[{"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).","article_processing_charge":"No","_id":"19386","ddc":["570","576"],"alternative_title":["ISTA Thesis"],"status":"public","OA_place":"publisher","oa":1,"file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-03-26T23:30:03Z","creator":"melkrewi","relation":"source_file","file_id":"19462","embargo_to":"open_access","file_name":"Thesis_Marwan_Elkrewi.docx","date_created":"2025-03-26T07:06:56Z","file_size":25019680,"checksum":"5549a8216c07e4c39281648912d72246"},{"file_name":"Thesis_Marwan_Elkrewi.pdf","checksum":"aed2ba9965aa89b3414deae1ae9f4321","date_created":"2025-03-26T07:06:22Z","file_size":17294844,"file_id":"19463","relation":"main_file","creator":"melkrewi","embargo":"2026-03-26","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-03-26T23:30:03Z"}],"supervisor":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"page":"170","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2025-03-11T12:54:31Z","day":"14","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"03","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.15479/AT-ISTA-19386","language":[{"iso":"eng"}],"date_published":"2025-03-14T00:00:00Z","corr_author":"1","has_accepted_license":"1","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"file_date_updated":"2026-03-26T23:30:03Z","title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","OA_embargo":"12","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12248"},{"id":"10767","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"15009"},{"id":"14613","status":"public","relation":"part_of_dissertation"},{"id":"17890","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10167"}]},"year":"2025","date_updated":"2026-07-06T13:48:33Z","type":"dissertation","publication_identifier":{"isbn":["9783990780534"],"eissn":["2663-337X"]},"citation":{"short":"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.","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","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>.","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>","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>"},"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. "}],"oa_version":"Published Version","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231"}]},{"article_processing_charge":"No","_id":"20798","das_tickbox":"1","ddc":["530"],"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"page":"152","supervisor":[{"last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur"}],"file":[{"checksum":"1be72faf529a5e8a2d03cb3d5f808b77","date_created":"2025-12-12T11:53:42Z","file_size":47536855,"file_name":"2025_Wald_Sebastian_Thesis.pdf","date_updated":"2026-06-15T22:30:03Z","content_type":"application/pdf","access_level":"open_access","embargo":"2026-06-15","file_id":"20809","relation":"main_file","creator":"swald"},{"embargo_to":"open_access","checksum":"8c3a1904dceb4bcd04bc9f14b2594bab","date_created":"2025-12-12T11:54:55Z","file_size":40127601,"file_name":"2025_Wald_Sebastian_Thesis.zip","date_updated":"2026-06-15T22:30:03Z","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"20810","relation":"source_file","creator":"swald"}],"oa":1,"keyword":["entanglement-enhanced atom interferometry","cavity QED","spin-squeezing","dipole trap","quantum optics"],"publication_status":"published","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"day":"11","date_created":"2025-12-11T11:48:11Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-20798","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"12","language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2026-06-15T22:30:03Z","corr_author":"1","date_published":"2025-12-11T00:00:00Z","year":"2025","related_material":{"record":[{"id":"14759","status":"public","relation":"part_of_dissertation"}]},"OA_embargo":"6","title":"Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry","publication_identifier":{"isbn":["978-3-99078-075-6"],"issn":["2663-337X"]},"type":"dissertation","date_updated":"2026-07-24T08:07:28Z","abstract":[{"lang":"eng","text":"Atom interferometers measure the relative phase shifts between coherent matter-wave paths\r\nthat arise from interactions with external fields or inertial forces. Due to their exceptional\r\nphase sensitivity, atom interferometers became an essential tool for precision measurements\r\nand fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However, their measurement precision is limited by quantum projection noise,\r\nwhich arises from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates with absolute precision. The generation of entanglement between the atoms offers a\r\npath to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis thesis reports on the development of an atom interferometer experiment designed to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity that mediates all relevant atom-light interactions. The\r\ncavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates on the fundamental theoretical framework, the cavity design, and the full\r\noptical setup, including the detailed configuration of the developed laser stabilization methods.\r\nExperimentally, continuous loading methods were explored, resulting in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control\r\nwas verified via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity coupling.\r\nThese presented results establish the experimental groundwork for the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry."}],"citation":{"short":"S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry, Institute of Science and Technology Austria, 2025.","mla":"Wald, Sebastian. <i>Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>.","ieee":"S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry,” Institute of Science and Technology Austria, 2025.","chicago":"Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>.","ista":"Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria.","ama":"Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>","apa":"Wald, S. (2025). <i>Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>"},"doi_confirm":"1","author":[{"full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","orcid":"0000-0002-5869-1604","first_name":"Sebastian","last_name":"Wald"}],"oa_version":"Published Version"},{"year":"2025","title":"Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans","OA_embargo":"6 months","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"type":"journal_article","date_updated":"2026-07-28T11:30:41Z","abstract":[{"lang":"eng","text":"A dynamic interplay between fast synaptic signals and slower neuromodulatory signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits. The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance remain uncertain. We designed a genetic screen to isolate genes involved in the peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin (snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1). We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans, and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies [developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C. elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1 signaling alters the synapsin and actin cytoskeleton and increases neuropeptide release by cholinergic motor neurons, which secondarily affects the presynaptic vesicle cycle. Together, these results clarify the dominant mechanisms of action of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I balance in DEE70."}],"article_number":"e1767232024","citation":{"ama":"Stratigi A, Soler-García M, Krout M, et al. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. 2025;45(13). doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>","apa":"Stratigi, A., Soler-García, M., Krout, M., Shukla, S., de Bono, M., Richmond, J. E., &#38; Laurent, P. (2025). Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>","short":"A. Stratigi, M. Soler-García, M. Krout, S. Shukla, M. de Bono, J.E. Richmond, P. Laurent, Journal of Neuroscience 45 (2025).","ieee":"A. Stratigi <i>et al.</i>, “Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans,” <i>Journal of Neuroscience</i>, vol. 45, no. 13. Society for Neuroscience, 2025.","mla":"Stratigi, Aikaterini, et al. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>, vol. 45, no. 13, e1767232024, Society for Neuroscience, 2025, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>.","ista":"Stratigi A, Soler-García M, Krout M, Shukla S, de Bono M, Richmond JE, Laurent P. 2025. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 45(13), e1767232024.","chicago":"Stratigi, Aikaterini, Miguel Soler-García, Mia Krout, Shikha Shukla, Mario de Bono, Janet E. Richmond, and Patrick Laurent. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2025. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>."},"author":[{"first_name":"Aikaterini","last_name":"Stratigi","full_name":"Stratigi, Aikaterini"},{"first_name":"Miguel","last_name":"Soler-García","full_name":"Soler-García, Miguel"},{"last_name":"Krout","first_name":"Mia","full_name":"Krout, Mia"},{"first_name":"Shikha","last_name":"Shukla","full_name":"Shukla, Shikha"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario","last_name":"De Bono","first_name":"Mario","orcid":"0000-0001-8347-0443"},{"last_name":"Richmond","first_name":"Janet E.","full_name":"Richmond, Janet E."},{"first_name":"Patrick","last_name":"Laurent","full_name":"Laurent, Patrick"}],"oa_version":"Published Version","doi":"10.1523/JNEUROSCI.1767-23.2024","month":"03","scopus_import":"1","article_type":"original","language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2025-09-27T22:30:02Z","volume":45,"date_published":"2025-03-26T00:00:00Z","publication_status":"published","intvolume":"        45","issue":"13","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"pmid":1,"day":"26","date_created":"2025-04-06T22:01:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"19498","OA_type":"hybrid","isi":1,"acknowledgement":"P.L. is a research associate of the Belgian National Fund for Scientific Research (FRS-FNRS). K.S., M.S.-G., S.S., and P.L. are supported by grants from the FRS-FNRS. This work was supported by an Advanced ERC Grant (269058 ACMO) to M.D.B. We thank the team of Alexander Gottschalk for the snn-1(S9A) strain. We thank the Imaging Facility of the Faculty of Medicine (LiMiF) of the Universite Libre de Bruxelles, supported by FRS-FNRS. This work made use of instruments in the Electron Microscopy Core of the University of Illinois Chicago Research Resources Center as well as the BioCryo facility of Northwestern University's NUANCE Center, which has received support from the SHyNE Resource (NSF ECCS-2025633), the IIN, and Northwestern's MRSEC program (NSF DMR-2308691). Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440).","ddc":["570"],"external_id":{"pmid":["39919830"],"isi":["001460952700001"]},"quality_controlled":"1","OA_place":"publisher","publication":"Journal of Neuroscience","status":"public","publisher":"Society for Neuroscience","department":[{"_id":"MaDe"}],"oa":1,"file":[{"checksum":"7befc0168f4cd5bd2b0fcff9e2a94784","file_size":3111735,"date_created":"2025-04-07T11:57:19Z","file_name":"2025_JourNeuroscience_Stratigi.pdf","date_updated":"2025-09-27T22:30:02Z","content_type":"application/pdf","access_level":"open_access","embargo":"2025-09-27","file_id":"19525","relation":"main_file","creator":"dernst"}]},{"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"department":[{"_id":"JoFi"},{"_id":"GradSch"}],"page":"135","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"access_level":"closed","date_updated":"2026-01-29T23:30:03Z","content_type":"application/x-zip-compressed","creator":"cchlebak","relation":"source_file","file_id":"18946","embargo_to":"open_access","file_name":"tex for upload.zip","date_created":"2025-01-29T08:38:08Z","file_size":18856130,"checksum":"71872702e8f46c275eaea44efc4d304f"},{"creator":"cchlebak","file_id":"18947","relation":"main_file","embargo":"2026-01-29","access_level":"open_access","date_updated":"2026-01-29T23:30:03Z","content_type":"application/pdf","file_name":"ISTThesisGA2022_final.pdf","date_created":"2025-01-29T08:38:34Z","file_size":17344760,"checksum":"dfaa06591970f4bff163705802fad56d"}],"supervisor":[{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","_id":"18871","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020 research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN) and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n","ddc":["530"],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"day":"24","date_created":"2025-01-24T10:28:39Z","degree_awarded":"PhD","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","acknowledged_ssus":[{"_id":"SSU"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"corr_author":"1","has_accepted_license":"1","file_date_updated":"2026-01-29T23:30:03Z","project":[{"call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"ec_funded":1,"date_published":"2025-01-24T00:00:00Z","month":"01","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","doi":"10.15479/at:ista:18871","citation":{"ama":"Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>","apa":"Arnold, G. M. (2025). <i>Microwave-optic interconnects for superconducting circuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>","short":"G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits, Institute of Science and Technology Austria, 2025.","ista":"Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria.","chicago":"Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>.","ieee":"G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,” Institute of Science and Technology Austria, 2025.","mla":"Arnold, Georg M. <i>Microwave-Optic Interconnects for Superconducting Circuits</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>."},"abstract":[{"text":"\"Can we do this with a new type of computer - a quantum computer?\". This famous\r\nquotation of the brilliant Richard Feynman within a conference talk on \"Simulating physics\r\nwith computers.” is often reverently praised as the origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical. Now, 43 years later, the theoretical framework of how such\r\na computer can operate has been developed. Two main important concepts for a potential\r\nquantum supremacy, superposition and entanglement, have been exploited to design quantum\r\nalgorithms to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis still far from being certain, in fact the race between the most promising platforms such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well\r\nas spin qubits has recently intensified. If one also includes the most mature applications of\r\nquantum communication technologies, secure quantum key distribution and quantum random\r\nnumber generators, as part of a quantum information technology ecosystem, we are confronted\r\nwith a plethora of different materials, concepts, and also operation frequencies. While\r\nsuperconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently, a quantum frequency converter or microwave-optic transducer is required\r\nto interface the different frequency domains or establish a long-range network connection\r\nwith suitable telecom fibers. In fact, the combination of different frequency regimes is also\r\nan essential part in our classical modern communication network, where computations are\r\nperformed in electrical circuits and the information exchange over longer distances happens\r\nvia optical fibers. However, the specific challenges specific to building a quantum computer,\r\nalso apply to the development of such a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the carrier of information, i.e. the smallest possible quantity, the signal\r\ncan easily be corrupted by other noise sources which needs to be avoided by all means. This\r\nis also the reason why microwave quantum computers operate at temperature environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals cannot be copied which would be a typical\r\nstrategy to account for errors in classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic transducers: While quantum computers are operating in one specific frequency\r\ndomain, microwave-optic transducers combine microwave and optical fields in one device.\r\nThis results in the particular challenge that high-energy optical radiation, which is usually\r\nwell-shielded from superconducting microwave quantum processors, are now an essential part\r\nof the device. The concomitant optical radiation in the operating transducer will inevitably\r\nhave a detrimental effect on the superconducting microwave components. Together with the\r\nrequirement of minimal background noise for quantum-limited operation as described above,\r\nv\r\nheating from the absorption of optical photons within the same device where single microwave\r\nexcitations are processed forms a formidable challenge.\r\nThis thesis aims to address this challenge by developing microwave-optic transducers where\r\nthe impact of optical absorption on superconducting circuits in general and superconducting\r\nqubits specifically can be mitigated. In our first approach, we developed a compact device\r\nwith optimized interaction strengths between the different frequency domains. This minimizes\r\nthe optical powers used for transducer operation and thus the optical absorption heating. This\r\nwork was - to the best of our knowledge - the first comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately, we saw that the optical absorption heating added\r\nnoise way above a single excitation. Consequently, a potential quantum signal would have\r\nbeen buried in the noise, added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional microwave-optic transducer instead\r\nof an integrated device. The larger heat capacity of the macroscopic device with a size\r\nof a few millimeters can absorb a larger fraction of the optical heating before it increases\r\nthe temperature of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat the microwave-optic transducer can be operated in a regime in which optical fields don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic\r\ntransducers in conjunction with microwave quantum processors and brings the integration and\r\nseamless orchestration of different frequency components in a quantum network a step closer.\r\n","lang":"eng"}],"author":[{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","first_name":"Georg M","last_name":"Arnold"}],"oa_version":"Published Version","year":"2025","title":"Microwave-optic interconnects for superconducting circuits","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6609"},{"status":"public","relation":"part_of_dissertation","id":"8529"},{"relation":"part_of_dissertation","status":"public","id":"18953"},{"relation":"part_of_dissertation","status":"public","id":"10924"},{"id":"9114","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"13200"}]},"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-16T12:20:43Z"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14274"}]},"OA_embargo":"6","title":"Adaptive strategies of dendritic cell migration in response to environmental cues","year":"2025","date_updated":"2026-06-18T17:34:48Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-058-9"]},"type":"dissertation","abstract":[{"lang":"eng","text":"Cell migration is a crucial process in animal development and maintenance. It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment, where cells can switch between\r\nmigration modes as they encounter new environmental cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration strategy when encountering geometrically,\r\nmechanically and chemically distinct environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy, extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable. Instead, the cells use topography of the\r\nenvironment to propel their cell body forward. To migrate efficiently in the maze of different\r\npore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions into much denser environments with limited choice of large pores. In such invasive\r\ntransitions it is unclear if the cells can cross tight pores without the use of adhesions and\r\nextracellular proteolysis and whether they maintain the nucleus in the cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen gels, geometrically defined\r\nmicrochannels with constrictions and simplistic under agarose migration assay, we provide\r\na comprehensive characterization of invasive migration of dendritic cells. We show that\r\nduring invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody into the dense environment. In collagen gels, we show that dendritic cells can invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading\r\nto a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile force is simultaneously necessary for reverting the nucleus back to\r\nthe cell front after invasion and maintaining this positioning during permissive migration.\r\nA functional role of the reorientation was uncovered in the first collaboration project.\r\nA prominent central actin pool was identified around the MTOC, especially pronounced in\r\ndense and compressive environments. The actin pool was shown to generate pushing forces\r\nto dilate the space for cell translocation. These forces are only necessary in non-permissive\r\nenvironments, where the nucleus reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive environments where space generation is dispensable, the\r\nMTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second collaboration project, we investigated the effects of distinct chemical\r\nenvironments on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas explained by their ability to modulate and even self-generate chemokine gradients. This\r\nallows the cells to migrate faster and more persistent in uniform chemokine fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial\r\nplayer in this process, both sensing the signal and internalizing the chemokine to create a sink."}],"citation":{"chicago":"Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>.","ista":"Canigova N. 2025. Adaptive strategies of dendritic cell migration in response to environmental cues. Institute of Science and Technology Austria.","mla":"Canigova, Nikola. <i>Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>.","ieee":"N. Canigova, “Adaptive strategies of dendritic cell migration in response to environmental cues,” Institute of Science and Technology Austria, 2025.","short":"N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues, Institute of Science and Technology Austria, 2025.","apa":"Canigova, N. (2025). <i>Adaptive strategies of dendritic cell migration in response to environmental cues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>","ama":"Canigova N. Adaptive strategies of dendritic cell migration in response to environmental cues. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>"},"oa_version":"Published Version","author":[{"last_name":"Canigova","first_name":"Nikola","orcid":"0000-0002-8518-5926","id":"3795523E-F248-11E8-B48F-1D18A9856A87","full_name":"Canigova, Nikola"}],"month":"05","doi":"10.15479/AT-ISTA-19745","language":[{"iso":"eng"}],"date_published":"2025-05-27T00:00:00Z","ec_funded":1,"has_accepted_license":"1","file_date_updated":"2025-11-27T23:30:02Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"}],"corr_author":"1","publication_status":"published","day":"27","date_created":"2025-05-26T08:49:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","acknowledgement":"This project has received funding from the Austrian Science Fund (FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","article_processing_charge":"No","_id":"19745","ddc":["570"],"status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","supervisor":[{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"oa":1,"file":[{"relation":"source_file","file_id":"19748","creator":"cchlebak","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-11-27T23:30:02Z","file_name":"NikolaCanigova_Thesis_final.docx","checksum":"1a2d1525d19347fbb879ef57c02951bf","date_created":"2025-05-28T07:38:17Z","file_size":103879193,"embargo_to":"open_access"},{"file_size":194530600,"date_created":"2025-05-28T07:39:53Z","checksum":"c1d8f9a40a8e19fcf895373f4b773a46","file_name":"NikolaCanigova_Thesis_final_PDFA2a_fixed.pdf","content_type":"application/pdf","date_updated":"2025-11-27T23:30:02Z","access_level":"open_access","embargo":"2025-11-27","creator":"cchlebak","file_id":"19749","relation":"main_file"}],"publisher":"Institute of Science and Technology Austria","page":"133","department":[{"_id":"MiSi"},{"_id":"GradSch"}]},{"language":[{"iso":"eng"}],"corr_author":"1","has_accepted_license":"1","file_date_updated":"2026-02-01T23:30:02Z","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"ec_funded":1,"date_published":"2025-03-04T00:00:00Z","doi":"10.15479/AT-ISTA-19271","month":"03","citation":{"ama":"Önal C. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19271\">10.15479/AT-ISTA-19271</a>","apa":"Önal, C. (2025). <i>Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19271\">https://doi.org/10.15479/AT-ISTA-19271</a>","short":"C. Önal, Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula, Institute of Science and Technology Austria, 2025.","chicago":"Önal, Cihan. “Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19271\">https://doi.org/10.15479/AT-ISTA-19271</a>.","ista":"Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria.","mla":"Önal, Cihan. <i>Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19271\">10.15479/AT-ISTA-19271</a>.","ieee":"C. Önal, “Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula,” Institute of Science and Technology Austria, 2025."},"abstract":[{"lang":"eng","text":"The medial habenula (MHb) is implicated in regulating emotional responses\r\nto aversive events. Studies in zebrafish have identified a remarkable morphological\r\nleft-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian\r\nMHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in\r\nmodulating fear responses. However, there is little evidence for structural or\r\nfunctional lateralization in the mammalian MHb-IPN pathway.\r\nHere, I investigated the synaptic properties of the left and right MHb\r\nafferents to the IPN in mice and addressed whether these synaptic connections\r\nselectively influence the expression of conditioned fear in mice. My findings reveal\r\nthat each individual IPN neuron receives inputs from both left and right MHb.\r\nElectrophysiological recordings from the same postsynaptic IPN neurons\r\ndemonstrate that the left MHb-originating synapses exhibit lower release\r\nprobability and higher 𝛾-aminobutyric acid type B receptor (GABABR)-mediated\r\npotentiation compared to the right MHb-originating synapses. Interestingly,\r\nchemogenetic inhibition of cholinergic neurons in the left but not the right MHb\r\nsignificantly attenuated cue-dependent fear recall. Furthermore, conditional\r\ndeletion of GABABR in the left MHb interfered with the recall of cued fear memory,\r\nwhereas that in the right MHb neurons spared fear memory expression.\r\nCollectively, I demonstrate a functional asymmetry of the MHb in mice,\r\nrevealing a predominant role for GABABR-mediated signaling in the left MHb-IPN\r\npathway in the modulation of fear memories. These findings suggest that\r\nlateralized pathways could represent a fundamental principle in the neural\r\nregulation of emotion across species."}],"author":[{"full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal"}],"oa_version":"Published Version","year":"2025","title":"Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9437"},{"relation":"part_of_dissertation","status":"public","id":"15084"}]},"type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"date_updated":"2026-04-07T12:40:42Z","OA_place":"publisher","alternative_title":["ISTA Thesis"],"status":"public","department":[{"_id":"GradSch"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"creator":"hoenal","file_id":"19272","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-02-01T23:30:02Z","access_level":"closed","file_size":25869143,"date_created":"2025-02-28T13:57:01Z","checksum":"c1a4d75a7471de9f954697b06cd18d28","file_name":"Cihan_Onal_Thesis_Final.docx","embargo_to":"open_access"},{"access_level":"open_access","content_type":"application/pdf","date_updated":"2026-02-01T23:30:02Z","creator":"hoenal","relation":"main_file","file_id":"19273","embargo":"2026-02-01","file_name":"Cihan_Onal_Thesis_Final_pdfa.pdf","file_size":12077596,"date_created":"2025-02-28T13:57:04Z","checksum":"de4e62147ab9f04098dc8cd898c630da"}],"supervisor":[{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"article_processing_charge":"No","_id":"19271","acknowledgement":"I would like to thank the European Research Council and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to Ryuichi Shigemoto and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), and the Austrian Neuroscience Association for providing financial support and opportunities, which were important in allowing me to present my work. I also wish to thank the\r\nPreclinical Facility, especially Michael Schunn, for always welcoming me from my earliest days as an intern. My gratitude goes as well to the Miba Machine Shop, in particular Todor Asenov, Astrit Arslani, and Thomas Menner, whose technical expertise often saved the day.","ddc":["570","571","573","599"],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"date_created":"2025-02-28T14:15:53Z","day":"04","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"}]},{"publication_identifier":{"isbn":["978-3-99078-055-8"],"eissn":["2663-337X"]},"type":"dissertation","date_updated":"2026-04-07T11:46:32Z","year":"2025","title":"Regulation of Cytoplasmic RNA Polymerase II","author":[{"full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","last_name":"Hlavata"}],"oa_version":"Published Version","abstract":[{"text":"Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm.","lang":"eng"}],"citation":{"ieee":"A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025.","mla":"Hlavata, Annamaria. <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>.","chicago":"Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>.","ista":"Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria.","short":"A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025.","apa":"Hlavata, A. (2025). <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>","ama":"Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>"},"doi":"10.15479/10.15479/AT-ISTA-19431","month":"03","has_accepted_license":"1","file_date_updated":"2026-03-20T23:30:04Z","corr_author":"1","date_published":"2025-03-20T00:00:00Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","date_created":"2025-03-20T12:52:47Z","day":"20","ddc":["572"],"_id":"19431","article_processing_charge":"No","acknowledgement":"I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.","publisher":"Institute of Science and Technology Austria","page":"83","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"supervisor":[{"first_name":"Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"embargo_to":"open_access","checksum":"b7ddf424ffe95f8c767c53c8bb62d4f3","file_size":23506747,"date_created":"2025-03-24T12:48:36Z","file_name":"PhD_Thesis_Hlavata_final_submission.docx","date_updated":"2026-03-20T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"19448","creator":"ahlavata"},{"file_name":"PhD_Thesis_Hlavata_final_submission_update.pdf","checksum":"6c5a59c9bac467c3d0b3ffb8ea6d9fd4","date_created":"2025-03-24T12:51:10Z","file_size":9478591,"relation":"main_file","file_id":"19449","creator":"ahlavata","embargo":"2026-03-20","access_level":"open_access","date_updated":"2026-03-20T23:30:04Z","content_type":"application/pdf"}],"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"]},{"acknowledged_ssus":[{"_id":"LifeSc"}],"publication_status":"published","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"date_created":"2025-03-06T12:16:54Z","day":"24","ddc":["577"],"_id":"19302","article_processing_charge":"No","OA_type":"closed access","acknowledgement":"Thank you to the Lab Support Facility at ISTA. Thank you to the European Research Council (ERC) for their funding under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grant EPIDEMICSonCHIP, No. 771402, to Sylvia Cremer, and ERC Starting Grant DISEASE, No. 802628, to Nathalie Stroeymeyt).","page":"85","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-02-23T23:30:03Z","creator":"lsartori","relation":"source_file","file_id":"19310","embargo_to":"open_access","file_name":"Thesis_Linda_Sartoris.docx","file_size":7129583,"date_created":"2025-03-07T10:16:11Z","checksum":"7e9466dcf3681454211b74b5107e9f7b"},{"embargo_to":"open_access","checksum":"2ccfcf32f0590bb0ec1a488e606a73f5","description":"for printing purposes only","date_created":"2025-03-11T10:42:20Z","file_size":3199703,"file_name":"thesis_Sartoris_for_print.pdf","content_type":"application/pdf","date_updated":"2026-03-02T23:31:13Z","access_level":"closed","relation":"other","file_id":"19384","creator":"lsartori"},{"file_name":"Thesis_Linda_Sartoris.pdf","date_created":"2025-03-11T10:52:00Z","file_size":3183186,"checksum":"1d1f3c1279065b1a7f407ff6d1ee1503","access_level":"open_access","date_updated":"2026-02-23T23:30:03Z","content_type":"application/pdf","creator":"lsartori","relation":"main_file","file_id":"19385","embargo":"2026-02-23"}],"oa":1,"supervisor":[{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"date_updated":"2026-03-02T23:31:14Z","year":"2025","title":"The effect of circadian rhythm on organisational immunity of ant colonies","author":[{"last_name":"Sartoris","first_name":"Linda","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","full_name":"Sartoris, Linda"}],"oa_version":"Published Version","citation":{"ama":"Sartoris L. The effect of circadian rhythm on organisational immunity of ant colonies. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>","apa":"Sartoris, L. (2025). <i>The effect of circadian rhythm on organisational immunity of ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>","short":"L. Sartoris, The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies, Institute of Science and Technology Austria, 2025.","chicago":"Sartoris, Linda. “The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>.","ista":"Sartoris L. 2025. The effect of circadian rhythm on organisational immunity of ant colonies. Institute of Science and Technology Austria.","mla":"Sartoris, Linda. <i>The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>.","ieee":"L. Sartoris, “The effect of circadian rhythm on organisational immunity of ant colonies,” Institute of Science and Technology Austria, 2025."},"abstract":[{"text":"Social interaction networks of insect colonies facilitate efficient information exchange and\r\ndemonstrate adaptive changes to mitigate disease transmission. While circadian rhythms\r\ninfluence individual behaviour, their role in shaping colony-level defences against pathogens\r\nremains unexplored. Here, we investigate whether social networks of the black garden ant,\r\nLasius niger, exhibit circadian rhythms and how these rhythms influence disease vulnerability\r\nwhen colonies are exposed to a pathogen during the day or the night.\r\nWe first establish baseline daily variations in activity and network dynamics in pathogen-free\r\ncolonies, revealing constitutive daily fluctuations in disease susceptibility. Subsequently, we\r\nexamine pathogen-induced changes in sanitary care and network dynamics by exposing\r\nforagers to a natural pathogen (Metarhizium brunneum) during either the day or the night.\r\nIndividual pathogen loads were measured after a nine-hour post-exposure period to evaluate\r\ntransmission outcomes.\r\nOur results demonstrate that diurnal ant colonies maintain robust circadian patterns in network\r\nproperties while flexibly adapting to pathogen exposure. Ants upregulate sanitary care\r\nirrespective of exposure timing, prioritising the protection of the valuable colony centre\r\nconsisting of nurses and the queen. These findings underscore the robustness and adaptability\r\nof ant colonies in balancing circadian rhythms with effective social immune responses.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.15479/AT-ISTA-19302","month":"02","corr_author":"1","project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"has_accepted_license":"1","file_date_updated":"2026-03-02T23:31:13Z","ec_funded":1,"date_published":"2025-02-24T00:00:00Z","language":[{"iso":"eng"}]},{"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"page":"96","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2025-09-30T22:30:02Z","creator":"acumpeli","relation":"main_file","file_id":"19457","embargo":"2025-09-30","file_name":"2025_Thesis_Cumpelik_corrections_PDFA.pdf","file_size":11869040,"date_created":"2025-03-25T11:07:55Z","checksum":"1c7573303d8e5f6da3eb03d59055390f"},{"file_id":"19458","relation":"source_file","creator":"acumpeli","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-09-30T22:30:02Z","file_name":"2025_Thesis_Cumpelik_corrections.docx","checksum":"b93265ebd9a53f7a14100d0d48b4ff5b","date_created":"2025-03-25T11:08:05Z","file_size":20436467,"embargo_to":"open_access"}],"oa":1,"supervisor":[{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","_id":"19456","ddc":["612"],"day":"18","date_created":"2025-03-25T11:22:38Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","keyword":["neuroscience","decision making","learning","cognitive flexibility","medial prefrontal cortex","hippocampus","electrophysiology"],"publication_status":"published","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"corr_author":"1","file_date_updated":"2025-09-30T22:30:02Z","has_accepted_license":"1","date_published":"2025-02-18T00:00:00Z","doi":"10.15479/AT-ISTA-19456","month":"02","citation":{"short":"A.D. Cumpelik, The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task, Institute of Science and Technology Austria, 2025.","ieee":"A. D. Cumpelik, “The role of prefrontal spatial coding in supporting a contextual association task,” Institute of Science and Technology Austria, 2025.","mla":"Cumpelik, Andrea D. <i>The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>.","ista":"Cumpelik AD. 2025. The role of prefrontal spatial coding in supporting a contextual association task. Institute of Science and Technology Austria.","chicago":"Cumpelik, Andrea D. “The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>.","ama":"Cumpelik AD. The role of prefrontal spatial coding in supporting a contextual association task. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>","apa":"Cumpelik, A. D. (2025). <i>The role of prefrontal spatial coding in supporting a contextual association task</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>"},"abstract":[{"text":"Making decisions requires flexibly adapting to changing environments, a process that\r\ndepends on accurately interpreting current contingencies and integrating them with\r\npast experience. Two brain regions are particularly critical for this process, the medial\r\nprefrontal cortex (mPFC) and the hippocampus. Using contextual information from the\r\nhippocampus, the mPFC selects relevant cognitive frameworks and suppresses\r\nirrelevant ones to guide appropriate actions. Several studies have shown that some\r\nmPFC pyramidal neurons become spatially tuned when spatial information is required\r\nto guide goal-directed behavior. However, the role of prefrontal spatial representations\r\nin learning and decision making is not well understood. This work aims to characterize\r\nthe role of mPFC spatial tuning in supporting a contextual association task. Rats were\r\ntrained to learn two cue–location associations on a radial arm maze over multiple days,\r\nwhile we simultaneously recorded from dorsal CA1 of the hippocampus and the\r\nprelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and\r\nprefrontal pyramidal neurons that “flicker” between multiple spatial representations on\r\ndifferent trials, suggesting dynamic, context-dependent coding. This flickering may\r\nprovide a substrate for how the network reorganizes in response to task demands,\r\nlikely by enabling the flexible evaluation of competing representations. ","lang":"eng"}],"author":[{"full_name":"Cumpelik, Andrea D","id":"3F158B32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1727-6612","first_name":"Andrea D","last_name":"Cumpelik"}],"oa_version":"Published Version","year":"2025","OA_embargo":"6 months","title":"The role of prefrontal spatial coding in supporting a contextual association task","type":"dissertation","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-056-5"]},"date_updated":"2026-04-07T12:37:58Z"},{"title":" Quantum remote sensing and non-equilibrium phase transitions in the microwave regime","related_material":{"record":[{"relation":"research_data","status":"public","id":"18978"},{"relation":"part_of_dissertation","status":"public","id":"19280"},{"relation":"part_of_dissertation","status":"public","id":"17183"},{"status":"public","relation":"part_of_dissertation","id":"13117"}]},"year":"2025","date_updated":"2026-06-03T07:16:05Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"citation":{"short":"R. Sett,  Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025.","ista":"Sett R. 2025.  Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria.","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>.","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>.","ieee":"R. Sett, “ Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025.","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>","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>"},"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"}],"oa_version":"Published Version","author":[{"id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","last_name":"Sett","orcid":"0000-0001-7641-8348","first_name":"Riya"}],"doi":"10.15479/AT-ISTA-19533","month":"04","language":[{"iso":"eng"}],"ec_funded":1,"date_published":"2025-04-01T00:00:00Z","corr_author":"1","project":[{"call_identifier":"H2020","grant_number":"862644","_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"}],"has_accepted_license":"1","file_date_updated":"2025-10-11T22:30:02Z","publication_status":"published","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"],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"day":"1","date_created":"2025-04-09T16:44:26Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"degree_awarded":"PhD","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","_id":"19533","article_processing_charge":"No","ddc":["530"],"status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","file":[{"file_name":"PhD_Thesis_Riya_Sett_pdfa.pdf","file_size":4129208,"date_created":"2025-04-10T11:33:22Z","checksum":"ba6cd2289d0141a160a14fc97df1632f","creator":"rsett","relation":"main_file","file_id":"19538","embargo":"2025-10-11","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-10-11T22:30:02Z"},{"access_level":"closed","date_updated":"2025-10-11T22:30:02Z","content_type":"application/x-zip-compressed","relation":"source_file","file_id":"19539","creator":"rsett","embargo_to":"open_access","file_name":"PhD Thesis Riya Sett.zip","checksum":"ee63a94cb8f7adf5e766903028b81ed6","file_size":6646110,"date_created":"2025-04-10T11:34:08Z"}],"oa":1,"supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"page":"109","publisher":"Institute of Science and Technology Austria"},{"language":[{"iso":"eng"}],"article_type":"original","volume":134,"date_published":"2025-02-14T00:00:00Z","ec_funded":1,"project":[{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"}],"has_accepted_license":"1","file_date_updated":"2025-03-04T10:40:50Z","corr_author":"1","doi":"10.1103/PhysRevLett.134.063601","month":"02","scopus_import":"1","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."}],"citation":{"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>","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>","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).","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>.","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.","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>.","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."},"article_number":"063601","oa_version":"Published Version","author":[{"first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zens, M.","first_name":"M.","last_name":"Zens"},{"first_name":"Martin","orcid":"0009-0005-0878-3032","last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","first_name":"Farid"},{"full_name":"Sett, Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7641-8348","first_name":"Riya","last_name":"Sett"},{"full_name":"Zielinski, Przemyslaw D","id":"e198fcc4-f6e0-11ea-865d-b6a256760ee8","first_name":"Przemyslaw D","last_name":"Zielinski"},{"full_name":"Dhar, H. S.","last_name":"Dhar","first_name":"H. S."},{"last_name":"Krimer","first_name":"D. O.","full_name":"Krimer, D. O."},{"last_name":"Rotter","first_name":"S.","full_name":"Rotter, S."},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19533"}]},"title":"Observation of collapse and revival in a superconducting atomic frequency comb","year":"2025","date_updated":"2026-08-11T22:30:36Z","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"arxiv":1,"type":"journal_article","publication":"Physical Review Letters","status":"public","OA_place":"publisher","file":[{"relation":"main_file","file_id":"19291","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-03-04T10:40:50Z","file_name":"2025_PhysReviewLetters_Redchenko.pdf","checksum":"633d6c5ddd9b805da22c5839d3d48df6","date_created":"2025-03-04T10:40:50Z","file_size":2080408,"success":1}],"oa":1,"publisher":"American Physical Society","department":[{"_id":"JoFi"}],"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.","_id":"19280","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","isi":1,"ddc":["530"],"external_id":{"pmid":["40021171"],"isi":["001454696700003"],"arxiv":["2310.04200"]},"quality_controlled":"1","pmid":1,"date_created":"2025-03-02T23:01:52Z","day":"14","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"6","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       134","publication_status":"published","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"doi":"10.15479/AT-ISTA-19722","month":"05","language":[{"iso":"eng"}],"date_published":"2025-05-23T00:00:00Z","file_date_updated":"2026-05-23T22:30:02Z","has_accepted_license":"1","corr_author":"1","title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","OA_embargo":"12","year":"2025","date_updated":"2026-06-12T08:34:29Z","publication_identifier":{"isbn":["978-3-99078-059-6"],"issn":["2663-337X"]},"type":"dissertation","abstract":[{"text":"As root epidermal cells progress from a phase of elongation to differentiation, their\r\ncortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The\r\nhormone cytokinin, a key regulator of root development, facilitates these cytoskeletal\r\nchanges. However, the molecular mechanisms underlying hormone-mediated MT\r\nreorientation during root development are still unknown. Here, we find that MT reorientation\r\nin root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell\r\ndifferentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s\r\nassociation with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end\r\ncreated by katanin-mediated severing at crossovers. Notably, our findings suggest that\r\ndynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning\r\nof the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets\r\nof cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1\r\nassociation in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it\r\nincreases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives\r\nMT reorganization during cell development by simultaneously modulating several\r\nmicrotubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool\r\nduring this process.","lang":"eng"}],"citation":{"short":"S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025.","chicago":"Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>.","ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria.","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025.","mla":"Inumella, Syamala. <i>Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>.","ama":"Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>","apa":"Inumella, S. (2025). <i>Molecular mechanisms of microtubule reorganization in elongating root epidermal cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>"},"oa_version":"Published Version","author":[{"last_name":"Inumella","first_name":"Syamala","orcid":"0009-0002-5890-120X","id":"F8660870-D756-11E9-98C5-34DFE5697425","full_name":"Inumella, Syamala"}],"acknowledgement":"Special thanks to the Plant Facility.","_id":"19722","article_processing_charge":"No","ddc":["580"],"alternative_title":["ISTA Thesis"],"status":"public","OA_place":"publisher","supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"creator":"sinumell","relation":"main_file","file_id":"19757","embargo":"2026-05-23","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-05-23T22:30:02Z","file_name":"Final Thesis_Syamala Inumella.pdf","date_created":"2025-05-28T11:59:11Z","file_size":8292363,"checksum":"847ec70b2e40f50e0ddc7b8da201d52c"},{"file_name":"Final Thesis_Syamala Inumella.docx","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","date_created":"2025-05-28T11:59:11Z","file_size":7145703,"embargo_to":"open_access","relation":"source_file","file_id":"19758","creator":"sinumell","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-05-23T22:30:02Z"}],"publisher":"Institute of Science and Technology Austria","page":"113","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publication_status":"published","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"day":"23","date_created":"2025-05-23T15:21:29Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD"},{"doi":"10.15479/AT-ISTA-19763","month":"05","date_published":"2025-05-29T00:00:00Z","corr_author":"1","file_date_updated":"2025-11-30T23:30:02Z","has_accepted_license":"1","project":[{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"language":[{"iso":"eng"}],"date_updated":"2026-04-14T09:50:53Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","related_material":{"record":[{"id":"18601","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17148"},{"status":"public","relation":"part_of_dissertation","id":"18807"},{"relation":"part_of_dissertation","status":"public","id":"13136"}]},"year":"2025","oa_version":"Published Version","author":[{"last_name":"Rus","orcid":"0000-0001-8703-1093","first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie"}],"citation":{"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>","short":"S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025.","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>.","ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025.","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>.","ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria."},"abstract":[{"lang":"eng","text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation."}],"ddc":["570"],"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.","article_processing_charge":"No","_id":"19763","oa":1,"file":[{"creator":"cchlebak","relation":"main_file","file_id":"19764","embargo":"2025-11-30","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-11-30T23:30:02Z","file_name":"Thesis_Lehr_PDFA.pdf","file_size":42879974,"date_created":"2025-05-30T09:10:22Z","checksum":"8cd7fe3ca990adbcafdece119aa0973d"},{"file_name":"Thesis_Lehr_emptyPages.docx","date_created":"2025-05-30T09:31:15Z","file_size":18731094,"checksum":"0c87dd5fc803450a47b20736b5f86a2f","embargo_to":"open_access","creator":"cchlebak","file_id":"19765","relation":"source_file","access_level":"closed","date_updated":"2025-11-30T23:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"supervisor":[{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"}],"page":"129","department":[{"_id":"AnKi"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"status":"public","OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"publication_status":"published","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"29","date_created":"2025-05-30T09:14:58Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"scopus_import":"1","month":"02","doi":"10.1016/j.devcel.2024.10.024","volume":60,"date_published":"2025-02-24T00:00:00Z","has_accepted_license":"1","file_date_updated":"2025-04-16T10:54:07Z","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"corr_author":"1","language":[{"iso":"eng"}],"article_type":"original","date_updated":"2026-08-11T22:30:37Z","publication_identifier":{"issn":["1534-5807"]},"type":"journal_article","related_material":{"record":[{"id":"19763","status":"public","relation":"dissertation_contains"}]},"title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","year":"2025","oa_version":"Published Version","author":[{"last_name":"Rus","orcid":"0000-0001-8703-1093","first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975"},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","last_name":"Minchington","first_name":"Thomas"},{"id":"48A59534-F248-11E8-B48F-1D18A9856A87","full_name":"Greunz, Martina","last_name":"Greunz","first_name":"Martina"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"}],"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"}],"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>","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>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>","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, Elsevier, 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>.","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. Elsevier, pp. 567–580, 2025.","ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.","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>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>."},"ddc":["570"],"external_id":{"isi":["001434279000001"],"pmid":["39603235"]},"quality_controlled":"1","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).","_id":"18807","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","isi":1,"oa":1,"file":[{"date_updated":"2025-04-16T10:54:07Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"19584","success":1,"file_size":6994499,"date_created":"2025-04-16T10:54:07Z","checksum":"bb58db4a908a1f4aabe4004706154541","file_name":"2025_DevelopmentalCell_Lehr.pdf"}],"publisher":"Elsevier","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"page":"567-580","publication":"Developmental Cell","status":"public","OA_place":"publisher","intvolume":"        60","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"day":"24","date_created":"2025-01-09T11:25:47Z","issue":"4","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_status":"published","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2025-10-11T08:18:51Z","day":"10","ddc":["576"],"_id":"20449","article_processing_charge":"No","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso.","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"page":"114","publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/pdf","date_updated":"2026-06-01T22:30:04Z","access_level":"open_access","embargo":"2026-06-01","file_id":"20507","relation":"main_file","creator":"vbett","checksum":"26905c22bca417198a733d792d8ce422","file_size":18507283,"date_created":"2025-10-20T13:32:29Z","file_name":"2025_Bett_Vincent_Thesis.pdf"},{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-06-01T22:30:04Z","creator":"vbett","file_id":"20508","relation":"source_file","embargo_to":"open_access","file_name":"2025_Bett_Vincent_Thesis.docx","file_size":17163921,"date_created":"2025-10-20T13:35:34Z","checksum":"6a09a8d126d3628bfd8a35202735f267"}],"oa":1,"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-06-12T08:32:16Z","year":"2025","title":"Evolution and regulation of the Z chromosome","related_material":{"record":[{"id":"19735","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"15009"}]},"author":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K","last_name":"Bett","first_name":"Vincent K"}],"oa_version":"Published Version","citation":{"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>.","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>.","ista":"Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria.","short":"V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025.","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>","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>"},"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. "}],"month":"10","doi":"10.15479/AT-ISTA-20449","corr_author":"1","project":[{"grant_number":"PAT 8748323","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","name":"Sex chromosomes in evolution and development"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"has_accepted_license":"1","file_date_updated":"2026-06-01T22:30:04Z","date_published":"2025-10-10T00:00:00Z","language":[{"iso":"eng"}]},{"doi":"10.15479/AT-ISTA-20694","month":"11","language":[{"iso":"eng"}],"has_accepted_license":"1","project":[{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"},{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"file_date_updated":"2026-03-01T23:30:03Z","corr_author":"1","date_published":"2025-11-25T00:00:00Z","year":"2025","related_material":{"record":[{"id":"12159","relation":"part_of_dissertation","status":"public"},{"id":"14796","status":"public","relation":"part_of_dissertation"},{"id":"20190","status":"public","relation":"part_of_dissertation"}]},"title":"Using genealogies to study the genomic basis of species divergence","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_updated":"2026-04-28T13:20:36Z","abstract":[{"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.","lang":"eng"}],"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>","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.","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>.","ieee":"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>.","short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025."},"author":[{"full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","first_name":"Arka","last_name":"Pal"}],"oa_version":"Published Version","article_processing_charge":"No","_id":"20694","ddc":["576","578"],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"status":"public","publisher":"Institute of Science and Technology Austria","page":"268","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"oa":1,"file":[{"file_name":"2025_Pal_Arka_Thesis.pdf","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","file_size":42723135,"date_created":"2025-12-01T13:53:36Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-03-01T23:30:03Z","file_id":"20721","relation":"main_file","creator":"apal","embargo":"2026-03-01"},{"embargo_to":"open_access","file_name":"2025_Pal_Arka_Thesis.docx","checksum":"166d832b08d0434ce407f8f3cb930fe5","file_size":60632116,"date_created":"2025-12-01T13:53:39Z","access_level":"closed","date_updated":"2026-03-01T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20722","relation":"source_file","creator":"apal"}],"publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"25","date_created":"2025-11-25T13:19:11Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD"},{"intvolume":"        34","publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2025-08-17T22:01:37Z","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"22","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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. ","isi":1,"_id":"20190","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","external_id":{"isi":["001546622100001"]},"ddc":["570"],"status":"public","publication":"Molecular Ecology","OA_place":"publisher","oa":1,"file":[{"file_name":"2025_MolecEcology_Pal.pdf","date_created":"2026-01-05T13:47:47Z","file_size":9886694,"checksum":"c586fc674df4e7dd6e43aef87a52c6f6","success":1,"creator":"dernst","file_id":"20958","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-01-05T13:47:47Z"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","title":"Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20694"}],"link":[{"url":"https://ista.ac.at/en/news/snapdragon-secrets/","description":"News on ISTA website","relation":"press_release"}]},"year":"2025","date_updated":"2026-08-11T22:30:41Z","type":"journal_article","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"article_number":"e70067","citation":{"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>.","ista":"Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.","mla":"Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <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>.","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.","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).","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>","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>"},"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"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-4530-8469","first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"last_name":"Mcnairn","first_name":"Adrian J.","full_name":"Mcnairn, Adrian J."},{"full_name":"Grenier, Jennifer K.","first_name":"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"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"}],"month":"11","doi":"10.1111/mec.70067","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","PlanS_conform":"1","volume":34,"date_published":"2025-11-01T00:00:00Z","corr_author":"1","has_accepted_license":"1","file_date_updated":"2026-01-05T13:47:47Z","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}]},{"citation":{"short":"F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025.","ieee":"F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025.","mla":"Strahodinsky, Florian. <i>Social Immunity in a Tri-Partite Host-Pathogen Relationship</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>.","ista":"Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria.","chicago":"Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>.","ama":"Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>","apa":"Strahodinsky, F. (2025). <i>Social immunity in a tri-partite host-pathogen relationship</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>"},"abstract":[{"lang":"eng","text":"Ants are frequently challenged by different pathogens, which they counter with\r\nindividual and collective responses. Usually, the pathogens like fungi or viruses are\r\nsolitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These\r\nentomopathogenic nematodes are active parasites with an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated the basic biology of the host-pathogen relationship.\r\nWe tested different ant life stages and found that adult ants display defense behaviors\r\nand are generally resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker presence significantly reduces transmission risk. In the end, we were also able\r\nto disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial and nematode components.\r\nIn the second chapter, we studied the effect of multiple infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect of combined fungal and nematode\r\nexposure to better understand how the pathogens interact with each other in an ant\r\nhost. We found instances where combined exposure lead to higher mortality in a given\r\ntime frame in both, adult queens and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model to study worm infections\r\nin ants which extend our knowledge on collective disease defense."}],"oa_version":"Published Version","author":[{"id":"979E35EE-C996-11E9-8C7C-CF13E6697425","full_name":"Strahodinsky, Florian","last_name":"Strahodinsky","first_name":"Florian"}],"title":"Social immunity in a tri-partite host-pathogen relationship","year":"2025","date_updated":"2026-04-07T12:39:58Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"date_published":"2025-07-11T00:00:00Z","corr_author":"1","has_accepted_license":"1","file_date_updated":"2026-01-15T23:30:03Z","doi":"10.15479/AT-ISTA-19993","month":"07","date_created":"2025-07-10T14:12:20Z","day":"11","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"}],"status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","file":[{"access_level":"closed","date_updated":"2026-01-15T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"fstrahod","file_id":"20021","relation":"source_file","embargo_to":"open_access","file_name":"Thesis_Florian_Strahodinsky_DOCX.docx","date_created":"2025-07-14T13:18:37Z","file_size":9857392,"checksum":"df3a02f0d937ea9a3d79d5fb94fff097"},{"date_created":"2025-07-14T13:18:38Z","file_size":6439602,"checksum":"7164c21fe1946e839f7b8acd255ce803","file_name":"Thesis_Florian_Strahodinsky_PDF.pdf","content_type":"application/pdf","date_updated":"2026-01-15T23:30:03Z","access_level":"open_access","embargo":"2026-01-15","creator":"fstrahod","relation":"main_file","file_id":"20022"}],"oa":1,"supervisor":[{"last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"page":"138","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","_id":"19993","ddc":["570"]},{"language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2026-04-30T22:30:02Z","corr_author":"1","date_published":"2025-10-30T00:00:00Z","month":"10","doi":"10.15479/AT-ISTA-20470","abstract":[{"text":"Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems.","lang":"eng"}],"citation":{"short":"B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025.","ieee":"B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025.","mla":"Wu, Bryan. <i>An Examination on Phages as a Naturally Composable System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>.","chicago":"Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>.","ista":"Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria.","ama":"Wu B. An examination on phages as a naturally composable system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>","apa":"Wu, B. (2025). <i>An examination on phages as a naturally composable system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>"},"author":[{"full_name":"Wu, Bryan","id":"3C521EBA-F248-11E8-B48F-1D18A9856A87","first_name":"Bryan","last_name":"Wu"}],"oa_version":"Published Version","year":"2025","title":"An examination on phages as a naturally composable system","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_updated":"2026-05-06T08:01:28Z","OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaGu"}],"page":"102","supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"file":[{"file_name":"2025_Wu_Bryan_Thesis.docx","file_size":10603235,"date_created":"2025-10-21T17:33:27Z","checksum":"d32ea83f259f6b0506325cd57b1d44c3","embargo_to":"open_access","creator":"brwu","relation":"source_file","file_id":"20516","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-04-30T22:30:02Z"},{"creator":"brwu","relation":"main_file","file_id":"20517","embargo":"2026-04-30","access_level":"open_access","date_updated":"2026-04-30T22:30:02Z","content_type":"application/pdf","file_name":"2025_Wu_Bryan_Thesis.pdf","date_created":"2025-10-21T17:33:26Z","file_size":6251936,"checksum":"53590046fd3244c5550b4022282449d2"}],"oa":1,"_id":"20470","article_processing_charge":"No","ddc":["579"],"day":"30","date_created":"2025-10-15T13:30:21Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","publication_status":"published"},{"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"type":"journal_article","date_updated":"2026-08-11T22:30:43Z","year":"2025","related_material":{"record":[{"id":"20449","status":"public","relation":"dissertation_contains"},{"id":"20444","relation":"dissertation_contains","status":"deleted"}],"link":[{"relation":"software","url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git"}]},"title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","author":[{"first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Trejo Arellano","first_name":"Minerva S","orcid":"0000-0002-1982-3475","id":"2b681148-eed5-11eb-b81b-ae229e8620f8","full_name":"Trejo Arellano, Minerva S"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","abstract":[{"text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.","lang":"eng"}],"citation":{"short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).","ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025.","mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","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.","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>.","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>","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>"},"article_number":"msaf085","scopus_import":"1","month":"05","doi":"10.1093/molbev/msaf085","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","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"file_date_updated":"2025-05-28T09:34:36Z","has_accepted_license":"1","corr_author":"1","volume":42,"date_published":"2025-05-01T00:00:00Z","article_type":"original","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_status":"published","intvolume":"        42","DOAJ_listed":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"5","pmid":1,"day":"01","date_created":"2025-05-25T22:16:56Z","ddc":["570"],"quality_controlled":"1","external_id":{"pmid":["40202086"],"isi":["001483460200001"]},"_id":"19735","OA_type":"gold","article_processing_charge":"Yes","isi":1,"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.","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"DaZi"}],"file":[{"relation":"main_file","file_id":"19756","creator":"dernst","date_updated":"2025-05-28T09:34:36Z","content_type":"application/pdf","access_level":"open_access","checksum":"6c14b03f94b4aadf8869be2c4366d077","file_size":1282772,"date_created":"2025-05-28T09:34:36Z","file_name":"2025_MBE_Bett.pdf","success":1}],"oa":1,"OA_place":"publisher","publication":"Molecular Biology and Evolution","status":"public"}]