[{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"month":"03","year":"2025","degree_awarded":"PhD","_id":"19386","oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-19386","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"170","ddc":["570","576"],"type":"dissertation","publication_status":"published","date_published":"2025-03-14T00:00:00Z","has_accepted_license":"1","supervisor":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"My PhD work was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).","related_material":{"record":[{"id":"12248","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10767","status":"public"},{"id":"14613","status":"public","relation":"part_of_dissertation"},{"id":"10167","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"15009","relation":"part_of_dissertation"},{"id":"17890","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. "}],"file":[{"relation":"source_file","file_size":25019680,"access_level":"closed","file_name":"Thesis_Marwan_Elkrewi.docx","creator":"melkrewi","date_updated":"2026-03-26T23:30:03Z","date_created":"2025-03-26T07:06:56Z","file_id":"19462","checksum":"5549a8216c07e4c39281648912d72246","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","file_id":"19463","checksum":"aed2ba9965aa89b3414deae1ae9f4321","embargo":"2026-03-26","date_created":"2025-03-26T07:06:22Z","file_name":"Thesis_Marwan_Elkrewi.pdf","date_updated":"2026-03-26T23:30:03Z","creator":"melkrewi","access_level":"open_access","relation":"main_file","file_size":17294844}],"title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","day":"14","OA_embargo":"12","publication_identifier":{"eissn":["2663-337X"],"isbn":["9783990780534"]},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file_date_updated":"2026-03-26T23:30:03Z","citation":{"mla":"Elkrewi, Marwan N. <i>Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>.","short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>","ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","chicago":"Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>.","ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria."},"date_created":"2025-03-11T12:54:31Z","author":[{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231"}],"date_updated":"2026-09-24T11:17:37Z","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.15479/AT-ISTA-19386","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"corr_author":"1","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","status":"public"},{"has_accepted_license":"1","publication_status":"published","date_published":"2025-10-10T00:00:00Z","page":"114","ddc":["576"],"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-20449","_id":"20449","degree_awarded":"PhD","year":"2025","month":"10","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"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"}],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"corr_author":"1","OA_place":"publisher","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.15479/AT-ISTA-20449","author":[{"first_name":"Vincent K","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"}],"date_updated":"2026-09-24T11:11:01Z","date_created":"2025-10-11T08:18:51Z","citation":{"ista":"Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria.","apa":"Bett, V. K. (2025). <i>Evolution and regulation of the Z chromosome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>","mla":"Bett, Vincent K. <i>Evolution and Regulation of the Z Chromosome</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>.","short":"V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025.","ieee":"V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025.","chicago":"Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>.","ama":"Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>"},"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file_date_updated":"2026-06-01T22:30:04Z","day":"10","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Males and females of many  species differ in morphology, physiology, and behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises largely from sex-biased gene\r\nexpression, which varies across tissues, developmental stages, and lineages. Increasing\r\nevidence highlights chromatin configuration, which can exist in open or closed states, and can\r\nbe shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the Y or W chromosome further contributes to sex -specific differences by\r\naltering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances, many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand Cameraria  ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying this process. We further characterize sex -biased gene expression and its regulation\r\nthrough histone modifications. Our analyses also reveal that the A. franciscana genome is\r\nhighly repetitive, with many genes containing intronic transposable elements. We find that\r\nenrichment of histonemo difications associated with constitutive heterochromatin, positively\r\ncorrelates with variation in gene expression levels. Collectively, these findings underscore role\r\nof chromatin regulation in shaping the evolution of sex chromosomes and sexual\r\ndifferentiation. "}],"file":[{"access_level":"open_access","creator":"vbett","date_updated":"2026-06-01T22:30:04Z","file_name":"2025_Bett_Vincent_Thesis.pdf","embargo":"2026-06-01","date_created":"2025-10-20T13:32:29Z","file_size":18507283,"relation":"main_file","content_type":"application/pdf","file_id":"20507","checksum":"26905c22bca417198a733d792d8ce422"},{"checksum":"6a09a8d126d3628bfd8a35202735f267","file_id":"20508","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","relation":"source_file","file_size":17163921,"date_created":"2025-10-20T13:35:34Z","date_updated":"2026-06-01T22:30:04Z","creator":"vbett","file_name":"2025_Bett_Vincent_Thesis.docx","access_level":"closed"}],"title":"Evolution and regulation of the Z chromosome","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"19735"},{"id":"15009","status":"public","relation":"part_of_dissertation"}]},"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso.","supervisor":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"article_processing_charge":"No"},{"article_processing_charge":"Yes","title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","abstract":[{"lang":"eng","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."}],"file":[{"file_name":"2025_MBE_Bett.pdf","date_updated":"2025-05-28T09:34:36Z","creator":"dernst","date_created":"2025-05-28T09:34:36Z","access_level":"open_access","file_size":1282772,"relation":"main_file","success":1,"content_type":"application/pdf","checksum":"6c14b03f94b4aadf8869be2c4366d077","file_id":"19756"}],"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.","related_material":{"link":[{"url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git","relation":"software"}],"record":[{"status":"public","id":"20449","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"20444","status":"deleted"}]},"OA_type":"gold","oa_version":"Published Version","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"day":"01","citation":{"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.","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>","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>.","short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).","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>.","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.","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>"},"volume":42,"language":[{"iso":"eng"}],"file_date_updated":"2025-05-28T09:34:36Z","author":[{"full_name":"Bett, Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"},{"orcid":"0000-0002-1982-3475","first_name":"Minerva S","full_name":"Trejo Arellano, Minerva S","id":"2b681148-eed5-11eb-b81b-ae229e8620f8","last_name":"Trejo Arellano"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"date_created":"2025-05-25T22:16:56Z","date_updated":"2026-11-05T23:31:03Z","OA_place":"publisher","intvolume":"        42","corr_author":"1","department":[{"_id":"BeVi"},{"_id":"DaZi"}],"doi":"10.1093/molbev/msaf085","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"pmid":["40202086"],"isi":["001483460200001"]},"publisher":"Oxford University Press","status":"public","project":[{"grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"scopus_import":"1","article_type":"original","isi":1,"month":"05","article_number":"msaf085","year":"2025","issue":"5","pmid":1,"_id":"19735","fulldoi":"https://doi.org/10.1093/molbev/msaf085","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-05-01T00:00:00Z","publication_status":"published","type":"journal_article","DOAJ_listed":"1","ddc":["570"],"has_accepted_license":"1","publication":"Molecular Biology and Evolution"},{"has_accepted_license":"1","page":"156","type":"dissertation","ddc":["570","530"],"publication_status":"published","date_published":"2025-09-15T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-20357","_id":"20357","year":"2025","degree_awarded":"PhD","month":"09","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"}],"keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"status":"public","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}],"doi":"10.15479/AT-ISTA-20357","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"corr_author":"1","OA_place":"publisher","date_created":"2025-09-15T17:04:48Z","date_updated":"2026-10-02T10:15:31Z","author":[{"last_name":"Ruzickova","full_name":"Ruzickova, Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia"}],"alternative_title":["ISTA Thesis"],"file_date_updated":"2026-09-15T22:30:02Z","language":[{"iso":"eng"}],"citation":{"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>.","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025.","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>","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.","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>.","ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria."},"day":"15","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-066-4"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"18525","status":"public"}]},"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","file":[{"access_level":"closed","creator":"cchlebak","file_name":"2025_Ruzickova_Natalia_Thesis.zip","date_created":"2026-08-07T10:57:05Z","date_updated":"2026-09-15T22:30:02Z","file_size":56464803,"relation":"source_file","content_type":"application/x-zip-compressed","embargo_to":"open_access","file_id":"22661","checksum":"0582508d439b233497384f83a8307398"},{"file_size":30634378,"relation":"main_file","access_level":"open_access","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","embargo":"2026-09-15","creator":"cchlebak","date_created":"2026-08-07T10:57:34Z","date_updated":"2026-09-15T22:30:02Z","file_id":"22662","checksum":"b722289fd550abede63adc27b9c61784","content_type":"application/pdf"}],"title":"Effect propagation in biological networks","doi_confirm":"1","supervisor":[{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"article_processing_charge":"No"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-20563","has_accepted_license":"1","publication_status":"published","date_published":"2025-11-03T00:00:00Z","page":"240","ddc":["515","519"],"type":"dissertation","month":"11","keyword":["optimal transport","kinetic equations","boundary value problems","quantization","gradient flows","homogenization"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F06504"}],"_id":"20563","degree_awarded":"PhD","year":"2025","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"corr_author":"1","OA_place":"publisher","doi":"10.15479/AT-ISTA-20563","author":[{"first_name":"Filippo","full_name":"Quattrocchi, Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi","orcid":"0009-0000-9773-1931"}],"date_updated":"2026-10-02T11:24:55Z","date_created":"2025-10-28T13:10:49Z","status":"public","publisher":"Institute of Science and Technology Austria","file":[{"file_size":4326411,"relation":"main_file","date_created":"2025-11-17T21:04:15Z","date_updated":"2026-01-01T23:30:03Z","embargo":"2026-01-01","file_name":"2025_quattrocchi_filippo_thesis.pdf","creator":"fquattro","access_level":"open_access","checksum":"6f55275bdf99992be3a6457d949dd664","file_id":"20653","content_type":"application/pdf"},{"content_type":"application/zip","embargo_to":"open_access","file_id":"20654","checksum":"707e580f5d993a214c0dba456b75837b","file_name":"2025_quattrocchi_thesis.zip","date_updated":"2026-01-01T23:30:03Z","date_created":"2025-11-17T21:05:43Z","creator":"fquattro","access_level":"closed","file_size":11726509,"relation":"source_file"}],"abstract":[{"lang":"eng","text":"The theory of optimal transport provides an elegant and powerful description of many evolution\r\nequations as gradient flows. The primary objective of this thesis is to adapt and extend the\r\ntheory to deal with important equations that are not covered by the classical framework,\r\nspecifically boundary value problems and kinetic equations. Additionally, we establish new\r\nresults in periodic homogenization for discrete dynamical optimal transport and in quantization\r\nof measures.\r\nSection 1.1 serves as an invitation to the classical theory of optimal transport, including the\r\nmain definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the\r\nmain results of this thesis, outline the motivations, and review the current state of the art.\r\nIn Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet\r\nboundary conditions. We construct a time-discrete scheme involving a modification of the\r\nWasserstein distance and, under weak assumptions, prove its convergence to a solution of this\r\nboundary value problem. In dimension 1, we show that this solution is a gradient flow in a\r\nsuitable space of measures.\r\nChapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory\r\nof optimal transport to describe and study particle systems at the mesoscopic scale. We prove\r\nadapted versions of some fundamental theorems, including the Benamou–Brenier formula and\r\nthe identification of absolutely continuous curves of measures.\r\nChapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical\r\ntransportation functionals on periodic graphs in the large-scale limit when the cost functional\r\nis asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge\r\nto 1-Wasserstein distances constructed from crystalline norms on R\r\nd\r\n.\r\nChapter 5 concerns optimal empirical quantization: the problem of approximating a measure\r\nby the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein\r\ndistance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for\r\nthe minimal error as n tends to infinity.\r\n"}],"title":"Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures","acknowledgement":"The research contained in this thesis has received funding from the Austrian Science\r\nFund (FWF) project 10.55776/F65.","related_material":{"record":[{"id":"20569","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"20571","relation":"part_of_dissertation"},{"id":"20570","status":"public","relation":"part_of_dissertation"},{"id":"18706","status":"public","relation":"part_of_dissertation"}]},"supervisor":[{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"}],"article_processing_charge":"No","citation":{"ista":"Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria.","ama":"Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>","ieee":"F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025.","chicago":"Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>.","mla":"Quattrocchi, Filippo. <i>Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>.","short":"F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025.","apa":"Quattrocchi, F. (2025). <i>Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>"},"alternative_title":["ISTA Thesis"],"file_date_updated":"2026-01-01T23:30:03Z","language":[{"iso":"eng"}],"day":"03","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]}},{"month":"08","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"keyword":["optimal transport","kinetic theory","second-order discrepancy","Vlasov equation","Wasserstein splines."],"_id":"20569","article_number":"2502.15665","year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.48550/arXiv.2502.15665","oa":1,"arxiv":1,"publication":"arXiv","type":"preprint","date_published":"2025-08-10T00:00:00Z","publication_status":"draft","related_material":{"record":[{"id":"20563","status":"public","relation":"dissertation_contains"}]},"OA_type":"green","acknowledgement":"This work was partially inspired by an unpublished note from 2014 by Guillaume Carlier,\r\nJean Dolbeault, and Bruno Nazaret. GB deeply thanks Jean Dolbeault for proposing\r\nthis problem to him, guiding him into the subject, and sharing the aforementioned note.\r\nWe are grateful to Karthik Elamvazhuthi for making us aware of the work [20].\r\nThe work of GB has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement\r\nNo 101034413.\r\nJM and FQ gratefully acknowledge support from the Austrian Science Fund (FWF)\r\nproject 10.55776/F65.","title":"Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures","abstract":[{"lang":"eng","text":"This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov's equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov's equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov's equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"apa":"Brigati, G., Maas, J., &#38; Quattrocchi, F. (n.d.). Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>","short":"G. Brigati, J. Maas, F. Quattrocchi, ArXiv (n.d.).","mla":"Brigati, Giovanni, et al. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” <i>ArXiv</i>, 2502.15665, doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>.","chicago":"Brigati, Giovanni, Jan Maas, and Filippo Quattrocchi. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>.","ieee":"G. Brigati, J. Maas, and F. Quattrocchi, “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures,” <i>arXiv</i>. .","ama":"Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>","ista":"Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv, 2502.15665."},"oa_version":"Preprint","day":"10","doi":"10.48550/arXiv.2502.15665","external_id":{"arxiv":["2502.15665"]},"OA_place":"repository","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"corr_author":"1","date_updated":"2026-11-05T23:31:09Z","author":[{"last_name":"Brigati","full_name":"Brigati, Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","first_name":"Giovanni"},{"first_name":"Jan","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","orcid":"0000-0002-0845-1338"},{"orcid":"0009-0000-9773-1931","first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi"}],"ec_funded":1,"date_created":"2025-10-28T13:12:08Z","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2502.15665","open_access":"1"}]},{"date_published":"2025-04-01T00:00:00Z","publication_status":"published","type":"dissertation","ddc":["530"],"page":"109","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT-ISTA-19533","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","degree_awarded":"PhD","year":"2025","_id":"19533","keyword":["phase transition","open quantum system","phase diagram","cavity quantum electrodynamics","superconducting qubits","semiclassical physics","quantum optics","josephson junction","parametric converter","phase conjugation","quantum radar","quantum entanglement","correlation","quantum sensing"],"project":[{"grant_number":"862644","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"month":"04","publisher":"Institute of Science and Technology Austria","status":"public","date_updated":"2026-10-15T09:08:00Z","ec_funded":1,"date_created":"2025-04-09T16:44:26Z","author":[{"first_name":"Riya","full_name":"Sett, Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett","orcid":"0000-0001-7641-8348"}],"OA_place":"publisher","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"doi":"10.15479/AT-ISTA-19533","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"day":"1","citation":{"ama":"Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>","chicago":"Sett, Riya. “Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>.","ieee":"R. Sett, “Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025.","short":"R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025.","mla":"Sett, Riya. <i>Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>.","apa":"Sett, R. (2025). <i>Quantum remote sensing and non-equilibrium phase transitions in the microwave regime</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>","ista":"Sett R. 2025. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria."},"language":[{"iso":"eng"}],"file_date_updated":"2025-10-11T22:30:02Z","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","supervisor":[{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M"}],"title":"Quantum remote sensing and non-equilibrium phase transitions in the microwave regime","doi_confirm":"1","file":[{"file_id":"19538","checksum":"ba6cd2289d0141a160a14fc97df1632f","content_type":"application/pdf","relation":"main_file","file_size":4129208,"creator":"rsett","embargo":"2025-10-11","file_name":"PhD_Thesis_Riya_Sett_pdfa.pdf","date_created":"2025-04-10T11:33:22Z","date_updated":"2025-10-11T22:30:02Z","access_level":"open_access"},{"embargo_to":"open_access","content_type":"application/x-zip-compressed","file_id":"19539","checksum":"ee63a94cb8f7adf5e766903028b81ed6","creator":"rsett","date_created":"2025-04-10T11:34:08Z","file_name":"PhD Thesis Riya Sett.zip","date_updated":"2025-10-11T22:30:02Z","access_level":"closed","file_size":6646110,"relation":"source_file"}],"abstract":[{"text":"This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n","lang":"eng"}],"acknowledgement":"I acknowledge the generous financial support of the Austrian Science Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop and the Institute of Science and Technology\r\nAustria nanofabrication facility for their technical assistance, which was instrumental in realizing\r\nthis work.","related_material":{"record":[{"relation":"research_data","status":"public","id":"18978"},{"relation":"part_of_dissertation","id":"19280","status":"public"},{"id":"13117","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"17183","relation":"part_of_dissertation"}]}},{"status":"public","publisher":"American Physical Society","corr_author":"1","department":[{"_id":"JoFi"}],"intvolume":"       134","OA_place":"publisher","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"arxiv":["2310.04200"],"isi":["001454696700003"],"pmid":["40021171"]},"doi":"10.1103/PhysRevLett.134.063601","quality_controlled":"1","author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"},{"full_name":"Zens, M.","last_name":"Zens","first_name":"M."},{"orcid":"0009-0005-0878-3032","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","full_name":"Peruzzo, Matilda","first_name":"Matilda","orcid":"0000-0002-3415-4628"},{"first_name":"Farid","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","orcid":"0000-0001-6937-5773"},{"orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","last_name":"Sett","first_name":"Riya"},{"full_name":"Zielinski, Przemyslaw D","last_name":"Zielinski","id":"e198fcc4-f6e0-11ea-865d-b6a256760ee8","first_name":"Przemyslaw D"},{"first_name":"H. S.","full_name":"Dhar, H. S.","last_name":"Dhar"},{"first_name":"D. O.","full_name":"Krimer, D. O.","last_name":"Krimer"},{"first_name":"S.","last_name":"Rotter","full_name":"Rotter, S."},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M"}],"date_updated":"2026-11-05T23:31:10Z","ec_funded":1,"date_created":"2025-03-02T23:01:52Z","volume":134,"citation":{"ista":"Redchenko E, Zens M, Zemlicka M, Peruzzo M, Hassani F, Sett R, Zielinski PD, Dhar HS, Krimer DO, Rotter S, Fink JM. 2025. Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. 134(6), 063601.","ama":"Redchenko E, Zens M, Zemlicka M, et al. Observation of collapse and revival in a superconducting atomic frequency comb. <i>Physical Review Letters</i>. 2025;134(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">10.1103/PhysRevLett.134.063601</a>","chicago":"Redchenko, Elena, M. Zens, Martin Zemlicka, Matilda Peruzzo, Farid Hassani, Riya Sett, Przemyslaw D Zielinski, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">https://doi.org/10.1103/PhysRevLett.134.063601</a>.","ieee":"E. Redchenko <i>et al.</i>, “Observation of collapse and revival in a superconducting atomic frequency comb,” <i>Physical Review Letters</i>, vol. 134, no. 6. American Physical Society, 2025.","mla":"Redchenko, Elena, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” <i>Physical Review Letters</i>, vol. 134, no. 6, 063601, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">10.1103/PhysRevLett.134.063601</a>.","short":"E. Redchenko, M. Zens, M. Zemlicka, M. Peruzzo, F. Hassani, R. Sett, P.D. Zielinski, H.S. Dhar, D.O. Krimer, S. Rotter, J.M. Fink, Physical Review Letters 134 (2025).","apa":"Redchenko, E., Zens, M., Zemlicka, M., Peruzzo, M., Hassani, F., Sett, R., … Fink, J. M. (2025). Observation of collapse and revival in a superconducting atomic frequency comb. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">https://doi.org/10.1103/PhysRevLett.134.063601</a>"},"file_date_updated":"2025-03-04T10:40:50Z","language":[{"iso":"eng"}],"day":"14","oa_version":"Published Version","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"abstract":[{"lang":"eng","text":"Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics."}],"file":[{"access_level":"open_access","date_created":"2025-03-04T10:40:50Z","file_name":"2025_PhysReviewLetters_Redchenko.pdf","date_updated":"2025-03-04T10:40:50Z","creator":"dernst","file_size":2080408,"relation":"main_file","content_type":"application/pdf","success":1,"file_id":"19291","checksum":"633d6c5ddd9b805da22c5839d3d48df6"}],"title":"Observation of collapse and revival in a superconducting atomic frequency comb","OA_type":"hybrid","acknowledgement":"The authors thank G. Arnold and R. Sahu for the discussions, L. Drmic for software development, the MIBA workshop and the ISTA nanofabrication facility for technical support, and VTT Technical Research Centre of Finland for providing us TWPAs for follow-up measurements. This work was supported by the Austrian Science Fund (FWF) [Grant DOI: 10.55776/F71] through BeyondC (F7105) and IST Austria. E. S. R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J. M. F. and M. Ž. acknowledge support from the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant.","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19533"}]},"article_processing_charge":"Yes (via OA deal)","publication":"Physical Review Letters","has_accepted_license":"1","arxiv":1,"publication_status":"published","date_published":"2025-02-14T00:00:00Z","ddc":["530"],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1103/PhysRevLett.134.063601","oa":1,"pmid":1,"issue":"6","_id":"19280","year":"2025","article_number":"063601","scopus_import":"1","article_type":"original","isi":1,"month":"02","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"project":[{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"},{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"}]},{"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"corr_author":"1","doi":"10.15479/AT-ISTA-20212","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_created":"2025-08-22T14:07:00Z","date_updated":"2026-10-02T12:16:56Z","author":[{"first_name":"Osvaldo","last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889"}],"status":"public","publisher":"Institute of Science and Technology Austria","title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM","doi_confirm":"1","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"20230","checksum":"3331f76bbef74ff4908e2d2c9262045c","access_level":"closed","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx","date_updated":"2026-08-26T22:30:02Z","date_created":"2025-08-26T09:03:50Z","creator":"omiranda","file_size":32887334,"relation":"source_file"},{"creator":"omiranda","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf","date_created":"2025-08-26T09:05:55Z","embargo":"2026-08-26","date_updated":"2026-08-26T22:30:02Z","access_level":"open_access","file_size":28636240,"relation":"main_file","content_type":"application/pdf","checksum":"02509d50cff8e35c5bcbf71e8d658176","file_id":"20231"}],"abstract":[{"lang":"eng","text":"Cortical development has been studied for many decades and with each passing year, we learn \r\nmore about the processes that govern the tightly regulated developmental program. Up until \r\nrecently, the field has struggled to gain reliable access to progenitors at the single-cell level, \r\nlimiting the resolution at which we can study cortical development in vivo. Therefore, much of \r\nthe data we have on mammalian cortical development is at the cell population level. The \r\nsubsequent pages of this thesis describe novel elements of cortical development in mice; \r\nacquired using a candidate gene approach in conjunction with Mosaic Analysis with Double \r\nMarkers (MADM) to achieve single cell resolution. In this thesis, I briefly provide an overview \r\nof the state of the field, describe the methodology used to quantify morphological \r\ncharacteristics of neurons and glia, and delve into the role of Phosphatase and tensin \r\nhomologue on chromosome ten (Pten) in neurogenesis and gliogenesis in the developing mouse \r\ncortex. By using MADM to generate genetic mosaics, in which only a small fraction of cells \r\nare mutated, to study population-level changes, we can bypass the early postnatal lethality \r\nreported in Pten conditional knockouts (cKOs) using Emx1-Cre. We used Emx1-CreERT2 to \r\ninduce clonal deletion of Pten, and quantify RGP neurogenic output at the single progenitor \r\nlevel. Pten-mutant neuron populations within the mosaics were significantly expanded. In the \r\nlatter parts of this thesis, we describe how Pten deletion leads to an increase in the abundance \r\nof astrocytes. We availed ourselves of the flexibility offered by the MADM system to generate \r\nPten mosaics within a series of distinct knockout tissues to test for the interactions between \r\nPten and a battery of genes involved in distinct pro-gliogenic signaling pathways. Our survey \r\nof Pten’s interactions with genes in key signaling pathways reveals that ERK1/2 are the critical \r\neffectors downstream of EGFR signaling essential for gliogenesis. Altogether, our results \r\ndemonstrate that Pten plays critical and distinct roles throughout cortical RGP lineage \r\nprogression. "}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"17425"}]},"acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253).","article_processing_charge":"No","supervisor":[{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"citation":{"ista":"Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria.","apa":"Miranda, O. (2025). <i>Unraveling the role of Pten in cortical stem cell lineage progression using MADM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>","mla":"Miranda, Osvaldo. <i>Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>.","short":"O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025.","ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025.","chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>.","ama":"Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>"},"file_date_updated":"2026-08-26T22:30:02Z","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-063-3"],"issn":["2663-337X"]},"oa_version":"Published Version","day":"22","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.15479/AT-ISTA-20212","oa":1,"has_accepted_license":"1","date_published":"2025-08-22T00:00:00Z","publication_status":"published","ddc":["570"],"type":"dissertation","page":"119","month":"08","keyword":["Pten","mtor","cortical development","MADM","Mapk"],"project":[{"grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"}],"_id":"20212","degree_awarded":"PhD","year":"2025"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.15479/AT-ISTA-20117","oa":1,"has_accepted_license":"1","publication_status":"published","date_published":"2025-08-04T00:00:00Z","page":"108","type":"dissertation","ddc":["580"],"month":"08","_id":"20117","degree_awarded":"PhD","year":"2025","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"corr_author":"1","OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.15479/AT-ISTA-20117","author":[{"first_name":"Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425","last_name":"Wang","full_name":"Wang, Yiqun"}],"date_created":"2025-08-04T15:24:21Z","date_updated":"2026-10-02T12:33:36Z","status":"public","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Auxin is essential for many aspects of plant growth and development, from \r\nembryogenesis to organ senescence. Polar auxin transport leads to local auxin maxima and \r\ngradients, which are important for regulating various plant development process, including \r\nembryogenesis, organogenesis and vascular tissue formation. The polar auxin transport is \r\nmediated by auxin influx carrier AUX1/LAX proteins and efflux carrier PIN proteins. The \r\nregulation of PIN proteins is a key convergence of crosstalk between auxin and other \r\nhormones, such as cytokinin. Cytokinin promotes the degradation of PIN1 in Arabidopsis \r\nroots, preferentially the dephosphorylated PIN1, and the process is independent of \r\ntranscription and translation (Marhavý et al., 2011; Marhavý et al., 2014). The internalization \r\nof PIN proteins from plasma membrane is controlled by clathrin-mediated endocytosis \r\n(Dhonukshe et al., 2007; Kitakura et al., 2011). However, whether cytokinin affects the PIN1 \r\ndegradation through regulating the phosphorylation of PIN1 or trafficking components is \r\nunknown. Here, we demonstrate that dynamin related protein DRP2s are required for the \r\ncytokinin regulated trafficking of PIN1 and PIN2 in Arabidopsis root epidermal cells. Despite \r\nthe reported redundancy of DRP2A and DRP2B in gametophyte development, we found that \r\nCK-mediated PIN1 degradation and –induced PIN2 membrane localization is affected in drp2a \r\nor drp2b single mutants. Interestingly, we found that cytokinin regulates the recruitment of \r\nDRP2A—but not DRP2B—to clathrin-coated pits, and affects the stability and plasma \r\nmembrane localization of DRP2A. Furthermore, we studied the involvement of cytokinin \r\nreceptors in the regulation of cytokinin on DRP2A. Additionally, the assembly and disassembly \r\ncycle of dynamin is mediated by its dephosphorylation and phosphotylation cycle; thus, we \r\ninvestigated the role of DRP2A phosphorylation in its cytokinin-regulated assembly and in \r\ncytokinin-regulated PIN trafficking. Altogether, we found that cytokinin regulated PIN \r\ntrafficking in Arabidopsis root epidermal cells involves modulation of the phosphorylation of \r\nendocytosis accessory protein DRP2A. ","lang":"eng"}],"file":[{"creator":"yiqwang","file_name":"2025_Wang_Yiqun_Thesis.docx","date_created":"2025-08-22T08:22:10Z","date_updated":"2026-09-03T22:30:03Z","access_level":"closed","file_size":25798848,"relation":"source_file","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20209","checksum":"36b87c17d12c7bf5955d6d812acb8d77"},{"checksum":"8d7a2383f66377da675d379ec30ea0fe","file_id":"20211","content_type":"application/pdf","file_size":12628313,"relation":"main_file","access_level":"open_access","creator":"yiqwang","date_created":"2025-08-22T10:32:30Z","file_name":"2025_Wang_Yiqun_Thesis.pdf","embargo":"2026-09-03","date_updated":"2026-09-03T22:30:03Z"}],"title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","doi_confirm":"1","acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"18063"}]},"supervisor":[{"first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"article_processing_charge":"No","citation":{"ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>.","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file_date_updated":"2026-09-03T22:30:03Z","day":"04","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]}},{"publication":"Plant Journal","has_accepted_license":"1","date_published":"2025-08-01T00:00:00Z","publication_status":"published","ddc":["580"],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"fulldoi":"https://doi.org/10.1111/tpj.70396","issue":"3","pmid":1,"_id":"20187","article_number":"e70396","year":"2025","article_type":"original","scopus_import":"1","month":"08","isi":1,"PlanS_conform":"1","project":[{"grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","publisher":"Wiley","intvolume":"       123","OA_place":"publisher","department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"corr_author":"1","quality_controlled":"1","doi":"10.1111/tpj.70396","external_id":{"isi":["001547884300001"],"pmid":["40782342"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_created":"2025-08-17T22:01:36Z","author":[{"id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic","full_name":"Babic, David","first_name":"David"},{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","last_name":"Abualia","first_name":"Rashed"},{"last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas"},{"orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","full_name":"Qi, Linlin","first_name":"Linlin"},{"full_name":"Tellier, Frédérique","last_name":"Tellier","first_name":"Frédérique"},{"last_name":"Smoljan","id":"cced8a85-223e-11ed-af04-b0596c55053b","full_name":"Smoljan, Adrijana","first_name":"Adrijana"},{"first_name":"Hana","full_name":"Rakusova, Hana","last_name":"Rakusova","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA"},{"first_name":"Petr","last_name":"Valošek","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","full_name":"Valošek, Petr"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva"},{"first_name":"Jean Denis","last_name":"Faure","full_name":"Faure, Jean Denis"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"date_updated":"2026-11-05T23:31:14Z","citation":{"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>","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>.","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).","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.","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>","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."},"volume":123,"language":[{"iso":"eng"}],"file_date_updated":"2025-09-01T14:09:31Z","publication_identifier":{"eissn":["1365-313X"],"issn":["0960-7412"]},"oa_version":"Published Version","day":"01","title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","file":[{"relation":"main_file","file_size":5791111,"date_created":"2025-09-01T14:09:31Z","creator":"dernst","file_name":"2025_PlantJournal_Babic.pdf","date_updated":"2025-09-01T14:09:31Z","access_level":"open_access","checksum":"1cdc3341d2d23101abca72521f1f23cb","file_id":"20264","success":1,"content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development."}],"OA_type":"hybrid","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).","related_material":{"record":[{"relation":"dissertation_contains","id":"20362","status":"public"}]},"article_processing_charge":"Yes (via OA deal)"},{"status":"public","publisher":"Institute of Science and Technology Austria","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/AT-ISTA-20362","date_created":"2025-09-17T13:28:01Z","author":[{"id":"db566d23-f6e0-11ea-865d-e6f270e968e7","full_name":"Babic, David","last_name":"Babic","first_name":"David"}],"date_updated":"2026-10-16T07:59:32Z","citation":{"short":"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>.","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>","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.","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>.","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file_date_updated":"2026-09-25T22:30:02Z","day":"18","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Arabidopsis embryo has long served as a model system for understanding how plant body \r\npatterning and axis establishment arise. Previous work established that auxin flows, directed \r\nby polar transport and reinforced by local biosynthesis, underpin axes formation, while recent \r\nstudies suggest that maternal tissue, membrane composition and surface receptor signaling add \r\nfurther regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which \r\nguide plant embryonic and post-embryonic development. We review methodological advances \r\nthat allow the embryo to be imaged and studied. These tools offer exciting venues for future \r\naddressing of outstanding research questions. Furthermore, we dissect the contribution of \r\nmaternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments \r\nlowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens \r\nthe initial apical maximum. The resulting deficit dampens downstream embryonic auxin \r\nbiosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided \r\nauxin controls auxin flows in the embryos on a larger scale than previously understood. \r\nIntriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases \r\nTMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be \r\npreferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK \r\nactivity arrests embryos, affects seedling development and persists into adult growth, \r\nsuggesting that maternal effect could shape development beyond fertilization and early \r\nembryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane \r\ncomposition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid \r\nmetabolism triggers widespread patterning errors. \r\nTogether, these results reposition early plant patterning as a hierarchical cascade that begins \r\nwith maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated \r\nby maternal receptor signaling and could ultimately be gated by the biophysical properties of \r\nthe membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking \r\ninto a single narrative, this thesis helps shifting the approach of viewing the embryo as an \r\nautonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal \r\ncontext."}],"file":[{"relation":"main_file","file_size":7501548,"access_level":"open_access","file_name":"2025_David_Babic_Thesis.pdf","embargo":"2026-09-25","date_updated":"2026-09-25T22:30:02Z","creator":"dbabic","date_created":"2025-09-24T13:43:14Z","file_id":"20388","checksum":"5ecf274281a54a41e0288bc79edf7492","content_type":"application/pdf"},{"checksum":"2703e548390de0a1af7a707137e8ab3b","file_id":"20389","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":23206052,"relation":"source_file","creator":"dbabic","file_name":"Thesis_Babic_draft.docx","date_created":"2025-09-24T13:43:14Z","date_updated":"2026-09-25T22:30:02Z","access_level":"closed"}],"doi_confirm":"1","title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","related_material":{"record":[{"status":"public","id":"20187","relation":"part_of_dissertation"}]},"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"}],"article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","date_published":"2025-09-18T00:00:00Z","page":"116","ddc":["580"],"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.15479/AT-ISTA-20362","oa":1,"_id":"20362","degree_awarded":"PhD","year":"2025","month":"09","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"main_file_link":[{"url":"https://doi.org/10.1101/2025.05.20.655037","open_access":"1"}],"status":"public","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}],"OA_place":"repository","doi":"10.1101/2025.05.20.655037","author":[{"full_name":"Dunajova, Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","last_name":"Tasciyan","first_name":"Saren","orcid":"0000-0003-1671-393X"},{"first_name":"Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","full_name":"Majek, Juraj","last_name":"Majek"},{"first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"first_name":"Erik","last_name":"Sahai","full_name":"Sahai, Erik"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"}],"date_created":"2026-03-11T08:40:06Z","date_updated":"2026-11-05T23:31:13Z","citation":{"ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. .","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.).","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>"},"language":[{"iso":"eng"}],"day":"25","oa_version":"Preprint","abstract":[{"text":"While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.","lang":"eng"}],"title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","related_material":{"record":[{"status":"public","id":"21439","relation":"research_data"},{"status":"public","id":"22963","relation":"later_version"},{"id":"21423","status":"public","relation":"dissertation_contains"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","acknowledgement":"European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360","das_tickbox":"1","article_processing_charge":"No","has_accepted_license":"1","publication":"bioRxiv","publication_status":"draft","date_published":"2025-09-25T00:00:00Z","ddc":["539","570"],"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1101/2025.05.20.655037","oa":1,"_id":"21427","year":"2025","month":"09","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"grant_number":"101071793","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"},{"grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}]},{"has_accepted_license":"1","type":"dissertation","ddc":["570"],"page":"102","date_published":"2025-09-24T00:00:00Z","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.15479/AT-ISTA-20393","oa":1,"_id":"20393","year":"2025","degree_awarded":"PhD","month":"09","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"status":"public","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT-ISTA-20393","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"OA_place":"publisher","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"AnKi"},{"_id":"EdHa"}],"author":[{"orcid":"0000-0001-6060-4795","last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","first_name":"Kasumi"}],"date_updated":"2026-10-16T08:31:16Z","date_created":"2025-09-25T10:08:10Z","file_date_updated":"2026-09-30T22:30:04Z","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"citation":{"ama":"Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>","ieee":"K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025.","chicago":"Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>.","mla":"Kishi, Kasumi. <i>Regulation of Notochord and Floor Plate Size during Mouse Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>.","short":"K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025.","apa":"Kishi, K. (2025). <i>Regulation of notochord and floor plate size during mouse development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>","ista":"Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria."},"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","day":"24","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"18481"}]},"doi_confirm":"1","title":"Regulation of notochord and floor plate size during mouse development","abstract":[{"text":"During vertebrate development, the morphogen Sonic Hedgehog (Shh) plays a key role in \r\npatterning the tissues of the extending body. This requires precise coordination between the \r\nsize of the source of Shh production and the embryo body. Shh is produced by the notochord, \r\nas well as floorplate of the neural tube. In this thesis, we investigated how the sizes of the \r\nnotochord and floorplate are regulated and how they impact the developing mouse embryo.  \r\nTo measure the size and shape of the developing mouse notochord and the cell behaviours \r\nwithin this organ, we performed high-resolution measurements in cleared embryos between \r\nE8.5 and E10.5 of development. Strikingly, our data revealed that the notochord maintains a \r\nconstant cross-sectional area throughout the trunk over time as it lengthens by cell \r\nproliferation. We show that this is achieved by a feedback between the notochord cell \r\nproliferation rate and both the cross-sectional area of the trunk notochord and elongation of \r\nthe embryo. Using live imaging, we further show that notochord cells undergo posteriorly\r\ndirected active cell migration and that this cell migration contributes to maintaining the \r\nstructural integrity of the notochord. Our results show a complex coordination of cell \r\nbehaviours that allow for robust notochord morphogenesis during mouse development and \r\nthe maintenance of a defined Shh source size.  \r\nShh produced by the notochord induces a secondary Shh-producing domain, the floor plate. \r\nHow the notochord and floor plate contribute to the formation of the Shh gradient in the \r\nneural tube and to the regulation of the floor plate size is poorly understood. Our theoretical \r\nand experimental analysis indicates that only the initial levels of notochord-derived Shh \r\ninfluence the size of the floor plate, and the floor plate is insensitive to its own production of \r\nShh. After its initial establishment, the floor plate expands by tissue growth, leading to scaling \r\nof the Shh gradient amplitude with tissue size.   \r\nAltogether, we show that the mechanisms regulating the sizes of the notochord and \r\nfloorplate in mouse development help to achieve size robustness of these tissues. Our data \r\ndemonstrate that the initial establishment of the Shh gradient in the neural tube is strongly \r\ndependent on the notochord and suggest that the robustness of notochord morphogenesis \r\nis essential for pattern formation. Later in development, the floor plate size and the Shh \r\ngradient are coupled to neural tube growth. Our findings provide new insights on how pattern \r\nformation, tissue growth and morphogenesis interact to ensure reproducible developmental \r\noutcomes. ","lang":"eng"}],"file":[{"relation":"source_file","file_size":41847994,"access_level":"closed","creator":"kkishi","file_name":"2025-Kishi-Kasumi-Thesis.zip","date_created":"2025-09-30T14:33:17Z","date_updated":"2026-09-30T22:30:04Z","checksum":"6bb5a7ce318dc3f7bd165f2523e77b89","file_id":"20413","content_type":"application/x-zip-compressed","embargo_to":"open_access"},{"content_type":"application/pdf","file_id":"20414","checksum":"88349b9177e1dcbe1242cd3884b36fdb","access_level":"open_access","date_updated":"2026-09-30T22:30:04Z","embargo":"2026-09-30","creator":"kkishi","date_created":"2025-09-30T14:33:22Z","file_name":"2025-Kishi-Kasumi-Thesis.pdf","file_size":55747072,"relation":"main_file"}],"article_processing_charge":"No","supervisor":[{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}]},{"month":"09","keyword":["Auxin Signaling","Plant Development"],"_id":"20364","year":"2025","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.15479/AT-ISTA-20364","oa":1,"has_accepted_license":"1","ddc":["580"],"type":"dissertation","page":"151","date_published":"2025-09-19T00:00:00Z","publication_status":"published","related_material":{"record":[{"status":"public","id":"12291","relation":"part_of_dissertation"},{"id":"19399","status":"public","relation":"part_of_dissertation"}]},"acknowledgement":"Plant Facility,\r\nProtein Service Facility","title":"Nuclear and cell surface auxin signaling in A. thaliana developmental transitions","doi_confirm":"1","file":[{"checksum":"536ba1701453b0b2346be14c046b2911","file_id":"20390","content_type":"application/pdf","relation":"main_file","file_size":14278965,"access_level":"open_access","embargo":"2026-09-30","creator":"cgiannin","date_updated":"2026-09-30T22:30:03Z","file_name":"2025_Giannini_Caterina_Thesis...pdf","date_created":"2025-09-24T14:46:34Z"},{"date_created":"2025-09-24T14:46:35Z","file_name":"2025_Giannini_Caterina_Thesis...docx","date_updated":"2026-09-30T22:30:03Z","creator":"cgiannin","access_level":"closed","relation":"source_file","file_size":24499022,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"192f55262f2da2ea0a59d9c23a1b8573","file_id":"20391"}],"abstract":[{"text":"Auxin is a central regulator of plant growth and development, orchestrating processes from \r\nembryogenesis to senescence through a complex network of biosynthesis, transport, and \r\nsignaling pathways.  \r\nIn Arabidopsis thaliana, canonical nuclear auxin signaling is mediated by the TIR1/AFB \r\nreceptors, which promote degradation of AUX/IAA repressors to enable ARF transcription \r\nfactors-driven transcriptional reprogramming. Parallel to this well-established nuclear \r\nmechanism, auxin also triggers rapid, non-transcriptional responses. In particular, at the cell \r\nsurface, most notably through ABP1 and TMKs. Despite decades of research, the integration \r\nof these pathways and their links to fundamental cellular processes remains not fully \r\nunderstood.  \r\nIn this study, we uncover a new role for TIR1/AFB signaling in rapidly activating \r\nmacroautophagy during developmental reprogramming. Auxin induces autophagy via \r\nTIR1/AFB adenylate cyclase activity, linking auxin perception to cAMP production and \r\ntranscriptional activation of autophagy machinery. Autophagy-deficient mutants exhibit \r\ndelayed meristem differentiation, impaired lateral root progression, and reduced shoot \r\norganogenesis, demonstrating its necessity for timely developmental transitions. \r\nWe also revisit the ABP1-TMK1 cell-surface auxin perception complex, providing \r\nbiochemical and mass photometry evidence for auxin-dependent complex formation. We show \r\nthat ABP1-TMK1 triggers an ultrafast global phosphorylation response targeting ~1000 \r\nproteins, including the auxin transporter PIN2, and Rho-of-plants (ROP) GTPases regulators. \r\nThis pathway directly regulates PIN2 phosphorylation, for gravitropism and auxin dependent \r\nROP activation. \r\nThese findings establish an integrated framework in which nuclear TIR1/AFB signaling and \r\ncell-surface ABP1-TMK signaling act in parallel to synchronize gene expression, cytoplasmic \r\nremodelling, and transporter regulation, thereby ensuring robust developmental plasticity in \r\nArabidopsis thaliana. ","lang":"eng"}],"article_processing_charge":"No","supervisor":[{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"file_date_updated":"2026-09-30T22:30:03Z","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"citation":{"ista":"Giannini C. 2025. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria.","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>","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>.","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>.","ieee":"C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025.","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>"},"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","day":"19","doi":"10.15479/AT-ISTA-20364","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"corr_author":"1","author":[{"first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina","last_name":"Giannini"}],"date_updated":"2026-10-16T08:24:09Z","date_created":"2025-09-19T12:23:38Z","status":"public","publisher":"Institute of Science and Technology Austria"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1101/2022.11.30.518503","oa":1,"publication":"bioRxiv","ddc":["580"],"type":"preprint","date_published":"2025-02-20T00:00:00Z","publication_status":"draft","month":"02","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425","name":"Cell surface receptor complexes for auxin signaling in plants"}],"_id":"19399","year":"2025","doi":"10.1101/2022.11.30.518503","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"OA_place":"repository","department":[{"_id":"JiFr"},{"_id":"XiFe"}],"corr_author":"1","date_updated":"2026-11-05T23:31:15Z","date_created":"2025-03-13T08:36:48Z","ec_funded":1,"author":[{"last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","orcid":"0000-0002-7244-7237"},{"full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","last_name":"Fiedler","first_name":"Lukas"},{"full_name":"Zou, Minxia","last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia"},{"first_name":"Caterina","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline"},{"full_name":"Vladimirtsev, Dmitrii","last_name":"Vladimirtsev","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","first_name":"Dmitrii"},{"first_name":"Marek","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch"},{"first_name":"Yongfan","full_name":"Yu, Yongfan","last_name":"Yu"},{"first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195"},{"full_name":"Chen, Meng","last_name":"Chen","first_name":"Meng"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang","orcid":"0000-0002-0471-8285"},{"orcid":"0000-0001-8295-2926","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","last_name":"Hörmayer"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"last_name":"Marques-Bueno","full_name":"Marques-Bueno, Maria Mar","first_name":"Maria Mar"},{"full_name":"Quddoos, Zainab","last_name":"Quddoos","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","first_name":"Zainab"},{"last_name":"Molnar","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"full_name":"Kulich, Ivan","last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan"},{"last_name":"Jaillais","full_name":"Jaillais, Yvon","first_name":"Yvon"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.11.30.518503"}],"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","related_material":{"record":[{"relation":"dissertation_contains","id":"19395","status":"public"},{"status":"public","id":"20656","relation":"later_version"},{"relation":"dissertation_contains","id":"20364","status":"public"}]},"title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","das_tickbox":"1","language":[{"iso":"eng"}],"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>.","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>. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/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.).","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>, doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">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>, n.d. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/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>. .","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>"},"oa_version":"Published Version","day":"20"},{"year":"2025","degree_awarded":"PhD","_id":"19763","project":[{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"month":"05","ddc":["570"],"type":"dissertation","page":"129","date_published":"2025-05-29T00:00:00Z","publication_status":"published","has_accepted_license":"1","oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-19763","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"day":"29","file_date_updated":"2025-11-30T23:30:02Z","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"citation":{"ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria.","chicago":"Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>.","ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025.","ama":"Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>","apa":"Rus, S. (2025). <i>Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>","mla":"Rus, Stefanie. <i>Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>.","short":"S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025."},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna"}],"acknowledgement":"My work would also not have been possible without the Imaging and Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has facilitated my research substantially. I\r\nalso want to thank the Graduate School Office for their never-ending support and their sincere\r\neffort to improve the PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank you for recognizing the importance of this project.","related_material":{"record":[{"relation":"part_of_dissertation","id":"13136","status":"public"},{"id":"17148","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18601"},{"id":"18807","status":"public","relation":"part_of_dissertation"}]},"title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","file":[{"access_level":"open_access","creator":"cchlebak","file_name":"Thesis_Lehr_PDFA.pdf","date_updated":"2025-11-30T23:30:02Z","embargo":"2025-11-30","date_created":"2025-05-30T09:10:22Z","file_size":42879974,"relation":"main_file","content_type":"application/pdf","checksum":"8cd7fe3ca990adbcafdece119aa0973d","file_id":"19764"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"0c87dd5fc803450a47b20736b5f86a2f","file_id":"19765","access_level":"closed","creator":"cchlebak","date_created":"2025-05-30T09:31:15Z","date_updated":"2025-11-30T23:30:02Z","file_name":"Thesis_Lehr_emptyPages.docx","relation":"source_file","file_size":18731094}],"abstract":[{"text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","status":"public","date_created":"2025-05-30T09:14:58Z","date_updated":"2026-10-20T08:57:07Z","author":[{"orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie","last_name":"Rus","first_name":"Stefanie"}],"doi":"10.15479/AT-ISTA-19763","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"OA_place":"publisher","department":[{"_id":"AnKi"},{"_id":"GradSch"}],"corr_author":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1016/j.devcel.2024.10.024","oa":1,"publication":"Developmental Cell","has_accepted_license":"1","ddc":["570"],"type":"journal_article","page":"567-580","date_published":"2025-02-24T00:00:00Z","publication_status":"published","month":"02","isi":1,"article_type":"original","scopus_import":"1","project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"dataavailabilitystatement":"RNA-seq data has been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. Code for the quantification of fluorescence intensity (FI) profiles in differentiated cells on stencils, as well as for model simulations, is available on GitHub (https://github.com/dbrueckner/NeuralTubeColonies, https://doi.org/10.5281/zenodo.13335390","_id":"18807","issue":"4","pmid":1,"year":"2025","doi":"10.1016/j.devcel.2024.10.024","quality_controlled":"1","external_id":{"pmid":["39603235"],"isi":["001434279000001"]},"OA_place":"publisher","intvolume":"        60","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"corr_author":"1","date_updated":"2026-11-05T23:31:16Z","date_created":"2025-01-09T11:25:47Z","author":[{"orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie"},{"orcid":"0000-0001-7205-2975","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","last_name":"Brückner"},{"first_name":"Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas"},{"first_name":"Martina","id":"48A59534-F248-11E8-B48F-1D18A9856A87","last_name":"Greunz","full_name":"Greunz, Martina"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publisher":"Cell Press","researchdata_availability":"yes","OA_type":"hybrid","related_material":{"record":[{"id":"19763","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","supplementarymaterial":"yes","title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","file":[{"access_level":"open_access","date_created":"2025-04-16T10:54:07Z","creator":"dernst","date_updated":"2025-04-16T10:54:07Z","file_name":"2025_DevelopmentalCell_Lehr.pdf","relation":"main_file","file_size":6994499,"content_type":"application/pdf","success":1,"file_id":"19584","checksum":"bb58db4a908a1f4aabe4004706154541"}],"abstract":[{"text":"Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","das_tickbox":"1","file_date_updated":"2025-04-16T10:54:07Z","language":[{"iso":"eng"}],"citation":{"ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>","chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Cell Press, pp. 567–580, 2025.","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580.","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Cell Press, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>.","apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>","ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580."},"volume":60,"oa_version":"Published Version","publication_identifier":{"issn":["1534-5807"]},"day":"24"},{"title":"Using genealogies to study the genomic basis of species divergence","abstract":[{"lang":"eng","text":"Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us."}],"file":[{"file_size":42723135,"relation":"main_file","access_level":"open_access","file_name":"2025_Pal_Arka_Thesis.pdf","creator":"apal","date_created":"2025-12-01T13:53:36Z","date_updated":"2026-03-01T23:30:03Z","embargo":"2026-03-01","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","file_id":"20721","content_type":"application/pdf"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20722","checksum":"166d832b08d0434ce407f8f3cb930fe5","access_level":"closed","date_created":"2025-12-01T13:53:39Z","file_name":"2025_Pal_Arka_Thesis.docx","date_updated":"2026-03-01T23:30:03Z","creator":"apal","relation":"source_file","file_size":60632116}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"12159","status":"public"},{"id":"20190","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14796","status":"public"}]},"article_processing_charge":"No","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"citation":{"apa":"Pal, A. (2025). <i>Using genealogies to study the genomic basis of species divergence</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>","short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025.","mla":"Pal, Arka. <i>Using Genealogies to Study the Genomic Basis of Species Divergence</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>.","ieee":"A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025.","chicago":"Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>.","ama":"Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria."},"language":[{"iso":"eng"}],"file_date_updated":"2026-03-01T23:30:03Z","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","day":"25","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"corr_author":"1","doi":"10.15479/AT-ISTA-20694","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","last_name":"Pal","first_name":"Arka"}],"date_created":"2025-11-25T13:19:11Z","date_updated":"2026-10-21T08:23:54Z","status":"public","publisher":"Institute of Science and Technology Austria","month":"11","project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"_id":"20694","degree_awarded":"PhD","year":"2025","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","fulldoi":"https://doi.org/10.15479/AT-ISTA-20694","oa":1,"has_accepted_license":"1","date_published":"2025-11-25T00:00:00Z","publication_status":"published","ddc":["576","578"],"type":"dissertation","page":"268"},{"status":"public","publisher":"Wiley","OA_place":"publisher","intvolume":"        34","department":[{"_id":"NiBa"}],"corr_author":"1","quality_controlled":"1","doi":"10.1111/mec.70067","external_id":{"isi":["001546622100001"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2025-08-17T22:01:37Z","author":[{"orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","full_name":"Pal, Arka","first_name":"Arka"},{"orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria"},{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"},{"full_name":"Mcnairn, Adrian J.","last_name":"Mcnairn","first_name":"Adrian J."},{"first_name":"Jennifer K.","full_name":"Grenier, Jennifer K.","last_name":"Grenier"},{"full_name":"Kucka, Marek","last_name":"Kucka","first_name":"Marek"},{"full_name":"Coop, Graham","last_name":"Coop","first_name":"Graham"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"}],"date_updated":"2026-11-05T23:31:17Z","citation":{"ista":"Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.","chicago":"Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K. Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>.","ieee":"A. Pal <i>et al.</i>, “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” <i>Molecular Ecology</i>, vol. 34, no. 22. Wiley, 2025.","ama":"Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. 2025;34(22). doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>","apa":"Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka, M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>","mla":"Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>, vol. 34, no. 22, e70067, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>.","short":"A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G. Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025)."},"volume":34,"file_date_updated":"2026-01-05T13:47:47Z","language":[{"iso":"eng"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"day":"01","title":"Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum","file":[{"content_type":"application/pdf","success":1,"file_id":"20958","checksum":"c586fc674df4e7dd6e43aef87a52c6f6","access_level":"open_access","file_name":"2025_MolecEcology_Pal.pdf","creator":"dernst","date_created":"2026-01-05T13:47:47Z","date_updated":"2026-01-05T13:47:47Z","relation":"main_file","file_size":9886694}],"abstract":[{"text":"A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"20694","status":"public"}],"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/snapdragon-secrets/","relation":"press_release"}]},"acknowledgement":"We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other Barton Group and Coop Lab members for stimulating discussions. We are grateful to all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón Mateu for her assistance in fieldwork logistics at the field station, El Serrat. We are grateful to Enrico Coen and his research group for providing the Antirrhinum molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up with sampling led by D.L.F. in 2017. The study was supported by Austrian Science Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.). Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics and analyses was provided by ISTA High Performance Cluster. ","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Molecular Ecology","date_published":"2025-11-01T00:00:00Z","publication_status":"published","ddc":["570"],"type":"journal_article","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","fulldoi":"https://doi.org/10.1111/mec.70067","oa":1,"issue":"22","_id":"20190","article_number":"e70067","year":"2025","scopus_import":"1","article_type":"original","isi":1,"month":"11","PlanS_conform":"1","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}}]