file_name: 2025_Ruzickova_Natalia_Thesis.pdf file_size: 30634378 relation: main_file file_date_updated: 2026-09-15T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20357 has_accepted_license: '1' keyword: - gene regulation - networks - omnigenic model - pancreas - collective behaviour language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '156' project: - _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e name: Collective behaviour of cells in pancreatic Islets of Langerhans publication_identifier: isbn: - 978-3-99078-066-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18525' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Effect propagation in biological networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20563' abstract: - lang: eng text: "The theory of optimal transport provides an elegant and powerful description of many evolution\r\nequations as gradient flows. The primary objective of this thesis is to adapt and extend the\r\ntheory to deal with important equations that are not covered by the classical framework,\r\nspecifically boundary value problems and kinetic equations. Additionally, we establish new\r\nresults in periodic homogenization for discrete dynamical optimal transport and in quantization\r\nof measures.\r\nSection 1.1 serves as an invitation to the classical theory of optimal transport, including the\r\nmain definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the\r\nmain results of this thesis, outline the motivations, and review the current state of the art.\r\nIn Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet\r\nboundary conditions. We construct a time-discrete scheme involving a modification of the\r\nWasserstein distance and, under weak assumptions, prove its convergence to a solution of this\r\nboundary value problem. In dimension 1, we show that this solution is a gradient flow in a\r\nsuitable space of measures.\r\nChapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory\r\nof optimal transport to describe and study particle systems at the mesoscopic scale. We prove\r\nadapted versions of some fundamental theorems, including the Benamou–Brenier formula and\r\nthe identification of absolutely continuous curves of measures.\r\nChapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical\r\ntransportation functionals on periodic graphs in the large-scale limit when the cost functional\r\nis asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge\r\nto 1-Wasserstein distances constructed from crystalline norms on R\r\nd\r\n.\r\nChapter 5 concerns optimal empirical quantization: the problem of approximating a measure\r\nby the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein\r\ndistance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for\r\nthe minimal error as n tends to infinity.\r\n" acknowledgement: "The research contained in this thesis has received funding from the Austrian Science\r\nFund (FWF) project 10.55776/F65." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:10.15479/AT-ISTA-20563 apa: Quattrocchi, F. (2025). Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20563 chicago: Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20563. ieee: F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025. ista: Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria. mla: Quattrocchi, Filippo. Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20563. short: F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-28T13:10:49Z date_published: 2025-11-03T00:00:00Z date_updated: 2026-10-02T11:24:55Z day: '03' ddc: - '515' - '519' degree_awarded: PhD department: - _id: GradSch - _id: JaMa doi: 10.15479/AT-ISTA-20563 file: - access_level: open_access checksum: 6f55275bdf99992be3a6457d949dd664 content_type: application/pdf creator: fquattro date_created: 2025-11-17T21:04:15Z date_updated: 2026-01-01T23:30:03Z embargo: 2026-01-01 file_id: '20653' file_name: 2025_quattrocchi_filippo_thesis.pdf file_size: 4326411 relation: main_file - access_level: closed checksum: 707e580f5d993a214c0dba456b75837b content_type: application/zip creator: fquattro date_created: 2025-11-17T21:05:43Z date_updated: 2026-01-01T23:30:03Z embargo_to: open_access file_id: '20654' file_name: 2025_quattrocchi_thesis.zip file_size: 11726509 relation: source_file file_date_updated: 2026-01-01T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20563 has_accepted_license: '1' keyword: - optimal transport - kinetic equations - boundary value problems - quantization - gradient flows - homogenization language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '240' project: - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20569' relation: part_of_dissertation status: public - id: '20571' relation: part_of_dissertation status: public - id: '20570' relation: part_of_dissertation status: public - id: '18706' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: repository OA_type: green _id: '20569' abstract: - lang: eng text: 'This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov''s equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov''s equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov''s equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves.' acknowledgement: "This work was partially inspired by an unpublished note from 2014 by Guillaume Carlier,\r\nJean Dolbeault, and Bruno Nazaret. GB deeply thanks Jean Dolbeault for proposing\r\nthis problem to him, guiding him into the subject, and sharing the aforementioned note.\r\nWe are grateful to Karthik Elamvazhuthi for making us aware of the work [20].\r\nThe work of GB has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement\r\nNo 101034413.\r\nJM and FQ gratefully acknowledge support from the Austrian Science Fund (FWF)\r\nproject 10.55776/F65." article_number: '2502.15665' article_processing_charge: No arxiv: 1 author: - first_name: Giovanni full_name: Brigati, Giovanni id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1 last_name: Brigati - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: 'Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv. doi:10.48550/arXiv.2502.15665' apa: 'Brigati, G., Maas, J., & Quattrocchi, F. (n.d.). Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv. https://doi.org/10.48550/arXiv.2502.15665' chicago: 'Brigati, Giovanni, Jan Maas, and Filippo Quattrocchi. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2502.15665.' ieee: 'G. Brigati, J. Maas, and F. Quattrocchi, “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures,” arXiv. .' ista: 'Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv, 2502.15665.' mla: 'Brigati, Giovanni, et al. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” ArXiv, 2502.15665, doi:10.48550/arXiv.2502.15665.' short: G. Brigati, J. Maas, F. Quattrocchi, ArXiv (n.d.). corr_author: '1' date_created: 2025-10-28T13:12:08Z date_published: 2025-08-10T00:00:00Z date_updated: 2026-11-04T23:31:11Z day: '10' department: - _id: GradSch - _id: JaMa doi: 10.48550/arXiv.2502.15665 ec_funded: 1 external_id: arxiv: - '2502.15665' fulldoi: https://doi.org/10.48550/arXiv.2502.15665 keyword: - optimal transport - kinetic theory - second-order discrepancy - Vlasov equation - Wasserstein splines. language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2502.15665 month: '08' oa: 1 oa_version: Preprint project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: arXiv publication_status: draft related_material: record: - id: '20563' relation: dissertation_contains status: public status: public title: 'Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '19533' abstract: - lang: eng text: "This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n" acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: NanoFab - _id: LifeSc - _id: SSU acknowledgement: "I acknowledge the generous financial support of the Austrian Science Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop and the Institute of Science and Technology\r\nAustria nanofabrication facility for their technical assistance, which was instrumental in realizing\r\nthis work." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 citation: ama: Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:10.15479/AT-ISTA-19533 apa: Sett, R. (2025). Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19533 chicago: Sett, Riya. “Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19533. ieee: R. Sett, “Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025. ista: Sett R. 2025. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. mla: Sett, Riya. Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19533. short: R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-09T16:44:26Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-10-15T09:08:00Z day: '1' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-19533 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: ba6cd2289d0141a160a14fc97df1632f content_type: application/pdf creator: rsett date_created: 2025-04-10T11:33:22Z date_updated: 2025-10-11T22:30:02Z embargo: 2025-10-11 file_id: '19538' file_name: PhD_Thesis_Riya_Sett_pdfa.pdf file_size: 4129208 relation: main_file - access_level: closed checksum: ee63a94cb8f7adf5e766903028b81ed6 content_type: application/x-zip-compressed creator: rsett date_created: 2025-04-10T11:34:08Z date_updated: 2025-10-11T22:30:02Z embargo_to: open_access file_id: '19539' file_name: PhD Thesis Riya Sett.zip file_size: 6646110 relation: source_file file_date_updated: 2025-10-11T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19533 has_accepted_license: '1' keyword: - phase transition - open quantum system - phase diagram - cavity quantum electrodynamics - superconducting qubits - semiclassical physics - quantum optics - josephson junction - parametric converter - phase conjugation - quantum radar - quantum entanglement - correlation - quantum sensing language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '109' project: - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18978' relation: research_data status: public - id: '19280' relation: part_of_dissertation status: public - id: '13117' relation: part_of_dissertation status: public - id: '17183' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Quantum remote sensing and non-equilibrium phase transitions in the microwave regime tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19280' abstract: - lang: eng text: Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: 'The authors thank G. Arnold and R. Sahu for the discussions, L. Drmic for software development, the MIBA workshop and the ISTA nanofabrication facility for technical support, and VTT Technical Research Centre of Finland for providing us TWPAs for follow-up measurements. This work was supported by the Austrian Science Fund (FWF) [Grant DOI: 10.55776/F71] through BeyondC (F7105) and IST Austria. E. S. R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J. M. F. and M. Ž. acknowledge support from the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant.' article_number: '063601' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: M. full_name: Zens, M. last_name: Zens - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka orcid: 0009-0005-0878-3032 - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 - first_name: Przemyslaw D full_name: Zielinski, Przemyslaw D id: e198fcc4-f6e0-11ea-865d-b6a256760ee8 last_name: Zielinski - first_name: H. S. full_name: Dhar, H. S. last_name: Dhar - first_name: D. O. full_name: Krimer, D. O. last_name: Krimer - first_name: S. full_name: Rotter, S. last_name: Rotter - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Redchenko E, Zens M, Zemlicka M, et al. Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. 2025;134(6). doi:10.1103/PhysRevLett.134.063601 apa: Redchenko, E., Zens, M., Zemlicka, M., Peruzzo, M., Hassani, F., Sett, R., … Fink, J. M. (2025). Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.134.063601 chicago: Redchenko, Elena, M. Zens, Martin Zemlicka, Matilda Peruzzo, Farid Hassani, Riya Sett, Przemyslaw D Zielinski, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.063601. ieee: E. Redchenko et al., “Observation of collapse and revival in a superconducting atomic frequency comb,” Physical Review Letters, vol. 134, no. 6. American Physical Society, 2025. ista: Redchenko E, Zens M, Zemlicka M, Peruzzo M, Hassani F, Sett R, Zielinski PD, Dhar HS, Krimer DO, Rotter S, Fink JM. 2025. Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. 134(6), 063601. mla: Redchenko, Elena, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” Physical Review Letters, vol. 134, no. 6, 063601, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.063601. short: E. Redchenko, M. Zens, M. Zemlicka, M. Peruzzo, F. Hassani, R. Sett, P.D. Zielinski, H.S. Dhar, D.O. Krimer, S. Rotter, J.M. Fink, Physical Review Letters 134 (2025). corr_author: '1' date_created: 2025-03-02T23:01:52Z date_published: 2025-02-14T00:00:00Z date_updated: 2026-11-04T23:31:12Z day: '14' ddc: - '530' department: - _id: JoFi doi: 10.1103/PhysRevLett.134.063601 ec_funded: 1 external_id: arxiv: - '2310.04200' isi: - '001454696700003' pmid: - '40021171' file: - access_level: open_access checksum: 633d6c5ddd9b805da22c5839d3d48df6 content_type: application/pdf creator: dernst date_created: 2025-03-04T10:40:50Z date_updated: 2025-03-04T10:40:50Z file_id: '19291' file_name: 2025_PhysReviewLetters_Redchenko.pdf file_size: 2080408 relation: main_file success: 1 file_date_updated: 2025-03-04T10:40:50Z fulldoi: https://doi.org/10.1103/PhysRevLett.134.063601 has_accepted_license: '1' intvolume: ' 134' isi: 1 issue: '6' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 26B354CA-B435-11E9-9278-68D0E5697425 name: Controllable Collective States of Superconducting Qubit Ensembles publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '19533' relation: dissertation_contains status: public scopus_import: '1' status: public title: Observation of collapse and revival in a superconducting atomic frequency comb tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 134 year: '2025' ... --- OA_place: publisher _id: '20212' abstract: - lang: eng text: "Cortical development has been studied for many decades and with each passing year, we learn \r\nmore about the processes that govern the tightly regulated developmental program. Up until \r\nrecently, the field has struggled to gain reliable access to progenitors at the single-cell level, \r\nlimiting the resolution at which we can study cortical development in vivo. Therefore, much of \r\nthe data we have on mammalian cortical development is at the cell population level. The \r\nsubsequent pages of this thesis describe novel elements of cortical development in mice; \r\nacquired using a candidate gene approach in conjunction with Mosaic Analysis with Double \r\nMarkers (MADM) to achieve single cell resolution. In this thesis, I briefly provide an overview \r\nof the state of the field, describe the methodology used to quantify morphological \r\ncharacteristics of neurons and glia, and delve into the role of Phosphatase and tensin \r\nhomologue on chromosome ten (Pten) in neurogenesis and gliogenesis in the developing mouse \r\ncortex. By using MADM to generate genetic mosaics, in which only a small fraction of cells \r\nare mutated, to study population-level changes, we can bypass the early postnatal lethality \r\nreported in Pten conditional knockouts (cKOs) using Emx1-Cre. We used Emx1-CreERT2 to \r\ninduce clonal deletion of Pten, and quantify RGP neurogenic output at the single progenitor \r\nlevel. Pten-mutant neuron populations within the mosaics were significantly expanded. In the \r\nlatter parts of this thesis, we describe how Pten deletion leads to an increase in the abundance \r\nof astrocytes. We availed ourselves of the flexibility offered by the MADM system to generate \r\nPten mosaics within a series of distinct knockout tissues to test for the interactions between \r\nPten and a battery of genes involved in distinct pro-gliogenic signaling pathways. Our survey \r\nof Pten’s interactions with genes in key signaling pathways reveals that ERK1/2 are the critical \r\neffectors downstream of EGFR signaling essential for gliogenesis. Altogether, our results \r\ndemonstrate that Pten plays critical and distinct roles throughout cortical RGP lineage \r\nprogression. " acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: "I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Osvaldo full_name: Miranda, Osvaldo id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425 last_name: Miranda orcid: 0000-0001-6618-6889 citation: ama: Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:10.15479/AT-ISTA-20212 apa: Miranda, O. (2025). Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20212 chicago: Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20212. ieee: O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025. ista: Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria. mla: Miranda, Osvaldo. Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20212. short: O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-22T14:07:00Z date_published: 2025-08-22T00:00:00Z date_updated: 2026-10-02T12:16:56Z day: '22' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/AT-ISTA-20212 doi_confirm: '1' file: - access_level: closed checksum: 3331f76bbef74ff4908e2d2c9262045c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: omiranda date_created: 2025-08-26T09:03:50Z date_updated: 2026-08-26T22:30:02Z embargo_to: open_access file_id: '20230' file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.docx file_size: 32887334 relation: source_file - access_level: open_access checksum: 02509d50cff8e35c5bcbf71e8d658176 content_type: application/pdf creator: omiranda date_created: 2025-08-26T09:05:55Z date_updated: 2026-08-26T22:30:02Z embargo: 2026-08-26 file_id: '20231' file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf file_size: 28636240 relation: main_file file_date_updated: 2026-08-26T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20212 has_accepted_license: '1' keyword: - Pten - mtor - cortical development - MADM - Mapk language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '119' project: - _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d grant_number: '26253' name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development publication_identifier: isbn: - 978-3-99078-063-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17425' relation: part_of_dissertation status: public status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Unraveling the role of Pten in cortical stem cell lineage progression using MADM type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20117' abstract: - lang: eng text: "Auxin is essential for many aspects of plant growth and development, from \r\nembryogenesis to organ senescence. Polar auxin transport leads to local auxin maxima and \r\ngradients, which are important for regulating various plant development process, including \r\nembryogenesis, organogenesis and vascular tissue formation. The polar auxin transport is \r\nmediated by auxin influx carrier AUX1/LAX proteins and efflux carrier PIN proteins. The \r\nregulation of PIN proteins is a key convergence of crosstalk between auxin and other \r\nhormones, such as cytokinin. Cytokinin promotes the degradation of PIN1 in Arabidopsis \r\nroots, preferentially the dephosphorylated PIN1, and the process is independent of \r\ntranscription and translation (Marhavý et al., 2011; Marhavý et al., 2014). The internalization \r\nof PIN proteins from plasma membrane is controlled by clathrin-mediated endocytosis \r\n(Dhonukshe et al., 2007; Kitakura et al., 2011). However, whether cytokinin affects the PIN1 \r\ndegradation through regulating the phosphorylation of PIN1 or trafficking components is \r\nunknown. Here, we demonstrate that dynamin related protein DRP2s are required for the \r\ncytokinin regulated trafficking of PIN1 and PIN2 in Arabidopsis root epidermal cells. Despite \r\nthe reported redundancy of DRP2A and DRP2B in gametophyte development, we found that \r\nCK-mediated PIN1 degradation and –induced PIN2 membrane localization is affected in drp2a \r\nor drp2b single mutants. Interestingly, we found that cytokinin regulates the recruitment of \r\nDRP2A—but not DRP2B—to clathrin-coated pits, and affects the stability and plasma \r\nmembrane localization of DRP2A. Furthermore, we studied the involvement of cytokinin \r\nreceptors in the regulation of cytokinin on DRP2A. Additionally, the assembly and disassembly \r\ncycle of dynamin is mediated by its dephosphorylation and phosphotylation cycle; thus, we \r\ninvestigated the role of DRP2A phosphorylation in its cytokinin-regulated assembly and in \r\ncytokinin-regulated PIN trafficking. Altogether, we found that cytokinin regulated PIN \r\ntrafficking in Arabidopsis root epidermal cells involves modulation of the phosphorylation of \r\nendocytosis accessory protein DRP2A. " acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl acknowledgement: "I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Yiqun full_name: Wang, Yiqun id: 82F537F2-B517-11E9-84D7-6433E6697425 last_name: Wang citation: ama: Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:10.15479/AT-ISTA-20117 apa: Wang, Y. (2025). The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20117 chicago: Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20117. ieee: Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025. ista: Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. mla: Wang, Yiqun. The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20117. short: Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-04T15:24:21Z date_published: 2025-08-04T00:00:00Z date_updated: 2026-10-02T12:33:36Z day: '04' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-20117 doi_confirm: '1' file: - access_level: closed checksum: 36b87c17d12c7bf5955d6d812acb8d77 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: yiqwang date_created: 2025-08-22T08:22:10Z date_updated: 2026-09-03T22:30:03Z embargo_to: open_access file_id: '20209' file_name: 2025_Wang_Yiqun_Thesis.docx file_size: 25798848 relation: source_file - access_level: open_access checksum: 8d7a2383f66377da675d379ec30ea0fe content_type: application/pdf creator: yiqwang date_created: 2025-08-22T10:32:30Z date_updated: 2026-09-03T22:30:03Z embargo: 2026-09-03 file_id: '20211' file_name: 2025_Wang_Yiqun_Thesis.pdf file_size: 12628313 relation: main_file file_date_updated: 2026-09-03T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20117 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '108' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18063' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: The role of dynamin related protein 2A in cytokinin regulated plant growth and development type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20187' abstract: - lang: eng text: Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: LifeSc acknowledgement: "We gratefully acknowledge the Imaging and Optics, Electron Microscopy (especially Vanessa Zheden for technical assistance) and Life Science (in particular Dorota Jaworska) facilities at ISTA for their continuous support. Authors would like to thank Michelle Gallei for advice during the generation of the transgenic lines; Zuzana Gelová for advice with DR5rev::GFP analyses; Ivan Kulich for help and advice on trichome imaging; Aline Monzer for generous help with hypocotyl and root analyses; Shutang Tan for help with the NGS data analysis; and Milan Župunski for advice on abiotic stress experiments. We would like to thank Dolf Weijers for the SOSEKI (SOK) marker line seeds. This work has benefited from the support of IJPB's Plant Observatory platforms P0-Chem.\r\n\r\nThis work was supported by Austrian Science Fund (FWF) (I 6123-B) and Science and Technology Department of Jiangxi Province (20223BCJ25037) to Huibin Han. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007)." article_number: e70396 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Frédérique full_name: Tellier, Frédérique last_name: Tellier - first_name: Adrijana full_name: Smoljan, Adrijana id: cced8a85-223e-11ed-af04-b0596c55053b last_name: Smoljan - first_name: Hana full_name: Rakusova, Hana id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA last_name: Rakusova - first_name: Petr full_name: Valošek, Petr id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87 last_name: Valošek - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jean Denis full_name: Faure, Jean Denis last_name: Faure - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Babic D, Abualia R, Fiedler L, et al. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 2025;123(3). doi:10.1111/tpj.70396 apa: Babic, D., Abualia, R., Fiedler, L., Qi, L., Tellier, F., Smoljan, A., … Friml, J. (2025). Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. Wiley. https://doi.org/10.1111/tpj.70396 chicago: Babic, David, Rashed Abualia, Lukas Fiedler, Linlin Qi, Frédérique Tellier, Adrijana Smoljan, Hana Rakusova, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” Plant Journal. Wiley, 2025. https://doi.org/10.1111/tpj.70396. ieee: D. Babic et al., “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” Plant Journal, vol. 123, no. 3. Wiley, 2025. ista: Babic D, Abualia R, Fiedler L, Qi L, Tellier F, Smoljan A, Rakusova H, Valošek P, Han H, Benková E, Faure JD, Friml J. 2025. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 123(3), e70396. mla: Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” Plant Journal, vol. 123, no. 3, e70396, Wiley, 2025, doi:10.1111/tpj.70396. short: D. Babic, R. Abualia, L. Fiedler, L. Qi, F. Tellier, A. Smoljan, H. Rakusova, P. Valošek, H. Han, E. Benková, J.D. Faure, J. Friml, Plant Journal 123 (2025). corr_author: '1' date_created: 2025-08-17T22:01:36Z date_published: 2025-08-01T00:00:00Z date_updated: 2026-11-04T23:31:15Z day: '01' ddc: - '580' department: - _id: EvBe - _id: JiFr - _id: GradSch doi: 10.1111/tpj.70396 external_id: isi: - '001547884300001' pmid: - '40782342' file: - access_level: open_access checksum: 1cdc3341d2d23101abca72521f1f23cb content_type: application/pdf creator: dernst date_created: 2025-09-01T14:09:31Z date_updated: 2025-09-01T14:09:31Z file_id: '20264' file_name: 2025_PlantJournal_Babic.pdf file_size: 5791111 relation: main_file success: 1 file_date_updated: 2025-09-01T14:09:31Z fulldoi: https://doi.org/10.1111/tpj.70396 has_accepted_license: '1' intvolume: ' 123' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis publication: Plant Journal publication_identifier: eissn: - 1365-313X issn: - 0960-7412 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '20362' relation: dissertation_contains status: public scopus_import: '1' status: public title: Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 123 year: '2025' ... --- OA_place: publisher _id: '20362' abstract: - lang: eng text: "Arabidopsis embryo has long served as a model system for understanding how plant body \r\npatterning and axis establishment arise. Previous work established that auxin flows, directed \r\nby polar transport and reinforced by local biosynthesis, underpin axes formation, while recent \r\nstudies suggest that maternal tissue, membrane composition and surface receptor signaling add \r\nfurther regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which \r\nguide plant embryonic and post-embryonic development. We review methodological advances \r\nthat allow the embryo to be imaged and studied. These tools offer exciting venues for future \r\naddressing of outstanding research questions. Furthermore, we dissect the contribution of \r\nmaternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments \r\nlowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens \r\nthe initial apical maximum. The resulting deficit dampens downstream embryonic auxin \r\nbiosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided \r\nauxin controls auxin flows in the embryos on a larger scale than previously understood. \r\nIntriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases \r\nTMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be \r\npreferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK \r\nactivity arrests embryos, affects seedling development and persists into adult growth, \r\nsuggesting that maternal effect could shape development beyond fertilization and early \r\nembryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane \r\ncomposition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid \r\nmetabolism triggers widespread patterning errors. \r\nTogether, these results reposition early plant patterning as a hierarchical cascade that begins \r\nwith maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated \r\nby maternal receptor signaling and could ultimately be gated by the biophysical properties of \r\nthe membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking \r\ninto a single narrative, this thesis helps shifting the approach of viewing the embryo as an \r\nautonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal \r\ncontext." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic citation: ama: Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:10.15479/AT-ISTA-20362 apa: Babic, D. (2025). Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20362 chicago: Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20362. ieee: D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025. ista: Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria. mla: Babic, David. Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20362. short: D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-17T13:28:01Z date_published: 2025-09-18T00:00:00Z date_updated: 2026-10-16T07:59:32Z day: '18' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr - _id: EvBe doi: 10.15479/AT-ISTA-20362 doi_confirm: '1' file: - access_level: open_access checksum: 5ecf274281a54a41e0288bc79edf7492 content_type: application/pdf creator: dbabic date_created: 2025-09-24T13:43:14Z date_updated: 2026-09-25T22:30:02Z embargo: 2026-09-25 file_id: '20388' file_name: 2025_David_Babic_Thesis.pdf file_size: 7501548 relation: main_file - access_level: closed checksum: 2703e548390de0a1af7a707137e8ab3b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dbabic date_created: 2025-09-24T13:43:14Z date_updated: 2026-09-25T22:30:02Z embargo_to: open_access file_id: '20389' file_name: Thesis_Babic_draft.docx file_size: 23206052 relation: source_file file_date_updated: 2026-09-25T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20362 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '116' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20187' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository _id: '21427' abstract: - lang: eng text: While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo. acknowledgement: "European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360" article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Erik full_name: Sahai, Erik last_name: Sahai - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv. doi:10.1101/2025.05.20.655037 apa: Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., & Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv. https://doi.org/10.1101/2025.05.20.655037 chicago: Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.20.655037. ieee: Z. Dunajova et al., “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” bioRxiv. . ista: Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, 10.1101/2025.05.20.655037. mla: Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” BioRxiv, doi:10.1101/2025.05.20.655037. short: Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-03-11T08:40:06Z date_published: 2025-09-25T00:00:00Z date_updated: 2026-11-04T23:31:15Z day: '25' ddc: - '539' - '570' department: - _id: GradSch - _id: EdHa - _id: MiSi - _id: NanoFab - _id: AnSa doi: 10.1101/2025.05.20.655037 fulldoi: https://doi.org/10.1101/2025.05.20.655037 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.20.655037 month: '09' oa: 1 oa_version: Preprint project: - _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd grant_number: '101071793' name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces' - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication: bioRxiv publication_status: draft related_material: record: - id: '21439' relation: research_data status: public - id: '22963' relation: later_version status: public - id: '21423' relation: dissertation_contains status: public status: public title: Substrate heterogeneity promotes cancer cell dissemination through interface roughening tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20393' abstract: - lang: eng text: "During vertebrate development, the morphogen Sonic Hedgehog (Shh) plays a key role in \r\npatterning the tissues of the extending body. This requires precise coordination between the \r\nsize of the source of Shh production and the embryo body. Shh is produced by the notochord, \r\nas well as floorplate of the neural tube. In this thesis, we investigated how the sizes of the \r\nnotochord and floorplate are regulated and how they impact the developing mouse embryo. \r\nTo measure the size and shape of the developing mouse notochord and the cell behaviours \r\nwithin this organ, we performed high-resolution measurements in cleared embryos between \r\nE8.5 and E10.5 of development. Strikingly, our data revealed that the notochord maintains a \r\nconstant cross-sectional area throughout the trunk over time as it lengthens by cell \r\nproliferation. We show that this is achieved by a feedback between the notochord cell \r\nproliferation rate and both the cross-sectional area of the trunk notochord and elongation of \r\nthe embryo. Using live imaging, we further show that notochord cells undergo posteriorly\r\ndirected active cell migration and that this cell migration contributes to maintaining the \r\nstructural integrity of the notochord. Our results show a complex coordination of cell \r\nbehaviours that allow for robust notochord morphogenesis during mouse development and \r\nthe maintenance of a defined Shh source size. \r\nShh produced by the notochord induces a secondary Shh-producing domain, the floor plate. \r\nHow the notochord and floor plate contribute to the formation of the Shh gradient in the \r\nneural tube and to the regulation of the floor plate size is poorly understood. Our theoretical \r\nand experimental analysis indicates that only the initial levels of notochord-derived Shh \r\ninfluence the size of the floor plate, and the floor plate is insensitive to its own production of \r\nShh. After its initial establishment, the floor plate expands by tissue growth, leading to scaling \r\nof the Shh gradient amplitude with tissue size. \r\nAltogether, we show that the mechanisms regulating the sizes of the notochord and \r\nfloorplate in mouse development help to achieve size robustness of these tissues. Our data \r\ndemonstrate that the initial establishment of the Shh gradient in the neural tube is strongly \r\ndependent on the notochord and suggest that the robustness of notochord morphogenesis \r\nis essential for pattern formation. Later in development, the floor plate size and the Shh \r\ngradient are coupled to neural tube growth. Our findings provide new insights on how pattern \r\nformation, tissue growth and morphogenesis interact to ensure reproducible developmental \r\noutcomes. " acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi orcid: 0000-0001-6060-4795 citation: ama: Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:10.15479/AT-ISTA-20393 apa: Kishi, K. (2025). Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20393 chicago: Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20393. ieee: K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025. ista: Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria. mla: Kishi, Kasumi. Regulation of Notochord and Floor Plate Size during Mouse Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20393. short: K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-25T10:08:10Z date_published: 2025-09-24T00:00:00Z date_updated: 2026-10-16T08:31:16Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi - _id: EdHa doi: 10.15479/AT-ISTA-20393 doi_confirm: '1' file: - access_level: closed checksum: 6bb5a7ce318dc3f7bd165f2523e77b89 content_type: application/x-zip-compressed creator: kkishi date_created: 2025-09-30T14:33:17Z date_updated: 2026-09-30T22:30:04Z embargo_to: open_access file_id: '20413' file_name: 2025-Kishi-Kasumi-Thesis.zip file_size: 41847994 relation: source_file - access_level: open_access checksum: 88349b9177e1dcbe1242cd3884b36fdb content_type: application/pdf creator: kkishi date_created: 2025-09-30T14:33:22Z date_updated: 2026-09-30T22:30:04Z embargo: 2026-09-30 file_id: '20414' file_name: 2025-Kishi-Kasumi-Thesis.pdf file_size: 55747072 relation: main_file file_date_updated: 2026-09-30T22:30:04Z fulldoi: https://doi.org/10.15479/AT-ISTA-20393 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '102' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18481' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Regulation of notochord and floor plate size during mouse development tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20364' abstract: - lang: eng text: "Auxin is a central regulator of plant growth and development, orchestrating processes from \r\nembryogenesis to senescence through a complex network of biosynthesis, transport, and \r\nsignaling pathways. \r\nIn Arabidopsis thaliana, canonical nuclear auxin signaling is mediated by the TIR1/AFB \r\nreceptors, which promote degradation of AUX/IAA repressors to enable ARF transcription \r\nfactors-driven transcriptional reprogramming. Parallel to this well-established nuclear \r\nmechanism, auxin also triggers rapid, non-transcriptional responses. In particular, at the cell \r\nsurface, most notably through ABP1 and TMKs. Despite decades of research, the integration \r\nof these pathways and their links to fundamental cellular processes remains not fully \r\nunderstood. \r\nIn this study, we uncover a new role for TIR1/AFB signaling in rapidly activating \r\nmacroautophagy during developmental reprogramming. Auxin induces autophagy via \r\nTIR1/AFB adenylate cyclase activity, linking auxin perception to cAMP production and \r\ntranscriptional activation of autophagy machinery. Autophagy-deficient mutants exhibit \r\ndelayed meristem differentiation, impaired lateral root progression, and reduced shoot \r\norganogenesis, demonstrating its necessity for timely developmental transitions. \r\nWe also revisit the ABP1-TMK1 cell-surface auxin perception complex, providing \r\nbiochemical and mass photometry evidence for auxin-dependent complex formation. We show \r\nthat ABP1-TMK1 triggers an ultrafast global phosphorylation response targeting ~1000 \r\nproteins, including the auxin transporter PIN2, and Rho-of-plants (ROP) GTPases regulators. \r\nThis pathway directly regulates PIN2 phosphorylation, for gravitropism and auxin dependent \r\nROP activation. \r\nThese findings establish an integrated framework in which nuclear TIR1/AFB signaling and \r\ncell-surface ABP1-TMK signaling act in parallel to synchronize gene expression, cytoplasmic \r\nremodelling, and transporter regulation, thereby ensuring robust developmental plasticity in \r\nArabidopsis thaliana. " acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "Plant Facility,\r\nProtein Service Facility" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini citation: ama: Giannini C. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. 2025. doi:10.15479/AT-ISTA-20364 apa: Giannini, C. (2025). Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20364 chicago: Giannini, Caterina. “Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20364. ieee: C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025. ista: Giannini C. 2025. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria. mla: Giannini, Caterina. Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20364. short: C. Giannini, Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-19T12:23:38Z date_published: 2025-09-19T00:00:00Z date_updated: 2026-10-16T08:24:09Z day: '19' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr - _id: MaLo doi: 10.15479/AT-ISTA-20364 doi_confirm: '1' file: - access_level: open_access checksum: 536ba1701453b0b2346be14c046b2911 content_type: application/pdf creator: cgiannin date_created: 2025-09-24T14:46:34Z date_updated: 2026-09-30T22:30:03Z embargo: 2026-09-30 file_id: '20390' file_name: 2025_Giannini_Caterina_Thesis...pdf file_size: 14278965 relation: main_file - access_level: closed checksum: 192f55262f2da2ea0a59d9c23a1b8573 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cgiannin date_created: 2025-09-24T14:46:35Z date_updated: 2026-09-30T22:30:03Z embargo_to: open_access file_id: '20391' file_name: 2025_Giannini_Caterina_Thesis...docx file_size: 24499022 relation: source_file file_date_updated: 2026-09-30T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20364 has_accepted_license: '1' keyword: - Auxin Signaling - Plant Development language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '151' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '19399' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Nuclear and cell surface auxin signaling in A. thaliana developmental transitions type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '19399' abstract: - lang: eng text: Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova for help with manuscript preparation; J. Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at ISTA for their excellent service and assistance. The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant 32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural Science Foundation of China (32321001).' article_processing_charge: No author: - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Yongfan full_name: Yu, Yongfan last_name: Yu - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Meng full_name: Chen, Meng last_name: Chen - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Maria Mar full_name: Marques-Bueno, Maria Mar last_name: Marques-Bueno - first_name: Zainab full_name: Quddoos, Zainab id: 32ff3c64-04a0-11f0-a50f-d0c45bfac466 last_name: Quddoos - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Yvon full_name: Jaillais, Yvon last_name: Jaillais - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv. doi:10.1101/2022.11.30.518503 apa: Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv. https://doi.org/10.1101/2022.11.30.518503 chicago: Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” BioRxiv, n.d. https://doi.org/10.1101/2022.11.30.518503. ieee: L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” bioRxiv. . ista: Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv, 10.1101/2022.11.30.518503. mla: Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” BioRxiv, doi:10.1101/2022.11.30.518503. short: L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais, J. Friml, BioRxiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2025-03-13T08:36:48Z date_published: 2025-02-20T00:00:00Z date_updated: 2026-11-04T23:31:16Z day: '20' ddc: - '580' department: - _id: JiFr - _id: XiFe doi: 10.1101/2022.11.30.518503 ec_funded: 1 fulldoi: https://doi.org/10.1101/2022.11.30.518503 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2022.11.30.518503 month: '02' oa: 1 oa_version: Published Version project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 26060676-B435-11E9-9278-68D0E5697425 grant_number: ALTF 985-2016 name: Cell surface receptor complexes for auxin signaling in plants publication: bioRxiv publication_status: draft related_material: record: - id: '19395' relation: dissertation_contains status: public - id: '20656' relation: later_version status: public - id: '20364' relation: dissertation_contains status: public status: public title: ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '19763' abstract: - lang: eng text: "Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation." acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc acknowledgement: "My work would also not have been possible without the Imaging and Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has facilitated my research substantially. I\r\nalso want to thank the Graduate School Office for their never-ending support and their sincere\r\neffort to improve the PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank you for recognizing the importance of this project." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 citation: ama: Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:10.15479/AT-ISTA-19763 apa: Rus, S. (2025). Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19763 chicago: Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19763. ieee: S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025. ista: Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria. mla: Rus, Stefanie. Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19763. short: S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-05-30T09:14:58Z date_published: 2025-05-29T00:00:00Z date_updated: 2026-10-20T08:57:07Z day: '29' ddc: - '570' degree_awarded: PhD department: - _id: AnKi - _id: GradSch doi: 10.15479/AT-ISTA-19763 file: - access_level: open_access checksum: 8cd7fe3ca990adbcafdece119aa0973d content_type: application/pdf creator: cchlebak date_created: 2025-05-30T09:10:22Z date_updated: 2025-11-30T23:30:02Z embargo: 2025-11-30 file_id: '19764' file_name: Thesis_Lehr_PDFA.pdf file_size: 42879974 relation: main_file - access_level: closed checksum: 0c87dd5fc803450a47b20736b5f86a2f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2025-05-30T09:31:15Z date_updated: 2025-11-30T23:30:02Z embargo_to: open_access file_id: '19765' file_name: Thesis_Lehr_emptyPages.docx file_size: 18731094 relation: source_file file_date_updated: 2025-11-30T23:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19763 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '129' project: - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13136' relation: part_of_dissertation status: public - id: '17148' relation: part_of_dissertation status: public - id: '18601' relation: part_of_dissertation status: public - id: '18807' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 title: Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18807' abstract: - lang: eng text: Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues. acknowledgement: We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Thomas full_name: Minchington, Thomas id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f last_name: Minchington - first_name: Martina full_name: Greunz, Martina id: 48A59534-F248-11E8-B48F-1D18A9856A87 last_name: Greunz - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 2025;60(4):567-580. doi:10.1016/j.devcel.2024.10.024 apa: Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., & Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2024.10.024 chicago: Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell. Cell Press, 2025. https://doi.org/10.1016/j.devcel.2024.10.024. ieee: S. Rus et al., “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” Developmental Cell, vol. 60, no. 4. Cell Press, pp. 567–580, 2025. ista: Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580. mla: Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell, vol. 60, no. 4, Cell Press, 2025, pp. 567–80, doi:10.1016/j.devcel.2024.10.024. short: S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: RNA-seq data has been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. Code for the quantification of fluorescence intensity (FI) profiles in differentiated cells on stencils, as well as for model simulations, is available on GitHub (https://github.com/dbrueckner/NeuralTubeColonies, https://doi.org/10.5281/zenodo.13335390 date_created: 2025-01-09T11:25:47Z date_published: 2025-02-24T00:00:00Z date_updated: 2026-11-04T23:31:17Z day: '24' ddc: - '570' department: - _id: AnKi - _id: EdHa - _id: NanoFab doi: 10.1016/j.devcel.2024.10.024 external_id: isi: - '001434279000001' pmid: - '39603235' file: - access_level: open_access checksum: bb58db4a908a1f4aabe4004706154541 content_type: application/pdf creator: dernst date_created: 2025-04-16T10:54:07Z date_updated: 2025-04-16T10:54:07Z file_id: '19584' file_name: 2025_DevelopmentalCell_Lehr.pdf file_size: 6994499 relation: main_file success: 1 file_date_updated: 2025-04-16T10:54:07Z fulldoi: https://doi.org/10.1016/j.devcel.2024.10.024 has_accepted_license: '1' intvolume: ' 60' isi: 1 issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 567-580 pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F7802 name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '19763' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2025' ... --- OA_place: publisher _id: '20694' abstract: - lang: eng text: "Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 citation: ama: Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:10.15479/AT-ISTA-20694 apa: Pal, A. (2025). Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20694 chicago: Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20694. ieee: A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025. ista: Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. mla: Pal, Arka. Using Genealogies to Study the Genomic Basis of Species Divergence. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20694. short: A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-11-25T13:19:11Z date_published: 2025-11-25T00:00:00Z date_updated: 2026-10-21T08:23:54Z day: '25' ddc: - '576' - '578' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20694 file: - access_level: open_access checksum: 7a10a738d58524aebb5dcbd9b34c21c5 content_type: application/pdf creator: apal date_created: 2025-12-01T13:53:36Z date_updated: 2026-03-01T23:30:03Z embargo: 2026-03-01 file_id: '20721' file_name: 2025_Pal_Arka_Thesis.pdf file_size: 42723135 relation: main_file - access_level: closed checksum: 166d832b08d0434ce407f8f3cb930fe5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: apal date_created: 2025-12-01T13:53:39Z date_updated: 2026-03-01T23:30:03Z embargo_to: open_access file_id: '20722' file_name: 2025_Pal_Arka_Thesis.docx file_size: 60632116 relation: source_file file_date_updated: 2026-03-01T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20694 has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '268' project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12159' relation: part_of_dissertation status: public - id: '20190' relation: part_of_dissertation status: public - id: '14796' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Using genealogies to study the genomic basis of species divergence tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20190' abstract: - lang: eng text: 'A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.' acknowledged_ssus: - _id: ScienComp acknowledgement: 'We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other Barton Group and Coop Lab members for stimulating discussions. We are grateful to all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón Mateu for her assistance in fieldwork logistics at the field station, El Serrat. We are grateful to Enrico Coen and his research group for providing the Antirrhinum molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up with sampling led by D.L.F. in 2017. The study was supported by Austrian Science Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.). Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics and analyses was provided by ISTA High Performance Cluster. ' article_number: e70067 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Alan full_name: Le Moan, Alan last_name: Le Moan - first_name: Adrian J. full_name: Mcnairn, Adrian J. last_name: Mcnairn - first_name: Jennifer K. full_name: Grenier, Jennifer K. last_name: Grenier - first_name: Marek full_name: Kucka, Marek last_name: Kucka - first_name: Graham full_name: Coop, Graham last_name: Coop - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: ama: Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 2025;34(22). doi:10.1111/mec.70067 apa: Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka, M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70067 chicago: Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K. Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” Molecular Ecology. Wiley, 2025. https://doi.org/10.1111/mec.70067. ieee: A. Pal et al., “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” Molecular Ecology, vol. 34, no. 22. Wiley, 2025. ista: Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067. mla: Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” Molecular Ecology, vol. 34, no. 22, e70067, Wiley, 2025, doi:10.1111/mec.70067. short: A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G. Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025). corr_author: '1' date_created: 2025-08-17T22:01:37Z date_published: 2025-11-01T00:00:00Z date_updated: 2026-11-04T23:31:18Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.70067 external_id: isi: - '001546622100001' file: - access_level: open_access checksum: c586fc674df4e7dd6e43aef87a52c6f6 content_type: application/pdf creator: dernst date_created: 2026-01-05T13:47:47Z date_updated: 2026-01-05T13:47:47Z file_id: '20958' file_name: 2025_MolecEcology_Pal.pdf file_size: 9886694 relation: main_file success: 1 file_date_updated: 2026-01-05T13:47:47Z fulldoi: https://doi.org/10.1111/mec.70067 has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/snapdragon-secrets/ record: - id: '20694' relation: dissertation_contains status: public scopus_import: '1' status: public title: Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 34 year: '2025' ... --- OA_place: publisher _id: '19271' abstract: - lang: eng text: "The medial habenula (MHb) is implicated in regulating emotional responses\r\nto aversive events. Studies in zebrafish have identified a remarkable morphological\r\nleft-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian\r\nMHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in\r\nmodulating fear responses. However, there is little evidence for structural or\r\nfunctional lateralization in the mammalian MHb-IPN pathway.\r\nHere, I investigated the synaptic properties of the left and right MHb\r\nafferents to the IPN in mice and addressed whether these synaptic connections\r\nselectively influence the expression of conditioned fear in mice. My findings reveal\r\nthat each individual IPN neuron receives inputs from both left and right MHb.\r\nElectrophysiological recordings from the same postsynaptic IPN neurons\r\ndemonstrate that the left MHb-originating synapses exhibit lower release\r\nprobability and higher \U0001D6FE-aminobutyric acid type B receptor (GABABR)-mediated\r\npotentiation compared to the right MHb-originating synapses. Interestingly,\r\nchemogenetic inhibition of cholinergic neurons in the left but not the right MHb\r\nsignificantly attenuated cue-dependent fear recall. Furthermore, conditional\r\ndeletion of GABABR in the left MHb interfered with the recall of cued fear memory,\r\nwhereas that in the right MHb neurons spared fear memory expression.\r\nCollectively, I demonstrate a functional asymmetry of the MHb in mice,\r\nrevealing a predominant role for GABABR-mediated signaling in the left MHb-IPN\r\npathway in the modulation of fear memories. These findings suggest that\r\nlateralized pathways could represent a fundamental principle in the neural\r\nregulation of emotion across species." acknowledged_ssus: - _id: PreCl - _id: M-Shop acknowledgement: "I would like to thank the European Research Council and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to Ryuichi Shigemoto and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), and the Austrian Neuroscience Association for providing financial support and opportunities, which were important in allowing me to present my work. I also wish to thank the\r\nPreclinical Facility, especially Michael Schunn, for always welcoming me from my earliest days as an intern. My gratitude goes as well to the Miba Machine Shop, in particular Todor Asenov, Astrit Arslani, and Thomas Menner, whose technical expertise often saved the day." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hüseyin C full_name: Önal, Hüseyin C id: 4659D740-F248-11E8-B48F-1D18A9856A87 last_name: Önal orcid: 0000-0002-2771-2011 citation: ama: Önal C. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. 2025. doi:10.15479/AT-ISTA-19271 apa: Önal, C. (2025). Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19271 chicago: Önal, Cihan. “Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19271. ieee: C. Önal, “Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula,” Institute of Science and Technology Austria, 2025. ista: Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria. mla: Önal, Cihan. Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19271. short: C. Önal, Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-02-28T14:15:53Z date_published: 2025-03-04T00:00:00Z date_updated: 2026-10-21T08:33:44Z day: '04' ddc: - '570' - '571' - '573' - '599' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/AT-ISTA-19271 ec_funded: 1 file: - access_level: closed checksum: c1a4d75a7471de9f954697b06cd18d28 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hoenal date_created: 2025-02-28T13:57:01Z date_updated: 2026-02-01T23:30:02Z embargo_to: open_access file_id: '19272' file_name: Cihan_Onal_Thesis_Final.docx file_size: 25869143 relation: source_file - access_level: open_access checksum: de4e62147ab9f04098dc8cd898c630da content_type: application/pdf creator: hoenal date_created: 2025-02-28T13:57:04Z date_updated: 2026-02-01T23:30:02Z embargo: 2026-02-01 file_id: '19273' file_name: Cihan_Onal_Thesis_Final_pdfa.pdf file_size: 12077596 relation: main_file file_date_updated: 2026-02-01T23:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19271 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9437' relation: part_of_dissertation status: public - id: '15084' relation: part_of_dissertation status: public status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19478' abstract: - lang: eng text: "Auxin is one of the most important phytohormones, playing a crucial role in plant growth and \r\ndevelopment. Genetic studies in Arabidopsis have identified core components of auxin \r\nsignalling and established the classical transcriptional regulation mechanism. This classical \r\nparadigm recognizes TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN \r\nSIGNALLING F-BOX (AFB) proteins as auxin receptors possessing E3 ubiquitin ligase \r\nactivity. Auxin functions as a \"molecular glue\" enhancing TIR1/AFB-Aux/IAA \r\n(AUXIN/INDOLE-3-ACETIC ACID) inhibitor interactions, leading to Aux/IAAs’ \r\nubiquitination and degradation. This process releases AUXIN RESPONSE FACTORs (ARFs) \r\nfrom repression, enabling transcriptional activation of auxin-responsive genes. Notably, the \r\ndiscovery of adenylate cyclase (AC) activity in TIR1/AFBs, catalysing cAMP production from \r\nATP, presents novel transcriptional regulatory possibilities, though cAMP's mechanistic role \r\nin auxin signalling remains unclear. Beyond transcriptional regulation (slow response) a non\r\ntranscriptional pathway (rapid response) mediated by AFB1 also exists, as auxin triggers rapid \r\nroot growth inhibition within 30 seconds. How TIR1 and AFB1, with their distinct subcellular \r\nlocalizations, differentially regulate transcriptional and non-transcriptional processes remains \r\nunclear. To address these two key questions, this study conducted the following investigations. \r\nTIR1 and AFB1 display distinct subcellular localization patterns, with AFB1 specifically \r\nmediating auxin-induced rapid root growth inhibition. To examine whether subcellular \r\nlocalization differences contribute to functional divergence between TIR1 and AFB1, we \r\nutilized microfluidic systems combined with genetic complementation assays. Nuclear export \r\nsignal-fused TIR1 failed to rescue the rapid response defects observed in afb1 mutants. In \r\ncontrast, nuclear localization signal-fused AFB1 exhibited dual functional deficiencies: it \r\nneither restored the rapid response impairment in afb1 mutants nor compensated for \r\ntranscriptional regulation defects in tir1 mutants which limitation stemmed from AFB1's \r\nintrinsic incapacity to assemble functional SCF complexes. These results collectively establish \r\nthat the functional specialization of TIR1 and AFB1 is governed by both their subcellular \r\ncompartmentalization and inherent biochemical characteristics. \r\nThe mechanism by which cAMP derived from the auxin receptor TIR1/AFB modulates \r\ntranscriptional regulation remains undefined. To address this, we genetically dissociated TIR1 \r\nAC activity from its E3 ubiquitin ligase function to investigate cAMP's signalling role. AC\r\ninactivating mutations preserved TIR1-mediated Aux/IAAs’ degradation but abolished ARF\r\ni \r\ndependent transcriptional activation. tir1afb2 mutants expressing AC-deficient TIR1 variants \r\nfailed to restore transcriptional responses. Crucially, compartmentalized cAMP accumulation \r\nwithin Aux/IAA - ARF complexes vicinity triggered auxin signalling independently of both \r\nauxin perception and Aux/IAAs’ degradation, confirming its secondary messenger identity. \r\nFurther mechanistic analysis demonstrated cAMP directly interact with ARF. cAMP \r\ndirectly promotes ARF dissociation from Aux/IAA repressors and enhances ARF \r\nhomodimerization. Genetic complementation assays revealed that ARF mutants lacking \r\nconserved cAMP-binding motifs exhibited partial functional recovery, providing direct \r\nevidence for cAMP-ARF physical interaction during signal propagation. \r\nThese findings collectively challenge the established model of auxin signalling and define \r\na novel TIR1-cAMP-ARF regulatory axis, substantially advancing our comprehension of \r\nauxin-mediated physiological regulation. " acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "This project was funded by the European Research Council Advanced Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian Science Fund (FWF; P\r\n37051-B)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen citation: ama: Chen H. The cAMP second messenger in auxin signalling. 2025. doi:10.15479/AT-ISTA-19478 apa: Chen, H. (2025). The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19478 chicago: Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19478. ieee: H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science and Technology Austria, 2025. ista: Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria. mla: Chen, Huihuang. The CAMP Second Messenger in Auxin Signalling. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19478. short: H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-04T07:48:24Z date_published: 2025-04-04T00:00:00Z date_updated: 2026-10-23T07:25:54Z day: '04' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-19478 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: b154973663a1bba505683faab7ae5ead content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hchen date_created: 2025-04-08T08:00:07Z date_updated: 2026-10-08T22:30:02Z embargo_to: open_access file_id: '19526' file_name: Thesis_0403_Huihuang.docx file_size: 16344814 relation: source_file - access_level: open_access checksum: 0099565f024388830c125ec17375c1a0 content_type: application/pdf creator: hchen date_created: 2025-04-08T08:00:06Z date_updated: 2026-10-09T22:30:03Z embargo: 2026-10-08 file_id: '19527' file_name: Thesis_0406_PDFA_Huihuang_1.pdf file_size: 8482147 relation: main_file file_date_updated: 2026-10-09T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-19478 has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '118' project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19421' relation: part_of_dissertation status: public - id: '13212' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: The cAMP second messenger in auxin signalling type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20467' abstract: - lang: eng text: "Prostaglandins play a central role in the inflammatory response. Prostaglandins are synthesized \r\nin a rate-limiting manner by the enzyme cyclooxygenase (Cox), which exists in two isoforms: \r\nthe Cox-2 and Cox-1 isoforms. Traditionally, Cox-1 is thought to mediate homeostatic \r\nfunctions due to its constitutive expression due to its constitutive expression, whereas Cox-2 is \r\ntemporary induced in response to inflammatory stimuli and is associated with the inflammatory \r\nresponse. Interestingly, in the central nervous system, Cox-1 is predominantly expressed in \r\nmicroglia. As the resident immune cells of the brain, microglia play a key role in inflammation. \r\nCox-1 expressing microglia are increased in neurodegenerative diseases, and both global \r\nknockout of Cox-1 and selective Cox-1 inhibition has been shown to ameliorate inflammatory \r\neffects in neurodegenerative diseases. However, direct evidence elucidating how microglial \r\nCox-1 expression influences their response to insults remains limited and warrants further \r\ninvestigation. \r\nFirst, I utilize the optic nerve crush (ONC) model to study the microglial response to injury and \r\ninflammation, confirming a reactive microglial response in both the crushed and uninjured \r\ncontralateral retina using CD68 expression and morphological analysis. While previous studies \r\nreported retinal ganglion cell (RGC) loss in the contralateral eye, I did not observe this, \r\nsuggesting that unilateral ONC induces microglial activation in the contralateral eye without \r\nRGC degeneration. To explore the role of Cox-1 in this response, I generated a mouse model \r\nwith microglia-specific deletion of Cox-1. After ONC, these mice exhibited an attenuated \r\nmicroglial response in both the ipsilateral and contralateral retinas, as well as in visual \r\nprocessing areas of the brain. Notably, Cox-2 does not show any expression after ONC in both \r\nwild-type and Cox-1 knockout mice Additionally, Cox-1KO mice show a reduction in \r\nphagocytic cups and a reduction in microglia proliferation after ONC. However, due to \r\nreproducibility problems of the observed phenotype, even after the generation of two new \r\nmouse models, I cannot draw any definitive conclusions based on the data. \r\nNext, due to the ambiguity of the mouse model, I explored an alternative route to investigate \r\nfunctional consequences of Cox-1 in microglia. I generated a COX1 knock-out human induced \r\npluripotent cell (hIPSC) line using CRISPR/Cas9. These cells are were differentiated in \r\nmicroglia-like cells and integrated in dissociated retinal organoids according to protocols \r\ndeveloped in our lab. In response to LPS and POLY(I:C) stimulation, the release and expression \r\nof cytokines and chemokines was decreased in COX1 knockout cells. However, the \r\nprostaglandin PGE2 was not increased in microglia-like cells in both control and COX1 \r\nknockout cells. \r\nOverall, the results from the COX1 knock-out microglia-like cells suggests that COX1 \r\nexpression in microglia play a role in neuroinflammation by affecting the release of \r\ninflammatory cytokines and chemokines. Hereby further challenging that the dogma of the \r\nCox-1 isoform involved in housekeeping functions and the Cox-2 isoform involved in \r\ninflammation applies for the central nervous system. " acknowledged_ssus: - _id: Bio - _id: SSU - _id: PreCl - _id: LifeSc acknowledgement: "The work presented in this Thesis was carried out at the Institute of Science and Technology\r\nAustria (ISTA), and was supported by the Austrian Science Fund (FWF) [10.55776/P37131].\r\nI would like to thank the Scientific Service Units (SSU) of ISTA for the provided resources,\r\nspecifically the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the\r\nPre-Clinical Facility (PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael\r\nSchunn, for mouse colony management and support. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Florianne E full_name: Miteva, Florianne E id: 3526230C-F248-11E8-B48F-1D18A9856A87 last_name: Miteva citation: ama: Miteva FE. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. 2025. doi:10.15479/AT-ISTA-20467 apa: Miteva, F. E. (2025). The role of cyclooxygenase 1 on microglial response to inflammatory stressors. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20467 chicago: Miteva, Florianne E. “The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20467. ieee: F. E. Miteva, “The role of cyclooxygenase 1 on microglial response to inflammatory stressors,” Institute of Science and Technology Austria, 2025. ista: Miteva FE. 2025. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. Institute of Science and Technology Austria. mla: Miteva, Florianne E. The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20467. short: F.E. Miteva, The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-14T10:24:41Z date_published: 2025-10-14T00:00:00Z date_updated: 2026-10-23T08:01:12Z day: '14' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/AT-ISTA-20467 doi_confirm: '1' file: - access_level: open_access checksum: 03537697be8c688d3a05cf948288e48f content_type: application/pdf creator: fschootu date_created: 2025-10-17T11:09:11Z date_updated: 2026-10-14T22:30:02Z embargo: 2026-10-14 file_id: '20484' file_name: 2025_Miteva_Florianne_thesis.pdf file_size: 13668588 relation: main_file - access_level: closed checksum: df4930d7211cf9cfe1254b77204dc1d3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: fschootu date_created: 2025-10-23T11:33:06Z date_updated: 2026-10-14T22:30:02Z embargo_to: open_access file_id: '20525' file_name: 2025_Miteva_florianne_thesis.docx file_size: 28991918 relation: source_file file_date_updated: 2026-10-14T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20467 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '99' project: - _id: 7be82147-9f16-11ee-852c-f44682d73140 grant_number: P37131 name: Dissecting the morpho-functional relationship of microglia publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19566' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: The role of cyclooxygenase 1 on microglial response to inflammatory stressors tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ...