[{"department":[{"_id":"GradSch"},{"_id":"MaDe"}],"OA_place":"publisher","file":[{"file_size":78812587,"file_id":"20311","relation":"source_file","creator":"hschoen","file_name":"2025_Schoen_Hanna_Thesis.docx","date_created":"2025-09-08T14:33:50Z","checksum":"b40c74404b8d9593802dabf57bfdf10f","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-09-09T08:57:04Z","access_level":"closed"},{"creator":"hschoen","embargo":"2026-09-15","access_level":"closed","date_created":"2025-09-11T14:20:59Z","checksum":"16abc3ff66396ce2457fe07ffa8bed90","date_updated":"2025-09-18T14:12:29Z","content_type":"application/pdf","file_name":"2025_Schoen_Hanna_Thesis.pdf","embargo_to":"open_access","file_size":9667057,"relation":"main_file","file_id":"20347"}],"doi":"10.15479/AT-ISTA-20167","file_date_updated":"2025-09-18T14:12:29Z","acknowledgement":"This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). ","day":"13","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs","ddc":["570"],"corr_author":"1","has_accepted_license":"1","type":"dissertation","degree_awarded":"PhD","date_updated":"2026-04-07T11:50:26Z","date_created":"2025-08-13T11:13:13Z","supervisor":[{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"article_processing_charge":"No","citation":{"chicago":"Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>.","apa":"Schön, H. (2025). <i>The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>","mla":"Schön, Hanna. <i>The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>.","ieee":"H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025.","ama":"Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>","ista":"Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria.","short":"H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025."},"date_published":"2025-08-13T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"20167","year":"2025","author":[{"full_name":"Schön, Hanna","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","first_name":"Hanna","last_name":"Schön"}],"publisher":"Institute of Science and Technology Austria","month":"08","oa_version":"Published Version","publication_identifier":{"isbn":["978-3-99078-061-9"],"issn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"project":[{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"},{"name":"Control of gene expression at the endoplasmic reticulum","_id":"23813290-32DE-11EA-91FC-C7463DDC885E","grant_number":"ALTF 302-2019"}],"page":"171"},{"isi":1,"year":"2025","article_type":"original","author":[{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","first_name":"David","last_name":"Babic"},{"full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed"},{"full_name":"Fiedler, Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas"},{"id":"44B04502-A9ED-11E9-B6FC-583AE6697425","first_name":"Linlin","last_name":"Qi","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401"},{"full_name":"Tellier, Frédérique","last_name":"Tellier","first_name":"Frédérique"},{"first_name":"Adrijana","id":"cced8a85-223e-11ed-af04-b0596c55053b","last_name":"Smoljan","full_name":"Smoljan, Adrijana"},{"full_name":"Rakusova, Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","last_name":"Rakusova"},{"id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Valošek","full_name":"Valošek, Petr"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"first_name":"Jean Denis","last_name":"Faure","full_name":"Faure, Jean Denis"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"publisher":"Wiley","oa_version":"Published Version","month":"08","oa":1,"date_updated":"2026-04-07T11:52:02Z","date_created":"2025-08-17T22:01:36Z","article_processing_charge":"Yes (via OA deal)","citation":{"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.","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).","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. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>","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.” <i>Plant Journal</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>.","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. <i>Plant Journal</i>. 2025;123(3). doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>","ieee":"D. Babic <i>et al.</i>, “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” <i>Plant Journal</i>, vol. 123, no. 3. Wiley, 2025.","mla":"Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>, vol. 123, no. 3, e70396, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>."},"_id":"20187","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_published":"2025-08-01T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"20362","status":"public"}]},"project":[{"grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis"}],"intvolume":"       123","article_number":"e70396","external_id":{"pmid":["40782342"],"isi":["001547884300001"]},"issue":"3","language":[{"iso":"eng"}],"PlanS_conform":"1","status":"public","publication_identifier":{"eissn":["1365-313X"],"issn":["0960-7412"]},"day":"01","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).","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","publication":"Plant Journal","ddc":["580"],"department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"OA_place":"publisher","file":[{"creator":"dernst","success":1,"checksum":"1cdc3341d2d23101abca72521f1f23cb","date_created":"2025-09-01T14:09:31Z","date_updated":"2025-09-01T14:09:31Z","content_type":"application/pdf","file_name":"2025_PlantJournal_Babic.pdf","access_level":"open_access","file_size":5791111,"file_id":"20264","relation":"main_file"}],"doi":"10.1111/tpj.70396","pmid":1,"file_date_updated":"2025-09-01T14:09:31Z","OA_type":"hybrid","quality_controlled":"1","type":"journal_article","scopus_import":"1","volume":123,"abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","corr_author":"1"},{"corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","type":"dissertation","doi":"10.15479/AT-ISTA-20362","file_date_updated":"2025-09-26T07:29:11Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"file":[{"content_type":"application/pdf","file_name":"2025_David_Babic_Thesis.pdf","date_updated":"2025-09-26T07:29:11Z","checksum":"5ecf274281a54a41e0288bc79edf7492","date_created":"2025-09-24T13:43:14Z","access_level":"closed","embargo":"2026-09-25","creator":"dbabic","file_id":"20388","relation":"main_file","embargo_to":"open_access","file_size":7501548},{"relation":"source_file","file_id":"20389","file_size":23206052,"access_level":"closed","file_name":"Thesis_Babic_draft.docx","date_created":"2025-09-24T13:43:14Z","date_updated":"2025-09-26T07:29:11Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"2703e548390de0a1af7a707137e8ab3b","creator":"dbabic"}],"title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","ddc":["580"],"day":"18","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"page":"116","related_material":{"record":[{"relation":"part_of_dissertation","id":"20187","status":"public"}]},"article_processing_charge":"No","citation":{"ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria.","short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","apa":"Babic, D. (2025). <i>Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>","chicago":"Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>.","ama":"Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>","ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025.","mla":"Babic, David. <i>Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>."},"date_published":"2025-09-18T00:00:00Z","_id":"20362","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_updated":"2026-04-07T11:52:02Z","date_created":"2025-09-17T13:28:01Z","supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"author":[{"full_name":"Babic, David","first_name":"David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","month":"09","year":"2025"},{"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Cell surface receptor complexes for auxin signaling in plants","grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"relation":"later_version","id":"20656","status":"public"},{"status":"public","id":"19395","relation":"dissertation_contains"},{"status":"public","id":"20364","relation":"dissertation_contains"}]},"status":"public","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory","oa_version":"Published Version","month":"02","author":[{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey"},{"full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","full_name":"Zou, Minxia"},{"first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini","full_name":"Giannini, Caterina"},{"last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"full_name":"Vladimirtsev, Dmitrii","last_name":"Vladimirtsev","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","first_name":"Dmitrii"},{"full_name":"Randuch, Marek","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch"},{"last_name":"Yu","first_name":"Yongfan","full_name":"Yu, Yongfan"},{"orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","last_name":"Hajny"},{"full_name":"Chen, Meng","last_name":"Chen","first_name":"Meng"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan"},{"last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"full_name":"Marques-Bueno, Maria Mar","last_name":"Marques-Bueno","first_name":"Maria Mar"},{"first_name":"Zainab","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","last_name":"Quddoos","full_name":"Quddoos, Zainab"},{"full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","last_name":"Kulich","full_name":"Kulich, Ivan"},{"full_name":"Jaillais, Yvon","last_name":"Jaillais","first_name":"Yvon"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"year":"2025","date_published":"2025-02-20T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"19399","citation":{"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, <a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","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.).","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. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>","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.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>.","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. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"article_processing_charge":"No","date_updated":"2026-04-07T11:52:15Z","date_created":"2025-03-13T08:36:48Z","oa":1,"type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2022.11.30.518503","open_access":"1"}],"corr_author":"1","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."}],"title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","publication":"bioRxiv","publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","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).","OA_type":"green","doi":"10.1101/2022.11.30.518503","ec_funded":1,"department":[{"_id":"JiFr"},{"_id":"XiFe"}],"OA_place":"repository"},{"status":"public","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"15357"},{"status":"public","relation":"part_of_dissertation","id":"12237"}]},"page":"144","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"},{"last_name":"Protesescu","first_name":"Loredana","full_name":"Protesescu, Loredana"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"}],"date_created":"2025-10-01T09:04:00Z","date_updated":"2026-04-07T11:52:32Z","date_published":"2025-10-01T00:00:00Z","_id":"20415","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_processing_charge":"No","citation":{"short":"S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025.","ista":"Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria.","ama":"Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>","ieee":"S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic solids,” Institute of Science and Technology Austria, 2025.","mla":"Lee, Seungho. <i>Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>.","apa":"Lee, S. (2025). <i>Nanoparticle-based precursors toward advanced crystalline inorganic solids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>","chicago":"Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>."},"year":"2025","oa_version":"Published Version","month":"10","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"}],"has_accepted_license":"1","corr_author":"1","type":"dissertation","degree_awarded":"PhD","file":[{"file_size":88706648,"file_id":"20420","relation":"source_file","creator":"slee","date_updated":"2025-10-07T08:57:14Z","file_name":"2025_Lee_Seungho_Thesis.docx","checksum":"fa6d5946feb37b678ee1c6dffb4fa167","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-10-03T12:29:43Z","access_level":"closed"},{"embargo":"2026-10-03","access_level":"closed","date_updated":"2025-10-03T12:29:25Z","file_name":"2025_Lee_Seungho_Thesis__.pdf","date_created":"2025-10-03T12:29:25Z","checksum":"c5ba6d464113ad0c5812a9d24b539b86","content_type":"application/pdf","creator":"slee","relation":"main_file","file_id":"20421","file_size":14587276,"embargo_to":"open_access"}],"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"OA_place":"publisher","file_date_updated":"2025-10-07T08:57:14Z","doi":"10.15479/AT-ISTA-20415","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","ddc":["540"],"title":"Nanoparticle-based precursors toward advanced crystalline inorganic solids"},{"alternative_title":["ISTA Thesis"],"page":"151","related_material":{"record":[{"relation":"part_of_dissertation","id":"12291","status":"public"},{"relation":"part_of_dissertation","id":"19399","status":"public"}]},"status":"public","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"year":"2025","author":[{"last_name":"Giannini","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"}],"publisher":"Institute of Science and Technology Austria","month":"09","oa_version":"Published Version","date_updated":"2026-04-07T11:52:16Z","date_created":"2025-09-19T12:23:38Z","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"article_processing_charge":"No","citation":{"ista":"Giannini C. 2025. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria.","short":"C. Giannini, Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions, Institute of Science and Technology Austria, 2025.","chicago":"Giannini, Caterina. “Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>.","apa":"Giannini, C. (2025). <i>Nuclear and cell surface auxin signaling in A. thaliana developmental transitions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>","ieee":"C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025.","mla":"Giannini, Caterina. <i>Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>.","ama":"Giannini C. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>"},"date_published":"2025-09-19T00:00:00Z","_id":"20364","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"type":"dissertation","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","keyword":["Auxin Signaling","Plant Development"],"acknowledgement":"Plant Facility,\r\nProtein Service Facility","day":"19","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Nuclear and cell surface auxin signaling in A. thaliana developmental transitions","ddc":["580"],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"OA_place":"publisher","file":[{"relation":"main_file","file_id":"20390","embargo_to":"open_access","file_size":14278965,"access_level":"closed","embargo":"2026-09-30","content_type":"application/pdf","checksum":"536ba1701453b0b2346be14c046b2911","date_created":"2025-09-24T14:46:34Z","file_name":"2025_Giannini_Caterina_Thesis...pdf","date_updated":"2025-09-30T14:31:29Z","creator":"cgiannin"},{"date_updated":"2025-09-24T14:46:35Z","date_created":"2025-09-24T14:46:35Z","file_name":"2025_Giannini_Caterina_Thesis...docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"192f55262f2da2ea0a59d9c23a1b8573","access_level":"closed","creator":"cgiannin","file_id":"20391","relation":"source_file","file_size":24499022}],"doi":"10.15479/AT-ISTA-20364","file_date_updated":"2025-09-30T14:31:29Z"},{"file_date_updated":"2025-10-28T13:10:26Z","doi":"10.15479/AT-ISTA-20441","file":[{"file_size":6846189,"file_id":"20567","relation":"main_file","success":1,"creator":"snaik","date_updated":"2025-10-28T13:10:08Z","date_created":"2025-10-28T13:10:08Z","file_name":"Thesis_PDFA_.pdf","checksum":"2892f04d4a5c18677871c3e06ac1244a","content_type":"application/pdf","access_level":"open_access"},{"creator":"snaik","content_type":"application/zip","file_name":"Thesis.zip","checksum":"15934d4465cd0e9b7c32678da9a33a2f","date_created":"2025-10-28T13:10:26Z","date_updated":"2025-10-28T13:10:26Z","access_level":"open_access","file_size":8839300,"file_id":"20568","relation":"source_file"}],"department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"OA_place":"publisher","ddc":["596","597","532"],"title":"Keratins act as global coordinators of tissue spreading through mechanosensitive feedback","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"acknowledgement":"I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences.","day":"12","has_accepted_license":"1","corr_author":"1","abstract":[{"lang":"eng","text":"Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium."}],"degree_awarded":"PhD","type":"dissertation","date_published":"2025-10-12T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"20441","citation":{"chicago":"Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>.","apa":"Naik, S. (2025). <i>Keratins act as global coordinators of tissue spreading through mechanosensitive feedback</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>","ieee":"S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025.","mla":"Naik, Suyash. <i>Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>.","ama":"Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>","ista":"Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria.","short":"S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025."},"article_processing_charge":"No","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T11:58:57Z","date_created":"2025-10-10T14:58:30Z","oa":1,"oa_version":"Published Version","month":"10","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Naik","first_name":"Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash"}],"year":"2025","status":"public","publication_identifier":{"isbn":["978-3-99078-069-5"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"PAT 5044023","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W 1250-B20","_id":"25AA5F24-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"105","related_material":{"record":[{"status":"public","id":"20465","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"]},{"author":[{"full_name":"Misova, Michaela","orcid":"0000-0003-2427-6856","last_name":"Misova","id":"495A3C32-F248-11E8-B48F-1D18A9856A87","first_name":"Michaela"}],"publisher":"Institute of Science and Technology Austria","month":"10","oa_version":"Published Version","year":"2025","article_processing_charge":"No","citation":{"ista":"Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria.","short":"M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System, Institute of Science and Technology Austria, 2025.","apa":"Misova, M. (2025). <i>Dissecting gap junction biology using the C. elegans nervous system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>","chicago":"Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans Nervous System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>.","ama":"Misova M. Dissecting gap junction biology using the C. elegans nervous system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>","mla":"Misova, Michaela. <i>Dissecting Gap Junction Biology Using the C. Elegans Nervous System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>.","ieee":"M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,” Institute of Science and Technology Austria, 2025."},"date_published":"2025-10-23T00:00:00Z","_id":"20485","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"date_updated":"2026-04-07T11:54:00Z","date_created":"2025-10-17T16:15:09Z","supervisor":[{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono"}],"alternative_title":["ISTA Thesis"],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"page":"155","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-068-8"]},"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"title":"Dissecting gap junction biology using the C. elegans nervous system","day":"23","acknowledgement":"I would also like to acknowledge the funding that I received from the European Union’s\r\nHorizon 2020 research and Innovation programme under the Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been possible without the contribution and support of people\r\nbehind the scientific service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit. I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC) Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. ","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT-ISTA-20485","file_date_updated":"2025-11-06T11:08:06Z","department":[{"_id":"GradSch"},{"_id":"MaDe"}],"OA_place":"publisher","ec_funded":1,"file":[{"file_size":75070995,"file_id":"20518","relation":"source_file","creator":"mmisova","file_name":"2025-Misova-Michaela-Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-11-06T11:08:06Z","checksum":"e042ea314e7e13fce76c6c95e126779a","date_created":"2025-10-23T08:22:35Z","access_level":"closed"},{"relation":"main_file","file_id":"20519","file_size":10974630,"embargo_to":"open_access","embargo":"2026-10-23","access_level":"closed","content_type":"application/pdf","date_updated":"2025-10-23T08:21:21Z","date_created":"2025-10-23T08:21:21Z","file_name":"2025-Misova-Michaela-Thesis.pdf","checksum":"fcd8973d6a025256eb0eb1a82c02172c","creator":"mmisova"}],"degree_awarded":"PhD","type":"dissertation","corr_author":"1","has_accepted_license":"1"},{"OA_place":"repository","date_updated":"2026-04-07T11:58:57Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"date_created":"2025-10-14T07:25:27Z","oa":1,"date_published":"2025-02-17T00:00:00Z","_id":"20465","article_processing_charge":"No","doi":"10.1101/2025.02.14.638262","citation":{"ista":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. bioRxiv, <a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>.","short":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, BioRxiv (n.d.).","apa":"Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., &#38; Heisenberg, C.-P. J. (n.d.). Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2025.02.14.638262\">https://doi.org/10.1101/2025.02.14.638262</a>","chicago":"Naik, Suyash, Yann-Edwin Keta, Kornelija Pranjic-Ferscha, Edouard B Hannezo, Silke Henkes, and Carl-Philipp J Heisenberg. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2025.02.14.638262\">https://doi.org/10.1101/2025.02.14.638262</a>.","ama":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>","ieee":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E. B. Hannezo, S. Henkes, and C.-P. J. Heisenberg, “Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","mla":"Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>."},"publication_status":"draft","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"day":"17","year":"2025","publisher":"Cold Spring Harbor Laboratory","month":"02","oa_version":"Preprint","title":"Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties","author":[{"orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash","last_name":"Naik","first_name":"Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yann-Edwin","last_name":"Keta","full_name":"Keta, Yann-Edwin"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henkes, Silke","first_name":"Silke","last_name":"Henkes"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"publication":"bioRxiv","status":"public","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2025.02.14.638262","open_access":"1"}],"corr_author":"1","abstract":[{"text":"For tissues to spread, they must be deformable while maintaining their structural integrity. How these opposing requirements are balanced within spreading tissues is not yet well understood. Here, we show that keratin intermediate filaments function in epithelial spreading by adapting tissue mechanical resilience to the stresses arising in the tissue during the spreading process. By analysing the expansion of the enveloping cell layer (EVL) over the large yolk cell in early zebrafish embryos in vivo, we found that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, which is essential for preventing tissue rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the force-generating processes pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production in the yolk cell and the mechanical resilience of the EVL against stresses generated by these pulling forces, thereby ensuring uniform and robust tissue spreading.","lang":"eng"}],"related_material":{"record":[{"id":"20441","relation":"dissertation_contains","status":"public"}]},"type":"preprint"},{"degree_awarded":"MS","type":"dissertation","has_accepted_license":"1","corr_author":"1","abstract":[{"text":"The internal dynamical properties of red giant stars have been explored extensively in recent\r\nyears as a result of the increase in high precision data availability from the space missions\r\nKepler and TESS (Transiting Exoplanet Survey Satellite), and in this exploration, it has been\r\ndiscovered that some of these stars are not behaving as expected. Red giants are stars that have\r\nevolved off of the main sequence after having completed fusing hydrogen into helium in their\r\ncore. Observational data shows that the cores are rotating significantly slower than models can\r\nrecreate consistently across evolutionary stages. This discrepancy has prompted investigation\r\ninto the efficiency of angular momentum transport mechanisms and mixing processes including\r\nmeridional circulation, shear instability, internal gravity waves, Tayler-Spruit dynamo, fossil\r\nmagnetic fields etc., to explain this behavior.\r\nAnalyzing seismic oscillations in stars, via asteroseismology, is a powerful tool as it is the only\r\nway in which the deep stellar interior can be probed and subsequently characterized; this is\r\npossible as global oscillations modulating the stellar surface are effected by internal processes.\r\nFor red giants, p-modes (pressure modes; resonating through the entire star) and g-modes\r\n(gravity-modes; resonating in the radiative interior) couple to create mixed modes. These\r\nmixed modes give access to the otherwise hidden stellar interior as g-modes couple to p-modes,\r\ndelivering information from the interior to the surface.\r\nInternal magnetic signatures have been observationally confirmed in red giant stars via\r\nasteroseismology and characterized in two ways. One being that dipole mixed modes with\r\nℓ = 1 will display a global asymmetric frequency shift of its azimuthal components; where\r\nthe m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted by two\r\ndifferent power laws, respectively. And the other being a reduced visibility of dipole mixed\r\nmode amplitudes in the power spectra, where stars presenting with this feature are denoted as\r\nsuppressed.\r\nSeveral studies of the suppressed dipole mixed mode amplitudes have been carried out, but thus\r\nfar, no dedicated studies of the asymmetric frequency shifts of suppressed red giants have been\r\nconducted; one reason being that the asymmetric frequency shifts cannot be characterized\r\nwhen the dipole mixed mode amplitudes are severely reduced in many of the suppressed stars.\r\nSincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed\r\nstars, that is, red giant stars presenting with suppressed dipole mixed modes in select parts of\r\ntheir power spectra rather than across the entire spectra, will be the subject of this study as\r\nthe respective mode amplitudes are still visible at high frequencies.\r\nAs such, this study will search for asymmetric frequency shifts on the dipole mixed\r\nmodes of partially suppressed red giant stars; the aim here is to investigate if both\r\nmode suppression and magnetic shifting of dipole mixed modes occur simultaneously.\r\nThisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters,\r\nuse the priors to model the power spectra with the stellar modeling code sloscillations_ISTA,\r\nand perform a Bayesian fit of the parameters with the simulated data on the star KIC 6975038,\r\na target with partially suppressed dipolar mode amplitudes identified in the literature, to fit its\r\nmagnetic parameters. I present a novel method to model the stellar power spectra of\r\npartially suppressed red giants by application of a sigmoid profile to the ℓ= 1 dipolar\r\nmode component of the spectra. With the results of this study I aim at constraining\r\nthe cause of this partial dipole mode amplitude suppression, allowing for more detailed\r\nstudies regarding their astrophysical nature. Furthermore, the long term hope for the method\r\nused in this study will be to expand the sample of partially suppressed red giants and fit their\r\nasteroseismic parameters accordingly.","lang":"eng"}],"keyword":["asteroseismology","stellar physics","red giant","magnetism","suppressed"],"ddc":["520"],"title":"Exploring internal magnetism in partially suppressed red giant stars","day":"08","acknowledgement":"I would like to give thanks to myself for my hard work on this document. This paper includes data collected by the Kepler mission and obtained from the MAST data\r\narchive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is\r\nprovided by the NASA Science Mission Directorate. STScI is operated by the Association of\r\nUniversities for Research in Astronomy, Inc., under NASA contract NAS 5–26555.\r\n","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT-ISTA-19853","file_date_updated":"2025-10-09T14:38:57Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"LiBu"}],"file":[{"file_size":8263624,"file_id":"20434","relation":"source_file","creator":"ksmith","file_name":"2025_Smith_Kanah_Thesis.zip","content_type":"application/zip","date_updated":"2025-10-08T09:45:33Z","checksum":"80d241d11b69af771c1fab0998be4f19","date_created":"2025-10-08T08:01:42Z","access_level":"closed"},{"file_id":"20439","relation":"main_file","file_size":9748339,"file_name":"2025_Smith_Kanah_Thesis.pdf","content_type":"application/pdf","checksum":"13cb48cc98e00fdfe32f3ff66f17aa26","date_created":"2025-10-09T14:38:57Z","date_updated":"2025-10-09T14:38:57Z","access_level":"open_access","success":1,"creator":"ksmith"}],"alternative_title":["ISTA Master's Thesis"],"page":"38","status":"public","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Smith, Kanah","last_name":"Smith","first_name":"Kanah","id":"7703505d-3211-11ee-a6a9-a2ab9d936c15"}],"publisher":"Institute of Science and Technology Austria","month":"10","oa_version":"Published Version","year":"2025","citation":{"short":"K. Smith, Exploring Internal Magnetism in Partially Suppressed Red Giant Stars, Institute of Science and Technology Austria, 2025.","ista":"Smith K. 2025. Exploring internal magnetism in partially suppressed red giant stars. Institute of Science and Technology Austria.","ieee":"K. Smith, “Exploring internal magnetism in partially suppressed red giant stars,” Institute of Science and Technology Austria, 2025.","mla":"Smith, Kanah. <i>Exploring Internal Magnetism in Partially Suppressed Red Giant Stars</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>.","ama":"Smith K. Exploring internal magnetism in partially suppressed red giant stars. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>","chicago":"Smith, Kanah. “Exploring Internal Magnetism in Partially Suppressed Red Giant Stars.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>.","apa":"Smith, K. (2025). <i>Exploring internal magnetism in partially suppressed red giant stars</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>"},"article_processing_charge":"No","date_published":"2025-10-08T00:00:00Z","_id":"19853","date_updated":"2026-04-07T12:01:37Z","date_created":"2025-06-20T13:27:08Z","oa":1,"supervisor":[{"first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle"}]},{"corr_author":"1","has_accepted_license":"1","abstract":[{"text":"The space of codimension-2 shapes, such as curves in 3D and surfaces in 4D, is an infinite-dimensional manifold. This thesis explores geometric structures and dynamics on this space, with emphasis on their implications for physics, particularly hydrodynamics.\r\n\r\nOur investigation ranges from theoretical studies of infinite-dimensional symplectic and prequantum geometry to numerical computation of the time evolution of shapes. The thesis presents four main contributions.\r\n\r\nIn the first part, we introduce implicit representations of codimension-2 shapes using a class of complex-valued functions, and prove that the space of these implicit representations forms a prequantum bundle over the codimension-2 shape space. This reveals a new geometric interpretation of the canonical symplectic structure on the codimension-2 shape space.\r\n\r\nIn the second part, we use implicit representations to develop a simulation method for the dynamics of space curves. To handle chaotic systems such as vortex filaments in hydrodynamics, we exploit the infinite degrees of freedom, hidden in both the configuration and dynamics of implicit representations.\r\n\r\nIn the third part, we introduce new symplectic structures on the space of space curves, which generalize the only previously known symplectic structure on this space, allowing for new Hamiltonian dynamics of space curves.\r\n\r\nIn the fourth part, we apply a symplectic viewpoint to a differential geometric problem with practical applications. We derive a new area formula for spherical polygons via prequantization. ","lang":"eng"}],"degree_awarded":"PhD","type":"dissertation","doi":"10.15479/AT-ISTA-20551","file_date_updated":"2025-11-10T08:45:05Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"ec_funded":1,"file":[{"file_size":72487812,"file_id":"20583","relation":"source_file","creator":"sishida","checksum":"4eef80afcb67691cbb6549c4756fa534","file_name":"Thesis_tex.zip","content_type":"application/zip","date_updated":"2025-11-01T18:26:14Z","date_created":"2025-11-01T18:26:14Z","access_level":"open_access"},{"access_level":"open_access","date_updated":"2025-11-10T08:45:05Z","date_created":"2025-11-10T08:45:05Z","content_type":"application/pdf","file_name":"Thesis_Sadashige_Ishida_PDFA.pdf","checksum":"1e5a557900bf2dce01966b211b15d0fe","success":1,"creator":"sishida","relation":"main_file","file_id":"20623","file_size":8945141}],"ddc":["516"],"title":"Symplectic-prequantum structures and dynamics on the codimension-2 shape space","acknowledgement":"Projects contained in this thesis were financially supported in part by the\r\nEuropean Research Council with grants 1. ERC Consolidator Grant 101045083 CoDiNA,\r\nand 2. the European Union’s Horizon 2020 research and innovation programme under grant\r\nagreement No. 638176.","day":"31","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-070-1"]},"status":"public","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12846"},{"status":"public","relation":"part_of_dissertation","id":"12431"},{"status":"public","id":"17361","relation":"part_of_dissertation"},{"id":"20580","relation":"part_of_dissertation","status":"public"}]},"page":"141","citation":{"ama":"Ishida S. Symplectic-prequantum structures and dynamics on the codimension-2 shape space. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20551\">10.15479/AT-ISTA-20551</a>","ieee":"S. Ishida, “Symplectic-prequantum structures and dynamics on the codimension-2 shape space,” Institute of Science and Technology Austria, 2025.","mla":"Ishida, Sadashige. <i>Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20551\">10.15479/AT-ISTA-20551</a>.","apa":"Ishida, S. (2025). <i>Symplectic-prequantum structures and dynamics on the codimension-2 shape space</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20551\">https://doi.org/10.15479/AT-ISTA-20551</a>","chicago":"Ishida, Sadashige. “Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20551\">https://doi.org/10.15479/AT-ISTA-20551</a>.","short":"S. Ishida, Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space, Institute of Science and Technology Austria, 2025.","ista":"Ishida S. 2025. Symplectic-prequantum structures and dynamics on the codimension-2 shape space. Institute of Science and Technology Austria."},"article_processing_charge":"No","date_published":"2025-10-31T00:00:00Z","acknowledged_ssus":[{"_id":"CampIT"}],"_id":"20551","date_updated":"2026-04-07T12:02:23Z","date_created":"2025-10-27T10:28:52Z","oa":1,"supervisor":[{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"},{"first_name":"Albert","last_name":"Chern","full_name":"Chern, Albert"}],"author":[{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","orcid":"0000-0002-3121-3100","full_name":"Ishida, Sadashige"}],"oa_version":"Published Version","month":"10","publisher":"Institute of Science and Technology Austria","year":"2025"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"draft","day":"15","year":"2025","month":"07","oa_version":"Preprint","title":"Implicit representations of codimension-2 submanifolds and their prequantum structure","publication":"arXiv","author":[{"last_name":"Chern","first_name":"Albert","full_name":"Chern, Albert"},{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","orcid":"0000-0002-3121-3100","full_name":"Ishida, Sadashige"}],"oa":1,"date_updated":"2026-04-07T12:02:23Z","date_created":"2025-10-30T18:36:56Z","OA_place":"repository","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"_id":"20580","date_published":"2025-07-15T00:00:00Z","article_processing_charge":"No","citation":{"ieee":"A. Chern and S. Ishida, “Implicit representations of codimension-2 submanifolds and their prequantum structure,” <i>arXiv</i>. .","mla":"Chern, Albert, and Sadashige Ishida. “Implicit Representations of Codimension-2 Submanifolds and Their Prequantum Structure.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2507.11727\">10.48550/ARXIV.2507.11727</a>.","ama":"Chern A, Ishida S. Implicit representations of codimension-2 submanifolds and their prequantum structure. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2507.11727\">10.48550/ARXIV.2507.11727</a>","chicago":"Chern, Albert, and Sadashige Ishida. “Implicit Representations of Codimension-2 Submanifolds and Their Prequantum Structure.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2507.11727\">https://doi.org/10.48550/ARXIV.2507.11727</a>.","apa":"Chern, A., &#38; Ishida, S. (n.d.). Implicit representations of codimension-2 submanifolds and their prequantum structure. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2507.11727\">https://doi.org/10.48550/ARXIV.2507.11727</a>","short":"A. Chern, S. Ishida, ArXiv (n.d.).","ista":"Chern A, Ishida S. Implicit representations of codimension-2 submanifolds and their prequantum structure. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2507.11727\">10.48550/ARXIV.2507.11727</a>."},"doi":"10.48550/ARXIV.2507.11727","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20551"}]},"type":"preprint","arxiv":1,"external_id":{"arxiv":["2507.11727"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2507.11727"}],"language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"This paper explores the geometry of the space of codimension-2 submanifolds. We implicitly represent these submanifolds by a class of complex-valued functions. This reveals a prequantum bundle structure over the space of submanifolds, equipped with the well-known Marsden-Weinstein symplectic structure. This bundle allows a new physical interpretation of the Marsden-Weinstein structure as the curvature of a connection form, which measures the average of volumes swept by the deformation of the S^1-family of hypersurfaces, defined as the phases of a complex function implicitly representing a submanifold."}],"corr_author":"1"},{"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-066-4"],"issn":["2663-337X"]},"status":"public","alternative_title":["ISTA Thesis"],"page":"160","related_material":{"record":[{"status":"public","id":"18525","relation":"part_of_dissertation"}]},"project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"}],"citation":{"apa":"Ruzickova, N. (2025). <i>Effect propagation in biological networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>","chicago":"Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>.","ama":"Ruzickova N. Effect propagation in biological networks. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>","ieee":"N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025.","mla":"Ruzickova, Natalia. <i>Effect Propagation in Biological Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>.","ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria.","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025."},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}],"_id":"20357","date_published":"2025-09-15T00:00:00Z","date_created":"2025-09-15T17:04:48Z","date_updated":"2026-04-07T12:02:39Z","supervisor":[{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}],"author":[{"last_name":"Ruzickova","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia","full_name":"Ruzickova, Natalia"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","month":"09","year":"2025","has_accepted_license":"1","corr_author":"1","keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"degree_awarded":"PhD","type":"dissertation","doi":"10.15479/AT-ISTA-20357","file_date_updated":"2025-11-27T10:00:25Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"file":[{"embargo_to":"open_access","title":"Effect propagation in biological networks","file_size":43518367,"file_id":"20360","relation":"main_file","creator":"nruzicko","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","checksum":"991e81bc16a76b4e0c352567728fd2c5","content_type":"application/pdf","date_updated":"2025-11-27T10:00:25Z","date_created":"2025-09-16T12:56:06Z","embargo":"2026-09-14","access_level":"closed"},{"relation":"source_file","file_id":"20361","file_size":53464789,"access_level":"closed","checksum":"c4ab257adad116083d8a97fac69b2dde","date_updated":"2025-09-16T12:59:23Z","content_type":"application/zip","file_name":"2025_Ruzickova_Natalia_Thesis_source.zip","date_created":"2025-09-16T12:59:23Z","creator":"nruzicko"}],"title":"Effect propagation in biological networks","ddc":["570","530"],"day":"15","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","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published"},{"abstract":[{"lang":"eng","text":"Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.\r\n\r\nIn this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.\r\n\r\n-------------------------------------------------------------------------------------------------------------------------------------------------------------- In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not\r\nendorse any of ISTA's products or services. Internal or personal use of this\r\nmaterial is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional\r\npurposes or for creating new collective works for resale or redistribution, please go to\r\nhttp://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from\r\nRightsLink.\r\n"}],"corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","type":"dissertation","file_date_updated":"2025-09-10T08:19:51Z","doi":"10.15479/AT-ISTA-20147","ec_funded":1,"file":[{"relation":"source_file","file_id":"20200","file_size":8884801,"access_level":"closed","date_created":"2025-08-21T09:40:28Z","checksum":"0f3015f1db36576a23d8d669afb60b41","date_updated":"2025-09-10T08:19:51Z","file_name":"2025_Sarac_NaciEge_Thesis.zip","content_type":"application/x-zip-compressed","creator":"esarac"},{"file_size":2955584,"relation":"main_file","file_id":"20201","success":1,"creator":"esarac","access_level":"open_access","checksum":"332ed2fe61f580641664ec3f05d30f14","content_type":"application/pdf","file_name":"2025_Sarac_NaciEge_Thesis.pdf","date_created":"2025-08-21T09:40:34Z","date_updated":"2025-08-21T09:40:34Z"}],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"title":"A monitoring-oriented theory and classification of quantitative specifications","ddc":["000"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","day":"07","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF)\r\nunder grant Z211-N23 (Wittgenstein Award) and the ERC-2020-AdG 101020093.\r\n","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","related_material":{"record":[{"id":"11775","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"13140","status":"deleted"},{"status":"public","id":"19741","relation":"part_of_dissertation"},{"id":"9356","relation":"part_of_dissertation","status":"public"},{"id":"19643","relation":"part_of_dissertation","status":"deleted"},{"status":"public","relation":"part_of_dissertation","id":"17634"},{"status":"public","relation":"part_of_dissertation","id":"20342"},{"relation":"part_of_dissertation","id":"13221","status":"public"}]},"page":"149","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"alternative_title":["ISTA Thesis"],"_id":"20147","date_published":"2025-08-07T00:00:00Z","article_processing_charge":"No","citation":{"chicago":"Sarac, Naci E. “A Monitoring-Oriented Theory and Classification of Quantitative Specifications.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>.","apa":"Sarac, N. E. (2025). <i>A monitoring-oriented theory and classification of quantitative specifications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>","mla":"Sarac, Naci E. <i>A Monitoring-Oriented Theory and Classification of Quantitative Specifications</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>.","ieee":"N. E. Sarac, “A monitoring-oriented theory and classification of quantitative specifications,” Institute of Science and Technology Austria, 2025.","ama":"Sarac NE. A monitoring-oriented theory and classification of quantitative specifications. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>","ista":"Sarac NE. 2025. A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria.","short":"N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative Specifications, Institute of Science and Technology Austria, 2025."},"supervisor":[{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"date_updated":"2026-04-07T12:02:57Z","date_created":"2025-08-07T15:57:57Z","month":"08","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","author":[{"full_name":"Sarac, Naci E","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"year":"2025"},{"article_type":"original","isi":1,"year":"2025","publisher":"EPI Sciences","oa_version":"Published Version","month":"04","author":[{"full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","last_name":"Boker"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi"},{"last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"DOAJ_listed":"1","oa":1,"date_created":"2025-09-11T12:17:52Z","date_updated":"2026-04-07T12:02:57Z","_id":"20342","date_published":"2025-04-08T00:00:00Z","article_processing_charge":"Yes","citation":{"short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025).","ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025.  Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE.  Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. 2025;21(2). doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “ Safety and liveness of quantitative properties and automata,” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2. EPI Sciences, 2025.","mla":"Boker, Udi, et al. “ Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>.","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2025).  Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “ Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>. EPI Sciences, 2025. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>."},"related_material":{"record":[{"relation":"earlier_version","id":"13221","status":"public"},{"status":"public","relation":"dissertation_contains","id":"20147"}]},"project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"arxiv":1,"article_number":"13149","intvolume":"        21","external_id":{"isi":["001468887900001"],"arxiv":["2307.06016"]},"issue":"2","PlanS_conform":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1860-5974"]},"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication.","day":"08","title":" Safety and liveness of quantitative properties and automata","publication":"Logical Methods in Computer Science","ddc":["000"],"file":[{"creator":"esarac","success":1,"access_level":"open_access","checksum":"0b4d477bd981379724c35a4de2c176e5","date_created":"2025-09-11T12:17:12Z","content_type":"application/pdf","file_name":"2307.06016.pdf","date_updated":"2025-09-11T12:17:12Z","file_size":709584,"relation":"main_file","file_id":"20343"}],"ec_funded":1,"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"OA_type":"gold","file_date_updated":"2025-09-11T12:17:12Z","doi":"10.46298/lmcs-21(2:2)2025","volume":21,"type":"journal_article","quality_controlled":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata."}],"has_accepted_license":"1","corr_author":"1"},{"related_material":{"record":[{"status":"public","id":"20147","relation":"dissertation_contains"}]},"page":"303-312","project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"alternative_title":["LNCS"],"arxiv":1,"intvolume":"     15696","external_id":{"arxiv":["2501.16088"]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031906428"],"issn":["0302-9743"]},"status":"public","year":"2025","month":"05","oa_version":"Published Version","publisher":"Springer Nature","author":[{"last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","full_name":"Chalupa, Marek"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi"},{"full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"oa":1,"date_created":"2025-05-25T22:17:07Z","date_updated":"2026-04-07T12:02:57Z","_id":"19741","date_published":"2025-05-01T00:00:00Z","article_processing_charge":"No","citation":{"chicago":"Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Automating the Analysis of Quantitative Automata with QuAK.” In <i>31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 15696:303–12. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-031-90643-5_16\">https://doi.org/10.1007/978-3-031-90643-5_16</a>.","apa":"Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2025). Automating the analysis of quantitative automata with QuAK. In <i>31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 15696, pp. 303–312). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-90643-5_16\">https://doi.org/10.1007/978-3-031-90643-5_16</a>","mla":"Chalupa, Marek, et al. “Automating the Analysis of Quantitative Automata with QuAK.” <i>31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 15696, Springer Nature, 2025, pp. 303–12, doi:<a href=\"https://doi.org/10.1007/978-3-031-90643-5_16\">10.1007/978-3-031-90643-5_16</a>.","ieee":"M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Automating the analysis of quantitative automata with QuAK,” in <i>31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 2025, vol. 15696, pp. 303–312.","ama":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. Automating the analysis of quantitative automata with QuAK. In: <i>31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 15696. Springer Nature; 2025:303-312. doi:<a href=\"https://doi.org/10.1007/978-3-031-90643-5_16\">10.1007/978-3-031-90643-5_16</a>","ista":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Automating the analysis of quantitative automata with QuAK. 31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems. , LNCS, vol. 15696, 303–312.","short":"M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2025, pp. 303–312."},"volume":15696,"type":"conference","quality_controlled":"1","scopus_import":"1","abstract":[{"text":"Quantitative automata model beyond-boolean aspects of systems: every execution is mapped to a real number by incorporating weighted transitions and value functions that generalize acceptance conditions of boolean w-automata. Despite the theoretical advances in systems analysis through quantitative automata, the first comprehensive software tool for quantitative automata (Quantitative Automata Kit, or QuAK) was developed only recently. QuAK implements algorithms for solving standard decision problems, e.g., emptiness and universality, as well as constructions for safety and liveness of quantitative automata. We present the architecture of QuAK, which reflects that all of these problems reduce to either checking inclusion between two quantitative automata or computing the highest value achievable by an automaton—its so-called top value. We improve QuAK by extending these two algorithms with an option to return, alongside their results, an ultimately periodic word witnessing the algorithm’s output, as well as implementing a new safety-liveness decomposition algorithm that can handle nondeterministic automata, making QuAK more informative and capable.","lang":"eng"}],"corr_author":"1","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.","day":"01","ddc":["000"],"title":"Automating the analysis of quantitative automata with QuAK","publication":"31st International Conference on Tools and Algorithms for the Construction and Analysis of Systems","ec_funded":1,"file":[{"file_size":420669,"relation":"main_file","file_id":"19768","creator":"dernst","success":1,"access_level":"open_access","checksum":"a27fa245be8d83421e9127b48a09c8af","file_name":"2025_TACAS_ChalupaMarek.pdf","date_created":"2025-06-02T08:13:11Z","content_type":"application/pdf","date_updated":"2025-06-02T08:13:11Z"}],"department":[{"_id":"ToHe"}],"OA_place":"publisher","file_date_updated":"2025-06-02T08:13:11Z","OA_type":"hybrid","doi":"10.1007/978-3-031-90643-5_16"},{"ddc":["572"],"title":"Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria","day":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","doi":"10.15479/AT-ISTA-20741","file_date_updated":"2025-12-10T13:09:58Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-12-10T13:09:58Z","date_created":"2025-12-10T13:09:58Z","file_name":"2025_marko_kojic_thesis.docx","checksum":"a3643d07e93134b2490a566b02a4517d","creator":"mkojic","relation":"source_file","file_id":"20774","file_size":142876975},{"creator":"mkojic","success":1,"access_level":"open_access","file_name":"2025_marko_kojic_thesis.pdf","date_updated":"2025-12-10T13:09:38Z","content_type":"application/pdf","checksum":"0a096f0af6ccc3a8329d5bb8797ad533","date_created":"2025-12-10T13:09:38Z","file_size":8597045,"relation":"main_file","file_id":"20775"}],"degree_awarded":"PhD","type":"dissertation","abstract":[{"lang":"eng","text":"Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. \r\n\r\nFirstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. \r\n\r\nNext, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. \r\n\r\nFinally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. "}],"has_accepted_license":"1","corr_author":"1","author":[{"first_name":"Marko","id":"73e7ecd4-dc85-11ea-9058-88a16394b160","last_name":"Kojic","orcid":"0000-0001-7244-8128","full_name":"Kojic, Marko"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","month":"12","year":"2025","article_processing_charge":"No","citation":{"ista":"Kojic M. 2025. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. Institute of Science and Technology Austria.","short":"M. Kojic, Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria, Institute of Science and Technology Austria, 2025.","chicago":"Kojic, Marko. “Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20741\">https://doi.org/10.15479/AT-ISTA-20741</a>.","apa":"Kojic, M. (2025). <i>Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20741\">https://doi.org/10.15479/AT-ISTA-20741</a>","ieee":"M. Kojic, “Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria,” Institute of Science and Technology Austria, 2025.","mla":"Kojic, Marko. <i>Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20741\">10.15479/AT-ISTA-20741</a>.","ama":"Kojic M. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20741\">10.15479/AT-ISTA-20741</a>"},"_id":"20741","acknowledged_ssus":[{"_id":"Bio"}],"date_published":"2025-12-09T00:00:00Z","oa":1,"date_created":"2025-12-09T13:08:11Z","date_updated":"2026-04-07T12:27:58Z","supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"15118"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-073-2"],"issn":["2663-337X"]},"status":"public"},{"date_published":"2025-06-25T00:00:00Z","_id":"19903","article_processing_charge":"No","citation":{"ista":"Hübner V. 2025. Reciprocity and inequality in social dilemmas. Institute of Science and Technology Austria.","short":"V. Hübner, Reciprocity and Inequality in Social Dilemmas, Institute of Science and Technology Austria, 2025.","chicago":"Hübner, Valentin. “Reciprocity and Inequality in Social Dilemmas.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>.","apa":"Hübner, V. (2025). <i>Reciprocity and inequality in social dilemmas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>","mla":"Hübner, Valentin. <i>Reciprocity and Inequality in Social Dilemmas</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>.","ieee":"V. Hübner, “Reciprocity and inequality in social dilemmas,” Institute of Science and Technology Austria, 2025.","ama":"Hübner V. Reciprocity and inequality in social dilemmas. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>"},"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"}],"date_created":"2025-06-25T13:50:10Z","date_updated":"2026-04-07T12:30:57Z","oa":1,"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","month":"06","author":[{"orcid":"0009-0001-5009-4987","full_name":"Hübner, Valentin","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","last_name":"Hübner"}],"year":"2025","publication_identifier":{"issn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"page":"157","related_material":{"record":[{"relation":"part_of_dissertation","id":"19843","status":"public"},{"id":"15083","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"19074"}]},"alternative_title":["ISTA Thesis"],"file_date_updated":"2025-07-09T13:37:00Z","doi":"10.15479/AT-ISTA-19903","ec_funded":1,"file":[{"file_size":6192760,"relation":"source_file","file_id":"19905","creator":"vhuebner","access_level":"closed","content_type":"application/x-xz","date_updated":"2025-06-25T13:38:07Z","date_created":"2025-06-25T13:38:07Z","file_name":"Thesis Valentin Hübner source.tar.xz","checksum":"794c02f8c82ca59ba6dda3bd7eed871a"},{"file_id":"19976","relation":"main_file","file_size":4837864,"file_name":"Thesis Valentin Hübner.pdf","checksum":"ac56063d81c81e40322b6ff5a8c4912e","content_type":"application/pdf","date_updated":"2025-07-09T13:37:00Z","date_created":"2025-07-09T13:37:00Z","access_level":"open_access","creator":"vhuebner"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"OA_place":"publisher","ddc":["519"],"title":"Reciprocity and inequality in social dilemmas","publication_status":"published","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"The research for this thesis was supported by the European Research Council\r\n(grant agreements No. 863818 and No. 850529), the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie grant agreement No. 754411),\r\nthe Austrian Science Fund (grant DOI 10.55776/COE12), the French Agence Nationale\r\nde la Recherche under the Programme d’investissements d’avenir (project reference 17-\r\nEURE-0010) and the Australian Government through the Australian Research Council\r\n(grant No. SR200100005, “Securing Antarctica’s Environmental Future”).","day":"25","has_accepted_license":"1","corr_author":"1","abstract":[{"text":"Cooperation, that is, one person paying a cost for another's benefit, is a fundamental principle without which no form of society could exist. The extent to which humans cooperate with each other is also an essential feature that differentiates them from other animals. Cooperation occurs even in the absence of altruistic motivations, when it is selfishly incentivised by the expectation of a future reward. For example, many economic interactions are well described that way. This kind of cooperation requires that people exhibit reciprocal behaviour that acts as a mechanism that rewards cooperation.\r\nWith game-theoretic models, it is possible to formally study potential such mechanisms and under what conditions they can exist. This thesis contributes to this effort by analysing recently introduced models of cooperation that advance on previous work by taking into account the potential for pre-existing inequality among cooperating individuals as well as the different forms that reciprocity can take.\r\nIndividuals may differ both intrinsically, in their abilities, as well as extrinsically, in the amount of resources they have available. Allowing for such differences in a model of cooperation helps to understand how inequality affects the potential for, and outcomes of, cooperation among unequals. In this thesis, it is shown that in the presence of intrinsic inequality, a similar unequal distribution of resources can increase the potential for cooperation. This effect is stronger the smaller the group is in which cooperation takes place. It is also shown that under particular assumptions, if the unequal members of a group vary the size of their contributions to a cooperative effort over time, they can thereby increase their efficiency and improve the collective outcome.\r\nCooperative behaviour in a two-person interaction can be rewarded either by direct reciprocation whenever the same two people interact again, or indirectly by a third party who observed the interaction. In the latter case of indirect reciprocity, individuals are proximally rewarded by a good reputation, which ultimately translates to being rewarded with cooperative behaviour by others. This mechanism can enable selfishly motivated cooperation even in circumstances where individuals are unlikely to meet again, akin to how money facilitates trade. While these two forms of reciprocity have mostly been studied in isolation, this thesis analyses both direct and indirect reciprocity in a general model in order to compare their relative effectiveness under different circumstances. The contribution of this thesis is an extension of previous work regarding a specific kind of interaction, whose parameters allow for convenient mathematical analysis, to the most general set of possible interactions.","lang":"eng"}],"degree_awarded":"PhD","type":"dissertation"},{"issue":"5","external_id":{"pmid":["40202086"],"isi":["001483460200001"]},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"status":"public","language":[{"iso":"eng"}],"project":[{"name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","grant_number":"PAT 8748323"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"20444","status":"private"},{"relation":"dissertation_contains","id":"20449","status":"public"}],"link":[{"url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git","relation":"software"}]},"article_number":"msaf085","intvolume":"        42","DOAJ_listed":"1","date_created":"2025-05-25T22:16:56Z","date_updated":"2026-04-07T12:28:15Z","oa":1,"date_published":"2025-05-01T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"19735","citation":{"chicago":"Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>.","apa":"Bett, V. K., Trejo Arellano, M. S., &#38; Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>","ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025.","mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","ama":"Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. 2025;42(5). doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>","ista":"Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.","short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025)."},"article_processing_charge":"Yes","article_type":"original","year":"2025","isi":1,"oa_version":"Published Version","publisher":"Oxford University Press","month":"05","author":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K"},{"full_name":"Trejo Arellano, Minerva S","orcid":"0000-0002-1982-3475","id":"2b681148-eed5-11eb-b81b-ae229e8620f8","first_name":"Minerva S","last_name":"Trejo Arellano"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"corr_author":"1","has_accepted_license":"1","abstract":[{"text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.","lang":"eng"}],"volume":42,"scopus_import":"1","type":"journal_article","quality_controlled":"1","file":[{"file_id":"19756","relation":"main_file","file_size":1282772,"file_name":"2025_MBE_Bett.pdf","date_updated":"2025-05-28T09:34:36Z","date_created":"2025-05-28T09:34:36Z","checksum":"6c14b03f94b4aadf8869be2c4366d077","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst"}],"department":[{"_id":"BeVi"},{"_id":"DaZi"}],"OA_place":"publisher","pmid":1,"file_date_updated":"2025-05-28T09:34:36Z","OA_type":"gold","doi":"10.1093/molbev/msaf085","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank the Vicoso lab for their help in maintaining Artemia and for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful technical advice and discussions. We are also grateful to the Scientific Unit at ISTA Austria for computational resources and assistance. This work was supported by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council (Vetenskapsrådet, grant number 2020-06424) to MSTA.","day":"01","title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","ddc":["570"],"publication":"Molecular Biology and Evolution"},{"author":[{"id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","last_name":"Hübner","full_name":"Hübner, Valentin","orcid":"0009-0001-5009-4987"},{"orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","last_name":"Schmid","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"month":"05","publisher":"Oxford University Press","oa_version":"Published Version","year":"2025","article_type":"original","citation":{"ama":"Hübner V, Schmid L, Hilbe C, Chatterjee K. Stable strategies of direct and indirect reciprocity across all social dilemmas. <i>PNAS Nexus</i>. 2025;4(5). doi:<a href=\"https://doi.org/10.1093/pnasnexus/pgaf154\">10.1093/pnasnexus/pgaf154</a>","mla":"Hübner, Valentin, et al. “Stable Strategies of Direct and Indirect Reciprocity across All Social Dilemmas.” <i>PNAS Nexus</i>, vol. 4, no. 5, pgaf154, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/pnasnexus/pgaf154\">10.1093/pnasnexus/pgaf154</a>.","ieee":"V. Hübner, L. Schmid, C. Hilbe, and K. Chatterjee, “Stable strategies of direct and indirect reciprocity across all social dilemmas,” <i>PNAS Nexus</i>, vol. 4, no. 5. Oxford University Press, 2025.","apa":"Hübner, V., Schmid, L., Hilbe, C., &#38; Chatterjee, K. (2025). Stable strategies of direct and indirect reciprocity across all social dilemmas. <i>PNAS Nexus</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pnasnexus/pgaf154\">https://doi.org/10.1093/pnasnexus/pgaf154</a>","chicago":"Hübner, Valentin, Laura Schmid, Christian Hilbe, and Krishnendu Chatterjee. “Stable Strategies of Direct and Indirect Reciprocity across All Social Dilemmas.” <i>PNAS Nexus</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/pnasnexus/pgaf154\">https://doi.org/10.1093/pnasnexus/pgaf154</a>.","short":"V. Hübner, L. Schmid, C. Hilbe, K. Chatterjee, PNAS Nexus 4 (2025).","ista":"Hübner V, Schmid L, Hilbe C, Chatterjee K. 2025. Stable strategies of direct and indirect reciprocity across all social dilemmas. PNAS Nexus. 4(5), pgaf154."},"article_processing_charge":"Yes","_id":"19843","date_published":"2025-05-01T00:00:00Z","oa":1,"date_created":"2025-06-15T22:01:30Z","date_updated":"2026-04-07T12:30:56Z","DOAJ_listed":"1","intvolume":"         4","article_number":"pgaf154","related_material":{"record":[{"status":"public","id":"19903","relation":"dissertation_contains"}]},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"status":"public","publication_identifier":{"eissn":["2752-6542"]},"external_id":{"pmid":["40417077"]},"issue":"5","ddc":["000"],"publication":"PNAS Nexus","title":"Stable strategies of direct and indirect reciprocity across all social dilemmas","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.).","day":"01","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","doi":"10.1093/pnasnexus/pgaf154","pmid":1,"OA_type":"gold","file_date_updated":"2025-06-23T08:09:50Z","department":[{"_id":"KrCh"}],"OA_place":"publisher","file":[{"creator":"dernst","success":1,"access_level":"open_access","checksum":"efd6648db3fc3ea0cdd7155d667e5f11","content_type":"application/pdf","date_created":"2025-06-23T08:09:50Z","file_name":"2025_PNASNexus_Huebner.pdf","date_updated":"2025-06-23T08:09:50Z","file_size":2551195,"relation":"main_file","file_id":"19867"}],"ec_funded":1,"type":"journal_article","quality_controlled":"1","scopus_import":"1","volume":4,"abstract":[{"lang":"eng","text":"Social dilemmas are collective-action problems where individual interests are at odds with group interests. Such dilemmas occur frequently at all scales of human interactions. When dealing with collective-action problems, people often act reciprocally. They adjust their behavior to match the previous behavior of the recipient. The literature distinguishes two kinds of reciprocity. According to direct reciprocity, individuals react to their immediate experiences with the recipient. They are more likely to cooperate if the recipient previously cooperated with them. According to indirect reciprocity, individuals react to the recipient’s general behavior, irrespectively of whether or not they benefited directly. In practice, the two kinds of reciprocity are often intertwined; people typically base their decisions on both direct experiences and indirect observations. Yet only recently have researchers begun to explore how the two kinds of reciprocity interact. So far, this research only addresses a single type of social dilemma, the donation game, where the effects of individual behaviors are independent. Instead, here we allow for all pairwise social dilemmas. By applying novel techniques to generalize the theory of zero-determinant strategies, we establish an important proof of principle: In all social dilemmas, socially optimal outcomes can be sustained as an equilibrium, using either direct or indirect reciprocity, or arbitrary mixtures thereof. These results neither require games to be repeated infinitely often, nor that individual opinions are synchronized. In this way, we considerably generalize the scope of models of reciprocity, and we build further bridges between the literatures on direct and indirect reciprocity."}],"has_accepted_license":"1","corr_author":"1"}]