[{"date_published":"2025-03-13T00:00:00Z","corr_author":"1","file_date_updated":"2025-04-01T07:55:27Z","has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.15479/AT-ISTA-19395","month":"03","oa_version":"Published Version","author":[{"first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"}],"citation":{"apa":"Monzer, A. (2025). <i>Cell-Surface Auxin Signaling: Linking molecular pathways to plant development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>","ama":"Monzer A. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>","chicago":"Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>.","ista":"Monzer A. 2025. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.","mla":"Monzer, Aline. <i>Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>.","ieee":"A. Monzer, “Cell-Surface Auxin Signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.","short":"A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025."},"abstract":[{"lang":"eng","text":"Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood."}],"date_updated":"2026-07-06T12:52:09Z","type":"dissertation","publication_identifier":{"eissn":["2663-337X"],"eisbn":["978-3-99078-054-1"]},"title":"Cell-Surface Auxin Signaling: Linking molecular pathways to plant development","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12291"},{"id":"14826","status":"public","relation":"part_of_dissertation"},{"id":"19399","relation":"part_of_dissertation","status":"public"},{"id":"19398","relation":"part_of_dissertation","status":"public"}]},"year":"2025","oa":1,"file":[{"file_id":"19396","relation":"main_file","creator":"amonzer","access_level":"open_access","date_updated":"2025-03-12T14:14:49Z","content_type":"application/pdf","file_name":"Final Thesis Aline Monzer.pdf","checksum":"9a3dd03bb4ec6b9907a325c3c4e8a1d7","date_created":"2025-03-12T14:14:49Z","file_size":13119670,"success":1},{"file_id":"19397","relation":"source_file","creator":"amonzer","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-04-01T07:55:27Z","access_level":"closed","checksum":"a353ce1ee2eabce37bca35499e76dbf1","date_created":"2025-03-12T14:15:19Z","file_size":13774837,"file_name":"Thesis Aline.docx"}],"supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"page":"160","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","ddc":["580"],"acknowledgement":"I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research.","_id":"19395","article_processing_charge":"No","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2025-03-12T14:25:42Z","day":"13","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published"},{"author":[{"last_name":"Karle","first_name":"Volker","orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker"}],"oa_version":"Published Version","abstract":[{"text":"Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.\r\nWhile most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.\r\nIn this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.\r\nWe begin by establishing a theoretical bridge between periodically kicked rotors and \"crystalline\" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear\r\nmolecules provide an ideal experimental platform due to their abovementioned precise controllability.\r\nThe core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through\r\nmolecular alignment and rotational level populations.\r\nThese findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental\r\nphysics and developing quantum technologies.","lang":"eng"}],"citation":{"apa":"Karle, V. (2025). <i>Non-equilibrium topological phases with periodically driven molecules and quantum rotors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>","ama":"Karle V. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>","ieee":"V. Karle, “Non-equilibrium topological phases with periodically driven molecules and quantum rotors,” Institute of Science and Technology Austria, 2025.","mla":"Karle, Volker. <i>Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>.","ista":"Karle V. 2025. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria.","chicago":"Karle, Volker. “Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>.","short":"V. Karle, Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors, Institute of Science and Technology Austria, 2025."},"publication_identifier":{"eissn":["2663-337X"]},"type":"dissertation","date_updated":"2026-07-29T08:59:30Z","year":"2025","related_material":{"record":[{"id":"14851","status":"public","relation":"part_of_dissertation"},{"id":"12788","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9903"},{"status":"public","relation":"part_of_dissertation","id":"15004"},{"status":"public","relation":"part_of_dissertation","id":"19425"}]},"title":"Non-equilibrium topological phases with periodically driven molecules and quantum rotors","file_date_updated":"2025-03-20T08:02:35Z","has_accepted_license":"1","corr_author":"1","date_published":"2025-03-13T00:00:00Z","language":[{"iso":"eng"}],"month":"03","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.15479/AT-ISTA-19393","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","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":"2025-03-12T13:04:59Z","day":"13","publication_status":"published","publisher":"Institute of Science and Technology Austria","page":"192","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"supervisor":[{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"file":[{"checksum":"d3ab25782c7ea38ce9910e57d25f6733","file_size":10625143,"date_created":"2025-03-12T12:56:46Z","file_name":"thesis_final.pdf","success":1,"relation":"main_file","file_id":"19394","creator":"vkarle","date_updated":"2025-03-12T12:56:46Z","content_type":"application/pdf","access_level":"open_access"},{"file_name":"thesis.zip","file_size":23119202,"date_created":"2025-03-13T13:15:10Z","checksum":"3ccfb0aeba4d860d71e18347913034e4","access_level":"closed","content_type":"application/zip","date_updated":"2025-03-20T08:02:35Z","creator":"vkarle","relation":"source_file","file_id":"19400"}],"oa":1,"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"ddc":["530"],"article_processing_charge":"No","_id":"19393","OA_type":"gold"},{"publisher":"Institute of Science and Technology Austria","page":"170","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"supervisor":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"file":[{"file_name":"Thesis_Marwan_Elkrewi.docx","file_size":25019680,"date_created":"2025-03-26T07:06:56Z","checksum":"5549a8216c07e4c39281648912d72246","embargo_to":"open_access","creator":"melkrewi","file_id":"19462","relation":"source_file","access_level":"closed","date_updated":"2026-03-26T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_updated":"2026-03-26T23:30:03Z","content_type":"application/pdf","access_level":"open_access","embargo":"2026-03-26","file_id":"19463","relation":"main_file","creator":"melkrewi","checksum":"aed2ba9965aa89b3414deae1ae9f4321","date_created":"2025-03-26T07:06:22Z","file_size":17294844,"file_name":"Thesis_Marwan_Elkrewi.pdf"}],"oa":1,"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"ddc":["570","576"],"article_processing_charge":"No","_id":"19386","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).","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","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":"2025-03-11T12:54:31Z","day":"14","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_status":"published","file_date_updated":"2026-03-26T23:30:03Z","has_accepted_license":"1","project":[{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"corr_author":"1","date_published":"2025-03-14T00:00:00Z","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","month":"03","doi":"10.15479/AT-ISTA-19386","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","first_name":"Marwan N"}],"oa_version":"Published Version","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. "}],"citation":{"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>.","ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.","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>.","short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>","ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>"},"publication_identifier":{"isbn":["9783990780534"],"eissn":["2663-337X"]},"type":"dissertation","date_updated":"2026-07-06T13:48:33Z","year":"2025","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12248"},{"id":"10767","status":"public","relation":"part_of_dissertation"},{"id":"15009","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14613"},{"status":"public","relation":"part_of_dissertation","id":"17890"},{"status":"public","relation":"part_of_dissertation","id":"10167"}]},"OA_embargo":"12","title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp"},{"abstract":[{"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.","lang":"eng"}],"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.","ista":"Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria.","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>.","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."},"oa_version":"Published Version","author":[{"first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal","full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"9437","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"15084"}]},"title":"Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula","year":"2025","date_updated":"2026-04-07T12:40:42Z","publication_identifier":{"eissn":["2663-337X"]},"type":"dissertation","language":[{"iso":"eng"}],"date_published":"2025-03-04T00:00:00Z","ec_funded":1,"has_accepted_license":"1","file_date_updated":"2026-02-01T23:30:02Z","project":[{"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","call_identifier":"H2020"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"corr_author":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"03","doi":"10.15479/AT-ISTA-19271","date_created":"2025-02-28T14:15:53Z","day":"04","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)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publication_status":"published","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"}],"status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","supervisor":[{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"}],"file":[{"embargo_to":"open_access","checksum":"c1a4d75a7471de9f954697b06cd18d28","date_created":"2025-02-28T13:57:01Z","file_size":25869143,"file_name":"Cihan_Onal_Thesis_Final.docx","date_updated":"2026-02-01T23:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"19272","creator":"hoenal"},{"access_level":"open_access","date_updated":"2026-02-01T23:30:02Z","content_type":"application/pdf","creator":"hoenal","file_id":"19273","relation":"main_file","embargo":"2026-02-01","file_name":"Cihan_Onal_Thesis_Final_pdfa.pdf","date_created":"2025-02-28T13:57:04Z","file_size":12077596,"checksum":"de4e62147ab9f04098dc8cd898c630da"}],"oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"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.","article_processing_charge":"No","_id":"19271","ddc":["570","571","573","599"]},{"date_updated":"2026-04-07T11:46:32Z","type":"dissertation","publication_identifier":{"eissn":["2663-337X"],"isbn":["978-3-99078-055-8"]},"title":"Regulation of Cytoplasmic RNA Polymerase II","year":"2025","oa_version":"Published Version","author":[{"full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","last_name":"Hlavata"}],"citation":{"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>","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>","short":"A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025.","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."},"abstract":[{"lang":"eng","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."}],"doi":"10.15479/10.15479/AT-ISTA-19431","month":"03","date_published":"2025-03-20T00:00:00Z","corr_author":"1","file_date_updated":"2026-03-20T23:30:04Z","has_accepted_license":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"publication_status":"published","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"20","date_created":"2025-03-20T12:52:47Z","ddc":["572"],"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.","_id":"19431","article_processing_charge":"No","file":[{"embargo_to":"open_access","file_name":"PhD_Thesis_Hlavata_final_submission.docx","checksum":"b7ddf424ffe95f8c767c53c8bb62d4f3","file_size":23506747,"date_created":"2025-03-24T12:48:36Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-03-20T23:30:04Z","relation":"source_file","file_id":"19448","creator":"ahlavata"},{"file_size":9478591,"date_created":"2025-03-24T12:51:10Z","checksum":"6c5a59c9bac467c3d0b3ffb8ea6d9fd4","file_name":"PhD_Thesis_Hlavata_final_submission_update.pdf","content_type":"application/pdf","date_updated":"2026-03-20T23:30:04Z","access_level":"open_access","embargo":"2026-03-20","creator":"ahlavata","file_id":"19449","relation":"main_file"}],"oa":1,"supervisor":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036","first_name":"Carrie A"}],"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"page":"83","publisher":"Institute of Science and Technology Austria","status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher"},{"status":"public","alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"oa":1,"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-02-23T23:30:03Z","access_level":"closed","file_id":"19310","relation":"source_file","creator":"lsartori","embargo_to":"open_access","checksum":"7e9466dcf3681454211b74b5107e9f7b","file_size":7129583,"date_created":"2025-03-07T10:16:11Z","file_name":"Thesis_Linda_Sartoris.docx"},{"access_level":"closed","date_updated":"2026-03-02T23:31:13Z","content_type":"application/pdf","creator":"lsartori","file_id":"19384","relation":"other","embargo_to":"open_access","file_name":"thesis_Sartoris_for_print.pdf","description":"for printing purposes only","date_created":"2025-03-11T10:42:20Z","file_size":3199703,"checksum":"2ccfcf32f0590bb0ec1a488e606a73f5"},{"file_name":"Thesis_Linda_Sartoris.pdf","checksum":"1d1f3c1279065b1a7f407ff6d1ee1503","date_created":"2025-03-11T10:52:00Z","file_size":3183186,"access_level":"open_access","date_updated":"2026-02-23T23:30:03Z","content_type":"application/pdf","relation":"main_file","file_id":"19385","creator":"lsartori","embargo":"2026-02-23"}],"publisher":"Institute of Science and Technology Austria","page":"85","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"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).","_id":"19302","article_processing_charge":"No","OA_type":"closed access","ddc":["577"],"date_created":"2025-03-06T12:16:54Z","day":"24","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"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"date_published":"2025-02-24T00:00:00Z","ec_funded":1,"has_accepted_license":"1","file_date_updated":"2026-03-02T23:31:13Z","project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"}],"corr_author":"1","doi":"10.15479/AT-ISTA-19302","month":"02","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"}],"citation":{"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>","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>","ista":"Sartoris L. 2025. The effect of circadian rhythm on organisational immunity of ant colonies. Institute of Science and Technology Austria.","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>.","ieee":"L. Sartoris, “The effect of circadian rhythm on organisational immunity of ant colonies,” Institute of Science and Technology Austria, 2025.","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>.","short":"L. Sartoris, The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies, Institute of Science and Technology Austria, 2025."},"oa_version":"Published Version","author":[{"last_name":"Sartoris","first_name":"Linda","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","full_name":"Sartoris, Linda"}],"title":"The effect of circadian rhythm on organisational immunity of ant colonies","year":"2025","date_updated":"2026-03-02T23:31:14Z","publication_identifier":{"eissn":["2663-337X"]},"type":"dissertation"},{"publication_status":"published","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2020-09-28T07:33:38Z","day":"20","ddc":["570"],"article_processing_charge":"No","_id":"8574","oa":1,"file":[{"success":1,"file_name":"thesis_EnikoSzep_final.pdf","checksum":"20e71f015fbbd78fea708893ad634ed0","date_created":"2020-09-28T07:25:35Z","file_size":6354833,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-09-28T07:25:35Z","relation":"main_file","file_id":"8575","creator":"dernst"},{"checksum":"a8de2c14a1bb4e53c857787efbb289e1","date_created":"2020-09-28T07:25:37Z","file_size":23020401,"file_name":"thesisFiles_EnikoSzep.zip","file_id":"8576","relation":"source_file","creator":"dernst","date_updated":"2020-09-28T07:25:37Z","content_type":"application/x-zip-compressed","access_level":"closed"}],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"page":"158","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"status":"public","OA_place":"publisher","date_updated":"2026-04-08T07:21:44Z","type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"title":"Local adaptation in metapopulations","year":"2020","oa_version":"Published Version","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","last_name":"Szep","first_name":"Eniko"}],"citation":{"apa":"Szep, E. (2020). <i>Local adaptation in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. <i>Local Adaptation in Metapopulations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020."},"abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes,  such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"month":"09","doi":"10.15479/AT:ISTA:8574","date_published":"2020-09-20T00:00:00Z","corr_author":"1","file_date_updated":"2020-09-28T07:25:37Z","has_accepted_license":"1","language":[{"iso":"eng"}]},{"status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","file":[{"checksum":"451f8e64b0eb26bf297644ac72bfcbe9","date_created":"2020-01-12T11:49:49Z","file_size":21100497,"file_name":"thesis.zip","date_updated":"2020-07-14T12:47:52Z","content_type":"application/zip","access_level":"closed","file_id":"7255","relation":"source_file","creator":"jtkadlec"},{"access_level":"open_access","date_updated":"2020-07-14T12:47:52Z","content_type":"application/pdf","creator":"dernst","file_id":"7367","relation":"main_file","file_name":"2020_Tkadlec_Thesis.pdf","date_created":"2020-01-28T07:32:42Z","file_size":11670983,"checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985"}],"oa":1,"supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"page":"144","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","_id":"7196","ddc":["519"],"date_created":"2019-12-20T12:26:36Z","day":"12","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","language":[{"iso":"eng"}],"date_published":"2020-01-12T00:00:00Z","corr_author":"1","file_date_updated":"2020-07-14T12:47:52Z","has_accepted_license":"1","doi":"10.15479/AT:ISTA:7196","month":"01","citation":{"short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","mla":"Tkadlec, Josef. <i>A Role of Graphs in Evolutionary Processes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>.","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>","apa":"Tkadlec, J. (2020). <i>A role of graphs in evolutionary processes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>"},"abstract":[{"lang":"eng","text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time."}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"title":"A role of graphs in evolutionary processes","related_material":{"record":[{"id":"5751","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"7210"},{"id":"7212","relation":"dissertation_contains","status":"public"}]},"year":"2020","date_updated":"2026-04-16T08:32:37Z","type":"dissertation","publication_identifier":{"eissn":["2663-337X"]}},{"language":[{"iso":"eng"}],"corr_author":"1","file_date_updated":"2021-10-31T23:30:05Z","has_accepted_license":"1","date_published":"2020-04-24T00:00:00Z","month":"04","doi":"10.15479/AT:ISTA:7680","citation":{"short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7680\">https://doi.org/10.15479/AT:ISTA:7680</a>.","mla":"Kainrath, Stephanie. <i>Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7680\">10.15479/AT:ISTA:7680</a>.","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7680\">10.15479/AT:ISTA:7680</a>","apa":"Kainrath, S. (2020). <i>Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7680\">https://doi.org/10.15479/AT:ISTA:7680</a>"},"abstract":[{"lang":"eng","text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."}],"author":[{"full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","orcid":"0000-0002-6709-2195","last_name":"Kainrath"}],"oa_version":"None","year":"2020","title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","related_material":{"record":[{"id":"1028","status":"public","relation":"dissertation_contains"}]},"type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"date_updated":"2026-07-08T05:54:07Z","status":"public","alternative_title":["ISTA Thesis"],"department":[{"_id":"CaGu"}],"page":"98","publisher":"Institute of Science and Technology Austria","file":[{"embargo":"2021-10-30","relation":"main_file","file_id":"7692","creator":"stgingl","content_type":"application/pdf","date_updated":"2021-10-31T23:30:05Z","access_level":"open_access","checksum":"fb9a4468eb27be92690728e35c823796","date_created":"2020-04-28T11:19:21Z","file_size":3268017,"file_name":"Thesis_without-signatures_PDFA.pdf"},{"access_level":"closed","content_type":"application/octet-stream","date_updated":"2021-10-31T23:30:05Z","creator":"stgingl","relation":"source_file","file_id":"7693","embargo_to":"open_access","file_name":"Thesis_without signatures.docx","date_created":"2020-04-28T11:19:24Z","file_size":5167703,"checksum":"f6c80ca97104a631a328cb79a2c53493"}],"oa":1,"supervisor":[{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"article_processing_charge":"No","_id":"7680","ddc":["570"],"date_created":"2020-04-24T16:00:51Z","day":"24","degree_awarded":"PhD","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"ddc":["000"],"article_processing_charge":"No","_id":"6894","supervisor":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:43Z","content_type":"application/pdf","creator":"mgiacobbe","file_id":"6916","relation":"main_file","file_name":"giacobbe_thesis.pdf","date_created":"2019-09-27T14:15:05Z","file_size":4100685,"checksum":"773beaf4a85dc2acc2c12b578fbe1965"},{"checksum":"97f1c3da71feefd27e6e625d32b4c75b","file_size":7959732,"date_created":"2019-09-27T14:22:04Z","file_name":"giacobbe_thesis_src.tar.gz","content_type":"application/gzip","date_updated":"2020-07-14T12:47:43Z","access_level":"closed","file_id":"6917","relation":"source_file","creator":"mgiacobbe"}],"oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"page":"132","status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","date_created":"2019-09-22T14:08:44Z","day":"30","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"},"doi":"10.15479/AT:ISTA:6894","month":"09","date_published":"2019-09-30T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:43Z","corr_author":"1","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:55:03Z","publication_identifier":{"eissn":["2663-337X"]},"type":"dissertation","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"647"},{"id":"631","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"140"}]},"title":"Automatic time-unbounded reachability analysis of hybrid systems","year":"2019","oa_version":"Published Version","author":[{"full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco","last_name":"Giacobbe"}],"abstract":[{"lang":"eng","text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks."}],"citation":{"apa":"Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","mla":"Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>.","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019."}},{"author":[{"last_name":"Paranjape","first_name":"Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","full_name":"Paranjape, Chaitanya S"}],"oa_version":"Published Version","citation":{"ista":"Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria.","chicago":"Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6957\">https://doi.org/10.15479/AT:ISTA:6957</a>.","mla":"Paranjape, Chaitanya S. <i>Onset of Turbulence in Plane Poiseuille Flow</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6957\">10.15479/AT:ISTA:6957</a>.","ieee":"C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute of Science and Technology Austria, 2019.","short":"C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of Science and Technology Austria, 2019.","apa":"Paranjape, C. S. (2019). <i>Onset of turbulence in plane Poiseuille flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6957\">https://doi.org/10.15479/AT:ISTA:6957</a>","ama":"Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6957\">10.15479/AT:ISTA:6957</a>"},"abstract":[{"text":"In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow,  etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable.  The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent.  In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.\r\n\r\nThe aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest.  \r\n\r\nWhile the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different.  \r\n\r\nIn shear flows, turbulence at onset is transient in nature.  Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence.","lang":"eng"}],"type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"date_updated":"2026-04-08T07:46:58Z","year":"2019","title":"Onset of turbulence in plane Poiseuille flow","corr_author":"1","file_date_updated":"2020-07-14T12:47:46Z","has_accepted_license":"1","date_published":"2019-10-24T00:00:00Z","language":[{"iso":"eng"}],"month":"10","doi":"10.15479/AT:ISTA:6957","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2019-10-22T12:08:43Z","day":"24","keyword":["Instabilities","Turbulence","Nonlinear dynamics"],"publication_status":"published","page":"138","department":[{"_id":"BjHo"}],"publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"checksum":"7ba298ba0ce7e1d11691af6b8eaf0a0a","file_size":45828099,"date_created":"2019-10-23T09:54:43Z","file_name":"Chaitanya_Paranjape_source_files_tex_figures.zip","date_updated":"2020-07-14T12:47:46Z","content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"6962","creator":"cparanjape"},{"file_name":"Chaitanya_Paranjape_Thesis.pdf","checksum":"642697618314e31ac31392da7909c2d9","date_created":"2019-10-23T10:37:09Z","file_size":19504197,"access_level":"open_access","date_updated":"2020-07-14T12:47:46Z","content_type":"application/pdf","file_id":"6963","relation":"main_file","creator":"cparanjape"}],"supervisor":[{"first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"ddc":["532"],"article_processing_charge":"No","_id":"6957"},{"citation":{"ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","mla":"Vasileva, Mina K. <i>Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>.","ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","chicago":"Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","apa":"Vasileva, M. K. (2019). <i>Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>"},"abstract":[{"lang":"eng","text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes."}],"author":[{"first_name":"Mina K","last_name":"Vasileva","full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","year":"2019","title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","related_material":{"record":[{"id":"449","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6377"},{"status":"public","relation":"part_of_dissertation","id":"1346"}]},"type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"date_updated":"2026-04-08T13:54:45Z","language":[{"iso":"eng"}],"corr_author":"1","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:51Z","date_published":"2019-12-12T00:00:00Z","month":"12","doi":"10.15479/AT:ISTA:7172","date_created":"2019-12-11T21:24:39Z","day":"12","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"department":[{"_id":"JiFr"}],"page":"192","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"creator":"mvasilev","relation":"source_file","file_id":"7175","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:47:51Z","access_level":"closed","date_created":"2019-12-12T09:32:36Z","file_size":20454014,"checksum":"ef981c1a3b1d9da0edcbedcff4970d37","file_name":"Thesis_Mina_final_upload_7.docx"},{"access_level":"open_access","date_updated":"2020-07-14T12:47:51Z","content_type":"application/pdf","file_id":"7176","relation":"main_file","creator":"mvasilev","file_name":"Thesis_Mina_final_upload_7.pdf","checksum":"3882c4585e46c9cfb486e4225cad54ab","date_created":"2019-12-12T09:33:10Z","file_size":11565025}],"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"_id":"7172","article_processing_charge":"No","ddc":["570"]},{"alternative_title":["ISTA Thesis"],"status":"public","OA_place":"publisher","file":[{"access_level":"closed","date_updated":"2020-10-17T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6950","relation":"source_file","creator":"akopf","embargo_to":"open_access","file_name":"Kopf_PhD_Thesis.docx","checksum":"00d100d6468e31e583051e0a006b640c","file_size":74735267,"date_created":"2019-10-15T05:28:42Z"},{"embargo":"2020-10-16","creator":"akopf","relation":"main_file","file_id":"6951","content_type":"application/pdf","date_updated":"2020-10-17T22:30:03Z","access_level":"open_access","date_created":"2019-10-15T05:28:47Z","file_size":52787224,"checksum":"5d1baa899993ae6ca81aebebe1797000","file_name":"Kopf_PhD_Thesis1.pdf"}],"oa":1,"supervisor":[{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"page":"171","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","_id":"6891","article_processing_charge":"No","ddc":["570"],"day":"24","date_created":"2019-09-19T08:19:44Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"publication_status":"published","language":[{"iso":"eng"}],"date_published":"2019-07-24T00:00:00Z","corr_author":"1","has_accepted_license":"1","file_date_updated":"2020-10-17T22:30:03Z","project":[{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"month":"07","doi":"10.15479/AT:ISTA:6891","citation":{"chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","mla":"Kopf, Aglaja. <i>The Implication of Cytoskeletal Dynamics on Leukocyte Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>.","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","apa":"Kopf, A. (2019). <i>The implication of cytoskeletal dynamics on leukocyte migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>"},"abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","first_name":"Aglaja","last_name":"Kopf"}],"title":"The implication of cytoskeletal dynamics on leukocyte migration","related_material":{"record":[{"id":"6877","relation":"part_of_dissertation","status":"public"},{"id":"6328","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"15"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/feeling-like-a-cell/"}]},"year":"2019","date_updated":"2026-06-18T17:44:11Z","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]}}]