[{"file":[{"creator":"sinumell","date_updated":"2026-05-23T22:30:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"847ec70b2e40f50e0ddc7b8da201d52c","embargo":"2026-05-23","file_size":8292363,"date_created":"2025-05-28T11:59:11Z","file_name":"Final Thesis_Syamala Inumella.pdf","file_id":"19757"},{"file_size":7145703,"date_created":"2025-05-28T11:59:11Z","file_name":"Final Thesis_Syamala Inumella.docx","embargo_to":"open_access","file_id":"19758","creator":"sinumell","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-05-23T22:30:02Z","access_level":"closed","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","relation":"source_file"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","citation":{"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>.","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>.","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025.","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>","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>","ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria."},"year":"2025","acknowledgement":"Special thanks to the Plant Facility.","supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"day":"23","oa_version":"Published Version","status":"public","_id":"19722","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/AT-ISTA-19722","date_published":"2025-05-23T00:00:00Z","has_accepted_license":"1","ddc":["580"],"abstract":[{"lang":"eng","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."}],"file_date_updated":"2026-05-23T22:30:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_embargo":"12","date_updated":"2026-06-12T08:34:29Z","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","article_processing_charge":"No","date_created":"2025-05-23T15:21:29Z","month":"05","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"language":[{"iso":"eng"}],"page":"113","type":"dissertation","doi":"10.15479/AT-ISTA-19722","oa":1,"title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-059-6"]},"author":[{"orcid":"0009-0002-5890-120X","first_name":"Syamala","full_name":"Inumella, Syamala","last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425"}],"corr_author":"1"},{"author":[{"full_name":"Wu, Bryan","id":"3C521EBA-F248-11E8-B48F-1D18A9856A87","last_name":"Wu","first_name":"Bryan"}],"corr_author":"1","doi":"10.15479/AT-ISTA-20470","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"An examination on phages as a naturally composable system","oa":1,"month":"10","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"CaGu"}],"publication_status":"published","page":"102","degree_awarded":"PhD","date_created":"2025-10-15T13:30:21Z","article_processing_charge":"No","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"}],"file_date_updated":"2026-04-30T22:30:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"date_updated":"2026-05-06T08:01:28Z","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/AT-ISTA-20470","ddc":["579"],"has_accepted_license":"1","date_published":"2025-10-30T00:00:00Z","citation":{"short":"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>.","ieee":"B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025.","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>","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>","ista":"Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria."},"year":"2025","publisher":"Institute of Science and Technology Austria","day":"30","supervisor":[{"first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C"}],"oa_version":"Published Version","status":"public","_id":"20470","file":[{"date_updated":"2026-04-30T22:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"brwu","access_level":"closed","checksum":"d32ea83f259f6b0506325cd57b1d44c3","relation":"source_file","file_name":"2025_Wu_Bryan_Thesis.docx","file_size":10603235,"date_created":"2025-10-21T17:33:27Z","embargo_to":"open_access","file_id":"20516"},{"file_id":"20517","file_name":"2025_Wu_Bryan_Thesis.pdf","file_size":6251936,"embargo":"2026-04-30","date_created":"2025-10-21T17:33:26Z","relation":"main_file","access_level":"open_access","checksum":"53590046fd3244c5550b4022282449d2","date_updated":"2026-04-30T22:30:02Z","content_type":"application/pdf","creator":"brwu"}]},{"file":[{"date_created":"2025-12-10T19:28:20Z","embargo":"2026-06-11","file_size":8105379,"file_name":"2025_Zivadinovic_Predrag_PhD_thesis.pdf","file_id":"20778","creator":"pzivadin","date_updated":"2026-06-11T22:30:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"aae9d1ed53f7b67f75e289c26a02b72f"},{"embargo_to":"open_access","file_id":"20779","file_name":"2025_Zivadinovic_Predrag_PhD_thesis_source.zip","date_created":"2025-12-10T19:28:10Z","file_size":8512240,"checksum":"8a08a3804ce7d9d625fdf1631113da8c","access_level":"closed","relation":"source_file","content_type":"application/zip","date_updated":"2026-06-11T22:30:02Z","creator":"pzivadin"}],"das_tickbox":"1","day":"11","supervisor":[{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"acknowledgement":"My work has been funded through the project \"Functional Advantages of Critical Brain\r\nDynamics\" of the ISTA interdisciplinary fund and through the FWF.\r\n","year":"2025","citation":{"apa":"Zivadinovic, P. (2025). <i>Scale-free activity as a basis for spatial learning and memory in the brain</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>","ieee":"P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory in the brain,” Institute of Science and Technology Austria, 2025.","ista":"Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria.","ama":"Zivadinovic P. Scale-free activity as a basis for spatial learning and memory in the brain. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>","mla":"Zivadinovic, Predrag. <i>Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>.","short":"P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain, Institute of Science and Technology Austria, 2025.","chicago":"Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>."},"publisher":"Institute of Science and Technology Austria","_id":"20777","status":"public","oa_version":"Published Version","OA_place":"publisher","ddc":["570","539","571"],"has_accepted_license":"1","date_published":"2025-12-11T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20777","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"A major challenge in neuroscience is deciphering how the brain orchestrates behavior in\r\nresponse to changes in environmental conditions. This process is characterized by several\r\nprocessing stages, from perception to the storage of important information. Information\r\nstorage is performed by a memory system implemented through complex networks of highly\r\ninterconnected neurons. The collective operational principles of neuronal networks that support\r\nformation and storage are the main topics of this thesis.\r\nTo investigate the collective dynamics of the hippocampus from the perspective of the brain\r\ncriticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches\r\n¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures\r\nderived from neuronal avalanches suggested that during wakefulness the hippocampus operated\r\nfurther away from criticality than during sleep/rest. In addition, neural activity propagated\r\ndifferently in these two brain states, as indicated by different collapses of the avalanche shapes.\r\nNext, the Phenomenological Renormalization Group approach also indicated conceptually\r\nsimilar differences, through the scaling exponent of activity variance α, which was higher during\r\nsleep/rest than during awake. These results confirmed that the activity of the hippocampus\r\nexhibits signatures of criticality and that these signatures change with the state of the brain.\r\nNext, I found that memory retention was predicted by the scaling exponent of activity variance\r\nα. The exponent α measured during the sleep/rest session that followed learning correlated\r\nwith memory retention during the subsequent unrewarded testing session. Moreover, α\r\npredicted performance even when controlled for reactivation that occurs in parallel. Second, α\r\nmeasured in the sleep/rest phase that preceded learning was correlated with the learning speed.\r\nI analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day\r\nvariability of these distributions, during sleep/rest that followed learning, correlated with the\r\nscaling exponent of activity variance α, as well as with memory retention. These findings\r\nconfirmed that variance scaling and functional heterogeneity provide behaviorally meaningful\r\nperspectives on hippocampal activity, as they are directly related to memory consolidation.\r\nI further investigated the process of memory acquisition and consolidation between the\r\nhippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards\r\nthe goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals\r\nduring sleep/rest that followed learning. This shift during sleep/rest was supported by the\r\nreactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and\r\nindependently of the hippocampal SWRs. Both types of reactivation predicted subsequent\r\nmemory retention, as well as the amount of goal-related remapping. Again, the day-to-day\r\nvariability of the distribution of the cell timescales correlated with the goal-related remapping,\r\nin CA1 during the learning session and in mEC during sleep/rest. These results suggest that\r\nin spatial navigation tasks, the functional responsibilities of CA1 and mEC change between\r\nlearning and sleep/rest and that their function benefits from increased functional heterogeneity\r\namong cells.\r\n","lang":"eng"}],"file_date_updated":"2026-06-11T22:30:02Z","date_updated":"2026-07-24T08:14:37Z","alternative_title":["ISTA Thesis"],"project":[{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318"}],"degree_awarded":"PhD","date_created":"2025-12-10T19:37:41Z","article_processing_charge":"No","month":"12","page":"104","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"publication_status":"published","doi_confirm":"1","publication_identifier":{"issn":["2663-337X"]},"title":"Scale-free activity as a basis for spatial learning and memory in the brain","oa":1,"doi":"10.15479/AT-ISTA-20777","type":"dissertation","author":[{"id":"68AA0E5A-AFDA-11E9-9994-141DE6697425","last_name":"Zivadinovic","full_name":"Zivadinovic, Predrag","first_name":"Predrag"}],"corr_author":"1"},{"publisher":"Institute of Science and Technology Austria","year":"2025","acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided\r\nby the MIBA Machine Shop and the Nanofabrication facility. We acknowledge the support from\r\nthe European Commission with the project Integrated Germanium Quantum Technology (with\r\nDOI:10.3030/101069515), the NOMIS Foundation, the HORIZON-RIA 101069515 project and\r\nthe FWF Projects Center for Correlated Quantum Materials and Solid State Quantum Systems:\r\nConventional and unconventional topological superconductors (with DOI:10.55776/F86) and\r\nHigh impedance circuit quantum electrodynamics with hole spins (with DOI:10.55776/I5060).\r\n","citation":{"ista":"Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria.","ama":"Saez Mollejo J. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>","ieee":"J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025.","apa":"Saez Mollejo, J. (2025). <i>Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>","chicago":"Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>.","mla":"Saez Mollejo, Jaime. <i>Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>.","short":"J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025."},"supervisor":[{"orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"day":"13","oa_version":"Published Version","_id":"19836","status":"public","file":[{"embargo_to":"open_access","file_id":"19849","file_name":"istaustriathesis-master - Copy.zip","file_size":59892829,"date_created":"2025-06-16T09:38:49Z","checksum":"643bfddead59857536cce4d57c775b32","access_level":"closed","relation":"source_file","date_updated":"2026-04-01T22:30:07Z","content_type":"application/x-zip-compressed","creator":"jsaezmol"},{"file_id":"19851","file_name":"SaezMollejo_PhDFinal_pdfa-1b.pdf","embargo":"2026-04-01","file_size":22382376,"date_created":"2025-06-18T08:50:16Z","checksum":"e3dcb767fcc2b1787a455fdda991cefb","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2026-04-01T22:30:07Z","creator":"jsaezmol"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"text":"Over the past century, researchers have been fascinated by the quantum nature of the\r\nphysical world, initially striving to understand its fundamental principles and consequences, and\r\neventually progressing toward engineering systems that can control and manipulate quantum\r\nproperties. Today, we stand at the dawn of the quantum technology era. While some quantum\r\ntechnologies follow well-defined roadmaps, others are still in the exciting and uncertain early\r\nstages of development. In the fields of quantum computing and quantum simulation, research\r\nis being conducted across a wide variety of platforms. Each of these demonstrates control over\r\nquantum properties but also faces challenges in scaling up to the level of a mature technology.\r\nThis thesis explores some of the fundamental properties of hole spin qubits in planar germanium.\r\nSemiconductor spin qubits are considered strong candidates for the realization of quantum\r\nprocessors, owing to their long relaxation and coherence times, as well as their compatibility\r\nwith existing semiconductor industry infrastructure. Among these, hole spin qubits in planar\r\ngermanium are particularly promising. Their advantages include a large effective mass, which\r\neases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit\r\ninteraction, which enables fast and purely electrical control. However, spin-orbit coupling also\r\nintroduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip\r\ntunneling, which might cause that the quantization axes are not aligned. In this thesis, we\r\ninvestigate the tilt between the quantization axes of two hole spins hosted in a double quantum\r\ndot as a function of both the magnetic field direction and various electrostatic configurations,\r\ndemonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove\r\nto be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the\r\nphysics governing spin qubit behavior.\r\n","lang":"eng"}],"file_date_updated":"2026-04-01T22:30:07Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"date_updated":"2026-07-29T12:55:59Z","OA_place":"publisher","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19836","date_published":"2025-06-13T00:00:00Z","has_accepted_license":"1","ddc":["530","539"],"license":"https://creativecommons.org/licenses/by/4.0/","month":"06","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"page":"175","related_material":{"record":[{"id":"19424","relation":"part_of_dissertation","status":"public"}]},"project":[{"grant_number":"101069515","name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"}],"degree_awarded":"PhD","article_processing_charge":"No","date_created":"2025-06-13T09:01:50Z","author":[{"last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime","first_name":"Jaime"}],"corr_author":"1","doi_confirm":"1","type":"dissertation","doi":"10.15479/AT-ISTA-19836","oa":1,"title":"Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ","publication_identifier":{"issn":["2663-337X"]}},{"OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19906","has_accepted_license":"1","date_published":"2025-06-26T00:00:00Z","ddc":["530"],"file_date_updated":"2025-12-27T23:30:02Z","abstract":[{"text":"Flows of ordinary fluids such as water or air transition from laminar to turbulent\r\nmotion as the velocity increases. This simple dependence of the flow state\r\nsolely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here\r\nvarious different instabilities and turbulent states can arise at low and even\r\nvanishing inertia, while high inertia turbulence counterintuitively is suppressed\r\nand its drag strongly reduced. We here show in experiments of a viscoelastic\r\nmodel fluid that the phenomena observed at low and high inertia have a\r\ncommon origin and that the same dynamical state, elasto-inertial turbulence,\r\npersists across four orders of magnitude in Reynolds number, ranging from\r\nvery low inertia, all the way to high inertia Maximum drag reduction (MDR)\r\nasymptote. We also explore the transitions from Newtonian turbulence to\r\nMDR, and specific cases of flow at high polymer concentrations, exploring the\r\nrelationship between flow at these wide range of control parameters.\r\n","lang":"eng"}],"ec_funded":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"date_updated":"2026-07-29T12:55:31Z","file":[{"content_type":"application/pdf","date_updated":"2025-12-27T23:30:02Z","creator":"cchlebak","access_level":"open_access","checksum":"302a07605a9e64ac247c2036d5f5b1cd","relation":"main_file","file_name":"Thesis_v9_PDFA2b.pdf","file_size":6504571,"date_created":"2025-06-26T08:40:53Z","embargo":"2025-12-27","file_id":"19907"},{"file_name":"Thesis Template - ISTA [istaustriathesis].zip","file_size":59092991,"date_created":"2025-06-26T08:41:24Z","embargo_to":"open_access","file_id":"19908","date_updated":"2025-12-27T23:30:02Z","content_type":"application/x-zip-compressed","creator":"cchlebak","access_level":"closed","checksum":"5d69d10bdacc24c27f02924379405bd9","relation":"source_file"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"This work was partially funded by the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie grant agreement\r\nNo. 665385.","citation":{"ama":"Suresh SS. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>","ista":"Suresh SS. 2025. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute of Science and Technology Austria.","apa":"Suresh, S. S. (2025). <i>Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>","ieee":"S. S. Suresh, “Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote,” Institute of Science and Technology Austria, 2025.","chicago":"Suresh, Sarath S. “Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>.","mla":"Suresh, Sarath S. <i>Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>.","short":"S.S. Suresh, Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote, Institute of Science and Technology Austria, 2025."},"year":"2025","supervisor":[{"first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"day":"26","oa_version":"Published Version","_id":"19906","status":"public","doi_confirm":"1","type":"dissertation","doi":"10.15479/AT-ISTA-19906","title":"Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote","oa":1,"publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Suresh, Sarath S","id":"3D126CC4-F248-11E8-B48F-1D18A9856A87","last_name":"Suresh","first_name":"Sarath S"}],"corr_author":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10299"}]},"degree_awarded":"PhD","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"article_processing_charge":"No","date_created":"2025-06-26T08:39:08Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"06","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"page":"82"},{"date_created":"2025-03-11T12:54:31Z","article_processing_charge":"No","degree_awarded":"PhD","project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12248"},{"relation":"part_of_dissertation","id":"10767","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14613"},{"status":"public","id":"10167","relation":"part_of_dissertation"},{"id":"15009","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"17890","relation":"part_of_dissertation"}]},"page":"170","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publication_status":"published","month":"03","publication_identifier":{"isbn":["9783990780534"],"eissn":["2663-337X"]},"oa":1,"title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","doi":"10.15479/AT-ISTA-19386","type":"dissertation","corr_author":"1","author":[{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"creator":"melkrewi","date_updated":"2026-03-26T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"5549a8216c07e4c39281648912d72246","access_level":"closed","file_size":25019680,"date_created":"2025-03-26T07:06:56Z","file_name":"Thesis_Marwan_Elkrewi.docx","file_id":"19462","embargo_to":"open_access"},{"relation":"main_file","checksum":"aed2ba9965aa89b3414deae1ae9f4321","access_level":"open_access","creator":"melkrewi","content_type":"application/pdf","date_updated":"2026-03-26T23:30:03Z","file_id":"19463","embargo":"2026-03-26","date_created":"2025-03-26T07:06:22Z","file_size":17294844,"file_name":"Thesis_Marwan_Elkrewi.pdf"}],"status":"public","_id":"19386","oa_version":"Published Version","day":"14","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"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).","citation":{"ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.","ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","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>","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.","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>."},"year":"2025","publisher":"Institute of Science and Technology Austria","ddc":["570","576"],"has_accepted_license":"1","date_published":"2025-03-14T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-19386","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_updated":"2026-09-24T11:17:37Z","OA_embargo":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. "}],"file_date_updated":"2026-03-26T23:30:03Z"},{"file":[{"file_name":"2025_Bett_Vincent_Thesis.pdf","date_created":"2025-10-20T13:32:29Z","embargo":"2026-06-01","file_size":18507283,"file_id":"20507","content_type":"application/pdf","date_updated":"2026-06-01T22:30:04Z","creator":"vbett","relation":"main_file","access_level":"open_access","checksum":"26905c22bca417198a733d792d8ce422"},{"date_created":"2025-10-20T13:35:34Z","file_size":17163921,"file_name":"2025_Bett_Vincent_Thesis.docx","embargo_to":"open_access","file_id":"20508","creator":"vbett","date_updated":"2026-06-01T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"6a09a8d126d3628bfd8a35202735f267","access_level":"closed","relation":"source_file"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"day":"10","publisher":"Institute of Science and Technology Austria","citation":{"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>","ieee":"V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025.","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>","ista":"Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria.","mla":"Bett, Vincent K. <i>Evolution and Regulation of the Z Chromosome</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>.","short":"V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025.","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>."},"year":"2025","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso.","_id":"20449","status":"public","oa_version":"Published Version","OA_place":"publisher","has_accepted_license":"1","date_published":"2025-10-10T00:00:00Z","ddc":["576"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-20449","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2026-06-01T22:30:04Z","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. "}],"date_updated":"2026-09-24T11:11:01Z","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","project":[{"grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"related_material":{"record":[{"id":"19735","relation":"part_of_dissertation","status":"public"},{"id":"15009","relation":"part_of_dissertation","status":"public"}]},"article_processing_charge":"No","date_created":"2025-10-11T08:18:51Z","month":"10","page":"114","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"oa":1,"title":"Evolution and regulation of the Z chromosome","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20449","author":[{"full_name":"Bett, Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"}],"corr_author":"1"},{"has_accepted_license":"1","date_published":"2025-09-15T00:00:00Z","ddc":["570","530"],"keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20357","OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-02T10:15:31Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2026-09-15T22:30:02Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}],"file":[{"file_name":"2025_Ruzickova_Natalia_Thesis.zip","file_size":56464803,"date_created":"2026-08-07T10:57:05Z","embargo_to":"open_access","file_id":"22661","date_updated":"2026-09-15T22:30:02Z","content_type":"application/x-zip-compressed","creator":"cchlebak","access_level":"closed","checksum":"0582508d439b233497384f83a8307398","relation":"source_file"},{"access_level":"open_access","checksum":"b722289fd550abede63adc27b9c61784","relation":"main_file","date_updated":"2026-09-15T22:30:02Z","content_type":"application/pdf","creator":"cchlebak","file_id":"22662","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","date_created":"2026-08-07T10:57:34Z","file_size":30634378,"embargo":"2026-09-15"}],"_id":"20357","status":"public","oa_version":"Published Version","supervisor":[{"full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"day":"15","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria.","ama":"Ruzickova N. Effect propagation in biological networks. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>","ieee":"N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025.","apa":"Ruzickova, N. (2025). <i>Effect propagation in biological networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>","chicago":"Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>.","mla":"Ruzickova, Natalia. <i>Effect Propagation in Biological Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>.","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025."},"year":"2025","acknowledgement":"I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n","title":"Effect propagation in biological networks","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-066-4"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20357","doi_confirm":"1","corr_author":"1","author":[{"full_name":"Ruzickova, Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","first_name":"Natalia"}],"article_processing_charge":"No","date_created":"2025-09-15T17:04:48Z","degree_awarded":"PhD","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18525"}]},"page":"156","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"GaTk"}],"month":"09"},{"OA_place":"publisher","has_accepted_license":"1","date_published":"2025-11-03T00:00:00Z","ddc":["515","519"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["optimal transport","kinetic equations","boundary value problems","quantization","gradient flows","homogenization"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20563","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"text":"The theory of optimal transport provides an elegant and powerful description of many evolution\r\nequations as gradient flows. The primary objective of this thesis is to adapt and extend the\r\ntheory to deal with important equations that are not covered by the classical framework,\r\nspecifically boundary value problems and kinetic equations. Additionally, we establish new\r\nresults in periodic homogenization for discrete dynamical optimal transport and in quantization\r\nof measures.\r\nSection 1.1 serves as an invitation to the classical theory of optimal transport, including the\r\nmain definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the\r\nmain results of this thesis, outline the motivations, and review the current state of the art.\r\nIn Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet\r\nboundary conditions. We construct a time-discrete scheme involving a modification of the\r\nWasserstein distance and, under weak assumptions, prove its convergence to a solution of this\r\nboundary value problem. In dimension 1, we show that this solution is a gradient flow in a\r\nsuitable space of measures.\r\nChapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory\r\nof optimal transport to describe and study particle systems at the mesoscopic scale. We prove\r\nadapted versions of some fundamental theorems, including the Benamou–Brenier formula and\r\nthe identification of absolutely continuous curves of measures.\r\nChapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical\r\ntransportation functionals on periodic graphs in the large-scale limit when the cost functional\r\nis asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge\r\nto 1-Wasserstein distances constructed from crystalline norms on R\r\nd\r\n.\r\nChapter 5 concerns optimal empirical quantization: the problem of approximating a measure\r\nby the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein\r\ndistance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for\r\nthe minimal error as n tends to infinity.\r\n","lang":"eng"}],"file_date_updated":"2026-01-01T23:30:03Z","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-02T11:24:55Z","file":[{"checksum":"6f55275bdf99992be3a6457d949dd664","access_level":"open_access","relation":"main_file","date_updated":"2026-01-01T23:30:03Z","content_type":"application/pdf","creator":"fquattro","file_id":"20653","file_name":"2025_quattrocchi_filippo_thesis.pdf","date_created":"2025-11-17T21:04:15Z","embargo":"2026-01-01","file_size":4326411},{"creator":"fquattro","date_updated":"2026-01-01T23:30:03Z","content_type":"application/zip","access_level":"closed","checksum":"707e580f5d993a214c0dba456b75837b","relation":"source_file","date_created":"2025-11-17T21:05:43Z","file_size":11726509,"file_name":"2025_quattrocchi_thesis.zip","embargo_to":"open_access","file_id":"20654"}],"supervisor":[{"orcid":"0000-0002-0845-1338","first_name":"Jan","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas"}],"day":"03","publisher":"Institute of Science and Technology Austria","acknowledgement":"The research contained in this thesis has received funding from the Austrian Science\r\nFund (FWF) project 10.55776/F65.","year":"2025","citation":{"ama":"Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>","ista":"Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria.","apa":"Quattrocchi, F. (2025). <i>Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>","ieee":"F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025.","chicago":"Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>.","mla":"Quattrocchi, Filippo. <i>Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>.","short":"F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025."},"status":"public","_id":"20563","oa_version":"Published Version","title":"Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures","oa":1,"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20563","author":[{"id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi","full_name":"Quattrocchi, Filippo","first_name":"Filippo","orcid":"0009-0000-9773-1931"}],"corr_author":"1","degree_awarded":"PhD","project":[{"grant_number":"F06504","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Differential Systems"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"20569","status":"public"},{"id":"20571","relation":"part_of_dissertation","status":"public"},{"id":"20570","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18706","relation":"part_of_dissertation"}]},"article_processing_charge":"No","date_created":"2025-10-28T13:10:49Z","month":"11","page":"240","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"language":[{"iso":"eng"}]},{"acknowledgement":"This work was partially inspired by an unpublished note from 2014 by Guillaume Carlier,\r\nJean Dolbeault, and Bruno Nazaret. GB deeply thanks Jean Dolbeault for proposing\r\nthis problem to him, guiding him into the subject, and sharing the aforementioned note.\r\nWe are grateful to Karthik Elamvazhuthi for making us aware of the work [20].\r\nThe work of GB has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement\r\nNo 101034413.\r\nJM and FQ gratefully acknowledge support from the Austrian Science Fund (FWF)\r\nproject 10.55776/F65.","year":"2025","citation":{"apa":"Brigati, G., Maas, J., &#38; Quattrocchi, F. (n.d.). Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>","ieee":"G. Brigati, J. Maas, and F. Quattrocchi, “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures,” <i>arXiv</i>. .","ista":"Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv, 2502.15665.","ama":"Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>","mla":"Brigati, Giovanni, et al. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” <i>ArXiv</i>, 2502.15665, doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>.","short":"G. Brigati, J. Maas, F. Quattrocchi, ArXiv (n.d.).","chicago":"Brigati, Giovanni, Jan Maas, and Filippo Quattrocchi. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>."},"arxiv":1,"day":"10","oa_version":"Preprint","_id":"20569","status":"public","external_id":{"arxiv":["2502.15665"]},"ec_funded":1,"abstract":[{"text":"This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov's equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov's equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov's equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-26T23:31:02Z","OA_place":"repository","fulldoi":"https://doi.org/10.48550/arXiv.2502.15665","keyword":["optimal transport","kinetic theory","second-order discrepancy","Vlasov equation","Wasserstein splines."],"date_published":"2025-08-10T00:00:00Z","OA_type":"green","month":"08","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"language":[{"iso":"eng"}],"publication_status":"draft","related_material":{"record":[{"status":"public","id":"20563","relation":"dissertation_contains"}]},"project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"date_created":"2025-10-28T13:12:08Z","article_processing_charge":"No","author":[{"first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","last_name":"Brigati","full_name":"Brigati, Giovanni"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338"},{"full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","orcid":"0009-0000-9773-1931","first_name":"Filippo"}],"publication":"arXiv","corr_author":"1","article_number":"2502.15665","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2502.15665","open_access":"1"}],"doi":"10.48550/arXiv.2502.15665","type":"preprint","title":"Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures","oa":1},{"month":"04","page":"109","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publication_status":"published","project":[{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"degree_awarded":"PhD","related_material":{"record":[{"relation":"research_data","id":"18978","status":"public"},{"status":"public","id":"19280","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"13117"},{"status":"public","relation":"part_of_dissertation","id":"17183"}]},"date_created":"2025-04-09T16:44:26Z","article_processing_charge":"No","author":[{"last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","orcid":"0000-0001-7641-8348","first_name":"Riya"}],"corr_author":"1","doi_confirm":"1","publication_identifier":{"issn":["2663-337X"]},"oa":1,"title":"Quantum remote sensing and non-equilibrium phase transitions in the microwave regime","doi":"10.15479/AT-ISTA-19533","type":"dissertation","day":"1","supervisor":[{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M"}],"citation":{"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>.","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.","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>","ieee":"R. Sett, “Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025.","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>"},"year":"2025","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.","publisher":"Institute of Science and Technology Austria","_id":"19533","status":"public","oa_version":"Published Version","file":[{"creator":"rsett","content_type":"application/pdf","date_updated":"2025-10-11T22:30:02Z","relation":"main_file","checksum":"ba6cd2289d0141a160a14fc97df1632f","access_level":"open_access","date_created":"2025-04-10T11:33:22Z","embargo":"2025-10-11","file_size":4129208,"file_name":"PhD_Thesis_Riya_Sett_pdfa.pdf","file_id":"19538"},{"file_id":"19539","embargo_to":"open_access","file_name":"PhD Thesis Riya Sett.zip","file_size":6646110,"date_created":"2025-04-10T11:34:08Z","relation":"source_file","checksum":"ee63a94cb8f7adf5e766903028b81ed6","access_level":"closed","content_type":"application/x-zip-compressed","date_updated":"2025-10-11T22:30:02Z","creator":"rsett"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-10-11T22:30:02Z","ec_funded":1,"abstract":[{"lang":"eng","text":"This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n"}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-15T09:08:00Z","OA_place":"publisher","ddc":["530"],"has_accepted_license":"1","date_published":"2025-04-01T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-19533","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"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"]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Cortical development has been studied for many decades and with each passing year, we learn \r\nmore about the processes that govern the tightly regulated developmental program. Up until \r\nrecently, the field has struggled to gain reliable access to progenitors at the single-cell level, \r\nlimiting the resolution at which we can study cortical development in vivo. Therefore, much of \r\nthe data we have on mammalian cortical development is at the cell population level. The \r\nsubsequent pages of this thesis describe novel elements of cortical development in mice; \r\nacquired using a candidate gene approach in conjunction with Mosaic Analysis with Double \r\nMarkers (MADM) to achieve single cell resolution. In this thesis, I briefly provide an overview \r\nof the state of the field, describe the methodology used to quantify morphological \r\ncharacteristics of neurons and glia, and delve into the role of Phosphatase and tensin \r\nhomologue on chromosome ten (Pten) in neurogenesis and gliogenesis in the developing mouse \r\ncortex. By using MADM to generate genetic mosaics, in which only a small fraction of cells \r\nare mutated, to study population-level changes, we can bypass the early postnatal lethality \r\nreported in Pten conditional knockouts (cKOs) using Emx1-Cre. We used Emx1-CreERT2 to \r\ninduce clonal deletion of Pten, and quantify RGP neurogenic output at the single progenitor \r\nlevel. Pten-mutant neuron populations within the mosaics were significantly expanded. In the \r\nlatter parts of this thesis, we describe how Pten deletion leads to an increase in the abundance \r\nof astrocytes. We availed ourselves of the flexibility offered by the MADM system to generate \r\nPten mosaics within a series of distinct knockout tissues to test for the interactions between \r\nPten and a battery of genes involved in distinct pro-gliogenic signaling pathways. Our survey \r\nof Pten’s interactions with genes in key signaling pathways reveals that ERK1/2 are the critical \r\neffectors downstream of EGFR signaling essential for gliogenesis. Altogether, our results \r\ndemonstrate that Pten plays critical and distinct roles throughout cortical RGP lineage \r\nprogression. ","lang":"eng"}],"file_date_updated":"2026-08-26T22:30:02Z","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-02T12:16:56Z","OA_place":"publisher","has_accepted_license":"1","date_published":"2025-08-22T00:00:00Z","ddc":["570"],"keyword":["Pten","mtor","cortical development","MADM","Mapk"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20212","supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"day":"22","publisher":"Institute of Science and Technology Austria","acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253).","citation":{"ista":"Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria.","ama":"Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>","ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025.","apa":"Miranda, O. (2025). <i>Unraveling the role of Pten in cortical stem cell lineage progression using MADM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>","chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>.","short":"O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025.","mla":"Miranda, Osvaldo. <i>Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>."},"year":"2025","status":"public","_id":"20212","oa_version":"Published Version","file":[{"embargo_to":"open_access","file_id":"20230","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx","file_size":32887334,"date_created":"2025-08-26T09:03:50Z","checksum":"3331f76bbef74ff4908e2d2c9262045c","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-08-26T22:30:02Z","creator":"omiranda"},{"file_id":"20231","file_size":28636240,"embargo":"2026-08-26","date_created":"2025-08-26T09:05:55Z","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf","checksum":"02509d50cff8e35c5bcbf71e8d658176","access_level":"open_access","relation":"main_file","creator":"omiranda","date_updated":"2026-08-26T22:30:02Z","content_type":"application/pdf"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"author":[{"orcid":"0000-0001-6618-6889","first_name":"Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Miranda","full_name":"Miranda, Osvaldo"}],"corr_author":"1","doi_confirm":"1","title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-063-3"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20212","month":"08","page":"119","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"project":[{"name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253"}],"degree_awarded":"PhD","related_material":{"record":[{"id":"17425","relation":"part_of_dissertation","status":"public"}]},"article_processing_charge":"No","date_created":"2025-08-22T14:07:00Z"},{"OA_place":"publisher","fulldoi":"https://doi.org/10.15479/AT-ISTA-20117","ddc":["580"],"date_published":"2025-08-04T00:00:00Z","has_accepted_license":"1","file_date_updated":"2026-09-03T22:30:03Z","abstract":[{"lang":"eng","text":"Auxin is essential for many aspects of plant growth and development, from \r\nembryogenesis to organ senescence. Polar auxin transport leads to local auxin maxima and \r\ngradients, which are important for regulating various plant development process, including \r\nembryogenesis, organogenesis and vascular tissue formation. The polar auxin transport is \r\nmediated by auxin influx carrier AUX1/LAX proteins and efflux carrier PIN proteins. The \r\nregulation of PIN proteins is a key convergence of crosstalk between auxin and other \r\nhormones, such as cytokinin. Cytokinin promotes the degradation of PIN1 in Arabidopsis \r\nroots, preferentially the dephosphorylated PIN1, and the process is independent of \r\ntranscription and translation (Marhavý et al., 2011; Marhavý et al., 2014). The internalization \r\nof PIN proteins from plasma membrane is controlled by clathrin-mediated endocytosis \r\n(Dhonukshe et al., 2007; Kitakura et al., 2011). However, whether cytokinin affects the PIN1 \r\ndegradation through regulating the phosphorylation of PIN1 or trafficking components is \r\nunknown. Here, we demonstrate that dynamin related protein DRP2s are required for the \r\ncytokinin regulated trafficking of PIN1 and PIN2 in Arabidopsis root epidermal cells. Despite \r\nthe reported redundancy of DRP2A and DRP2B in gametophyte development, we found that \r\nCK-mediated PIN1 degradation and –induced PIN2 membrane localization is affected in drp2a \r\nor drp2b single mutants. Interestingly, we found that cytokinin regulates the recruitment of \r\nDRP2A—but not DRP2B—to clathrin-coated pits, and affects the stability and plasma \r\nmembrane localization of DRP2A. Furthermore, we studied the involvement of cytokinin \r\nreceptors in the regulation of cytokinin on DRP2A. Additionally, the assembly and disassembly \r\ncycle of dynamin is mediated by its dephosphorylation and phosphotylation cycle; thus, we \r\ninvestigated the role of DRP2A phosphorylation in its cytokinin-regulated assembly and in \r\ncytokinin-regulated PIN trafficking. Altogether, we found that cytokinin regulated PIN \r\ntrafficking in Arabidopsis root epidermal cells involves modulation of the phosphorylation of \r\nendocytosis accessory protein DRP2A. "}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-10-02T12:33:36Z","alternative_title":["ISTA Thesis"],"file":[{"creator":"yiqwang","date_updated":"2026-09-03T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"36b87c17d12c7bf5955d6d812acb8d77","access_level":"closed","relation":"source_file","file_size":25798848,"date_created":"2025-08-22T08:22:10Z","file_name":"2025_Wang_Yiqun_Thesis.docx","embargo_to":"open_access","file_id":"20209"},{"checksum":"8d7a2383f66377da675d379ec30ea0fe","access_level":"open_access","relation":"main_file","creator":"yiqwang","date_updated":"2026-09-03T22:30:03Z","content_type":"application/pdf","file_id":"20211","date_created":"2025-08-22T10:32:30Z","embargo":"2026-09-03","file_size":12628313,"file_name":"2025_Wang_Yiqun_Thesis.pdf"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","citation":{"mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria.","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>"},"year":"2025","publisher":"Institute of Science and Technology Austria","day":"04","supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"}],"oa_version":"Published Version","status":"public","_id":"20117","doi_confirm":"1","doi":"10.15479/AT-ISTA-20117","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","oa":1,"author":[{"last_name":"Wang","id":"82F537F2-B517-11E9-84D7-6433E6697425","full_name":"Wang, Yiqun","first_name":"Yiqun"}],"corr_author":"1","related_material":{"record":[{"status":"public","id":"18063","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","date_created":"2025-08-04T15:24:21Z","article_processing_charge":"No","month":"08","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publication_status":"published","page":"108"},{"external_id":{"pmid":["40782342"],"isi":["001547884300001"]},"issue":"3","file":[{"success":1,"file_id":"20264","date_created":"2025-09-01T14:09:31Z","file_size":5791111,"file_name":"2025_PlantJournal_Babic.pdf","access_level":"open_access","checksum":"1cdc3341d2d23101abca72521f1f23cb","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2025-09-01T14:09:31Z"}],"intvolume":"       123","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"day":"01","isi":1,"year":"2025","citation":{"ieee":"D. Babic <i>et al.</i>, “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” <i>Plant Journal</i>, vol. 123, no. 3. Wiley, 2025.","apa":"Babic, D., Abualia, R., Fiedler, L., Qi, L., Tellier, F., Smoljan, A., … Friml, J. (2025). Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>","ama":"Babic D, Abualia R, Fiedler L, et al. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. 2025;123(3). doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>","ista":"Babic D, Abualia R, Fiedler L, Qi L, Tellier F, Smoljan A, Rakusova H, Valošek P, Han H, Benková E, Faure JD, Friml J. 2025. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 123(3), e70396.","short":"D. Babic, R. Abualia, L. Fiedler, L. Qi, F. Tellier, A. Smoljan, H. Rakusova, P. Valošek, H. Han, E. Benková, J.D. Faure, J. Friml, Plant Journal 123 (2025).","mla":"Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>, vol. 123, no. 3, e70396, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>.","chicago":"Babic, David, Rashed Abualia, Lukas Fiedler, Linlin Qi, Frédérique Tellier, Adrijana Smoljan, Hana Rakusova, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>."},"acknowledgement":"We gratefully acknowledge the Imaging and Optics, Electron Microscopy (especially Vanessa Zheden for technical assistance) and Life Science (in particular Dorota Jaworska) facilities at ISTA for their continuous support. Authors would like to thank Michelle Gallei for advice during the generation of the transgenic lines; Zuzana Gelová for advice with DR5rev::GFP analyses; Ivan Kulich for help and advice on trichome imaging; Aline Monzer for generous help with hypocotyl and root analyses; Shutang Tan for help with the NGS data analysis; and Milan Župunski for advice on abiotic stress experiments. We would like to thank Dolf Weijers for the SOSEKI (SOK) marker line seeds. This work has benefited from the support of IJPB's Plant Observatory platforms P0-Chem.\r\n\r\nThis work was supported by Austrian Science Fund (FWF) (I 6123-B) and Science and Technology Department of Jiangxi Province (20223BCJ25037) to Huibin Han. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","publisher":"Wiley","status":"public","_id":"20187","oa_version":"Published Version","OA_place":"publisher","ddc":["580"],"OA_type":"hybrid","has_accepted_license":"1","date_published":"2025-08-01T00:00:00Z","PlanS_conform":"1","fulldoi":"https://doi.org/10.1111/tpj.70396","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-09-01T14:09:31Z","abstract":[{"text":"Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.","lang":"eng"}],"date_updated":"2026-10-26T23:31:07Z","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"}],"quality_controlled":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"20362","status":"public"}]},"date_created":"2025-08-17T22:01:36Z","article_processing_charge":"Yes (via OA deal)","month":"08","volume":123,"department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"e70396","pmid":1,"publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","oa":1,"doi":"10.1111/tpj.70396","type":"journal_article","publication":"Plant Journal","author":[{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic","first_name":"David"},{"full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","orcid":"0000-0002-9357-9415"},{"first_name":"Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"first_name":"Linlin","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi"},{"first_name":"Frédérique","full_name":"Tellier, Frédérique","last_name":"Tellier"},{"first_name":"Adrijana","last_name":"Smoljan","id":"cced8a85-223e-11ed-af04-b0596c55053b","full_name":"Smoljan, Adrijana"},{"first_name":"Hana","full_name":"Rakusova, Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","last_name":"Rakusova"},{"full_name":"Valošek, Petr","last_name":"Valošek","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"},{"first_name":"Jean Denis","last_name":"Faure","full_name":"Faure, Jean Denis"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"}],"corr_author":"1","scopus_import":"1"},{"file":[{"file_name":"2025_David_Babic_Thesis.pdf","file_size":7501548,"embargo":"2026-09-25","date_created":"2025-09-24T13:43:14Z","file_id":"20388","content_type":"application/pdf","date_updated":"2026-09-25T22:30:02Z","creator":"dbabic","relation":"main_file","checksum":"5ecf274281a54a41e0288bc79edf7492","access_level":"open_access"},{"file_id":"20389","embargo_to":"open_access","file_name":"Thesis_Babic_draft.docx","file_size":23206052,"date_created":"2025-09-24T13:43:14Z","relation":"source_file","access_level":"closed","checksum":"2703e548390de0a1af7a707137e8ab3b","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-09-25T22:30:02Z","creator":"dbabic"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"citation":{"chicago":"Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>.","mla":"Babic, David. <i>Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>.","short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>","ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025.","apa":"Babic, D. (2025). <i>Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>"},"year":"2025","publisher":"Institute of Science and Technology Austria","day":"18","supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"oa_version":"Published Version","status":"public","_id":"20362","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/AT-ISTA-20362","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["580"],"has_accepted_license":"1","date_published":"2025-09-18T00:00:00Z","abstract":[{"text":"Arabidopsis embryo has long served as a model system for understanding how plant body \r\npatterning and axis establishment arise. Previous work established that auxin flows, directed \r\nby polar transport and reinforced by local biosynthesis, underpin axes formation, while recent \r\nstudies suggest that maternal tissue, membrane composition and surface receptor signaling add \r\nfurther regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which \r\nguide plant embryonic and post-embryonic development. We review methodological advances \r\nthat allow the embryo to be imaged and studied. These tools offer exciting venues for future \r\naddressing of outstanding research questions. Furthermore, we dissect the contribution of \r\nmaternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments \r\nlowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens \r\nthe initial apical maximum. The resulting deficit dampens downstream embryonic auxin \r\nbiosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided \r\nauxin controls auxin flows in the embryos on a larger scale than previously understood. \r\nIntriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases \r\nTMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be \r\npreferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK \r\nactivity arrests embryos, affects seedling development and persists into adult growth, \r\nsuggesting that maternal effect could shape development beyond fertilization and early \r\nembryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane \r\ncomposition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid \r\nmetabolism triggers widespread patterning errors. \r\nTogether, these results reposition early plant patterning as a hierarchical cascade that begins \r\nwith maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated \r\nby maternal receptor signaling and could ultimately be gated by the biophysical properties of \r\nthe membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking \r\ninto a single narrative, this thesis helps shifting the approach of viewing the embryo as an \r\nautonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal \r\ncontext.","lang":"eng"}],"file_date_updated":"2026-09-25T22:30:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-16T07:59:32Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"20187","status":"public"}]},"degree_awarded":"PhD","date_created":"2025-09-17T13:28:01Z","article_processing_charge":"No","month":"09","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","page":"116","doi_confirm":"1","doi":"10.15479/AT-ISTA-20362","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"oa":1,"title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","author":[{"first_name":"David","full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic"}],"corr_author":"1"},{"acknowledgement":"European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360","citation":{"chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>.","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.).","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. .","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>"},"year":"2025","das_tickbox":"1","day":"25","oa_version":"Preprint","_id":"21427","status":"public","OA_place":"repository","fulldoi":"https://doi.org/10.1101/2025.05.20.655037","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["539","570"],"date_published":"2025-09-25T00:00:00Z","has_accepted_license":"1","abstract":[{"text":"While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-26T23:31:06Z","related_material":{"record":[{"relation":"research_data","id":"21439","status":"public"},{"status":"public","id":"22963","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"21423"}]},"project":[{"grant_number":"101071793","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"date_created":"2026-03-11T08:40:06Z","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"09","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}],"publication_status":"draft","doi":"10.1101/2025.05.20.655037","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.20.655037"}],"type":"preprint","oa":1,"title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","author":[{"last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","first_name":"Zuzana"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","orcid":"0000-0003-1671-393X","first_name":"Saren"},{"first_name":"Juraj","last_name":"Majek","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","full_name":"Majek, Juraj"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"Sahai, Erik","last_name":"Sahai","first_name":"Erik"},{"full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B"}],"publication":"bioRxiv","corr_author":"1"},{"corr_author":"1","author":[{"last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","orcid":"0000-0001-6060-4795","first_name":"Kasumi"}],"title":"Regulation of notochord and floor plate size during mouse development","oa":1,"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20393","doi_confirm":"1","page":"102","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"AnKi"},{"_id":"EdHa"}],"month":"09","article_processing_charge":"No","date_created":"2025-09-25T10:08:10Z","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"18481","status":"public"}]},"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-16T08:31:16Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"During vertebrate development, the morphogen Sonic Hedgehog (Shh) plays a key role in \r\npatterning the tissues of the extending body. This requires precise coordination between the \r\nsize of the source of Shh production and the embryo body. Shh is produced by the notochord, \r\nas well as floorplate of the neural tube. In this thesis, we investigated how the sizes of the \r\nnotochord and floorplate are regulated and how they impact the developing mouse embryo.  \r\nTo measure the size and shape of the developing mouse notochord and the cell behaviours \r\nwithin this organ, we performed high-resolution measurements in cleared embryos between \r\nE8.5 and E10.5 of development. Strikingly, our data revealed that the notochord maintains a \r\nconstant cross-sectional area throughout the trunk over time as it lengthens by cell \r\nproliferation. We show that this is achieved by a feedback between the notochord cell \r\nproliferation rate and both the cross-sectional area of the trunk notochord and elongation of \r\nthe embryo. Using live imaging, we further show that notochord cells undergo posteriorly\r\ndirected active cell migration and that this cell migration contributes to maintaining the \r\nstructural integrity of the notochord. Our results show a complex coordination of cell \r\nbehaviours that allow for robust notochord morphogenesis during mouse development and \r\nthe maintenance of a defined Shh source size.  \r\nShh produced by the notochord induces a secondary Shh-producing domain, the floor plate. \r\nHow the notochord and floor plate contribute to the formation of the Shh gradient in the \r\nneural tube and to the regulation of the floor plate size is poorly understood. Our theoretical \r\nand experimental analysis indicates that only the initial levels of notochord-derived Shh \r\ninfluence the size of the floor plate, and the floor plate is insensitive to its own production of \r\nShh. After its initial establishment, the floor plate expands by tissue growth, leading to scaling \r\nof the Shh gradient amplitude with tissue size.   \r\nAltogether, we show that the mechanisms regulating the sizes of the notochord and \r\nfloorplate in mouse development help to achieve size robustness of these tissues. Our data \r\ndemonstrate that the initial establishment of the Shh gradient in the neural tube is strongly \r\ndependent on the notochord and suggest that the robustness of notochord morphogenesis \r\nis essential for pattern formation. Later in development, the floor plate size and the Shh \r\ngradient are coupled to neural tube growth. Our findings provide new insights on how pattern \r\nformation, tissue growth and morphogenesis interact to ensure reproducible developmental \r\noutcomes. ","lang":"eng"}],"file_date_updated":"2026-09-30T22:30:04Z","date_published":"2025-09-24T00:00:00Z","has_accepted_license":"1","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-20393","OA_place":"publisher","status":"public","_id":"20393","oa_version":"Published Version","supervisor":[{"orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}],"day":"24","publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>.","mla":"Kishi, Kasumi. <i>Regulation of Notochord and Floor Plate Size during Mouse Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>.","short":"K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025.","ista":"Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria.","ama":"Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>","apa":"Kishi, K. (2025). <i>Regulation of notochord and floor plate size during mouse development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>","ieee":"K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025."},"year":"2025","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"file":[{"embargo_to":"open_access","file_id":"20413","file_size":41847994,"date_created":"2025-09-30T14:33:17Z","file_name":"2025-Kishi-Kasumi-Thesis.zip","checksum":"6bb5a7ce318dc3f7bd165f2523e77b89","access_level":"closed","relation":"source_file","creator":"kkishi","date_updated":"2026-09-30T22:30:04Z","content_type":"application/x-zip-compressed"},{"relation":"main_file","access_level":"open_access","checksum":"88349b9177e1dcbe1242cd3884b36fdb","creator":"kkishi","content_type":"application/pdf","date_updated":"2026-09-30T22:30:04Z","file_id":"20414","file_size":55747072,"embargo":"2026-09-30","date_created":"2025-09-30T14:33:22Z","file_name":"2025-Kishi-Kasumi-Thesis.pdf"}]},{"doi_confirm":"1","oa":1,"title":"Nuclear and cell surface auxin signaling in A. thaliana developmental transitions","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20364","author":[{"first_name":"Caterina","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini"}],"corr_author":"1","degree_awarded":"PhD","related_material":{"record":[{"id":"12291","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"19399","relation":"part_of_dissertation"}]},"article_processing_charge":"No","date_created":"2025-09-19T12:23:38Z","month":"09","page":"151","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"language":[{"iso":"eng"}],"OA_place":"publisher","has_accepted_license":"1","date_published":"2025-09-19T00:00:00Z","ddc":["580"],"keyword":["Auxin Signaling","Plant Development"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20364","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2026-09-30T22:30:03Z","abstract":[{"lang":"eng","text":"Auxin is a central regulator of plant growth and development, orchestrating processes from \r\nembryogenesis to senescence through a complex network of biosynthesis, transport, and \r\nsignaling pathways.  \r\nIn Arabidopsis thaliana, canonical nuclear auxin signaling is mediated by the TIR1/AFB \r\nreceptors, which promote degradation of AUX/IAA repressors to enable ARF transcription \r\nfactors-driven transcriptional reprogramming. Parallel to this well-established nuclear \r\nmechanism, auxin also triggers rapid, non-transcriptional responses. In particular, at the cell \r\nsurface, most notably through ABP1 and TMKs. Despite decades of research, the integration \r\nof these pathways and their links to fundamental cellular processes remains not fully \r\nunderstood.  \r\nIn this study, we uncover a new role for TIR1/AFB signaling in rapidly activating \r\nmacroautophagy during developmental reprogramming. Auxin induces autophagy via \r\nTIR1/AFB adenylate cyclase activity, linking auxin perception to cAMP production and \r\ntranscriptional activation of autophagy machinery. Autophagy-deficient mutants exhibit \r\ndelayed meristem differentiation, impaired lateral root progression, and reduced shoot \r\norganogenesis, demonstrating its necessity for timely developmental transitions. \r\nWe also revisit the ABP1-TMK1 cell-surface auxin perception complex, providing \r\nbiochemical and mass photometry evidence for auxin-dependent complex formation. We show \r\nthat ABP1-TMK1 triggers an ultrafast global phosphorylation response targeting ~1000 \r\nproteins, including the auxin transporter PIN2, and Rho-of-plants (ROP) GTPases regulators. \r\nThis pathway directly regulates PIN2 phosphorylation, for gravitropism and auxin dependent \r\nROP activation. \r\nThese findings establish an integrated framework in which nuclear TIR1/AFB signaling and \r\ncell-surface ABP1-TMK signaling act in parallel to synchronize gene expression, cytoplasmic \r\nremodelling, and transporter regulation, thereby ensuring robust developmental plasticity in \r\nArabidopsis thaliana. "}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-16T08:24:09Z","file":[{"file_name":"2025_Giannini_Caterina_Thesis...pdf","embargo":"2026-09-30","date_created":"2025-09-24T14:46:34Z","file_size":14278965,"file_id":"20390","date_updated":"2026-09-30T22:30:03Z","content_type":"application/pdf","creator":"cgiannin","access_level":"open_access","checksum":"536ba1701453b0b2346be14c046b2911","relation":"main_file"},{"embargo_to":"open_access","file_id":"20391","file_name":"2025_Giannini_Caterina_Thesis...docx","date_created":"2025-09-24T14:46:35Z","file_size":24499022,"access_level":"closed","checksum":"192f55262f2da2ea0a59d9c23a1b8573","relation":"source_file","date_updated":"2026-09-30T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cgiannin"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"supervisor":[{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"}],"day":"19","publisher":"Institute of Science and Technology Austria","citation":{"short":"C. Giannini, Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions, Institute of Science and Technology Austria, 2025.","mla":"Giannini, Caterina. <i>Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>.","chicago":"Giannini, Caterina. “Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>.","apa":"Giannini, C. (2025). <i>Nuclear and cell surface auxin signaling in A. thaliana developmental transitions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>","ieee":"C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025.","ama":"Giannini C. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>","ista":"Giannini C. 2025. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria."},"year":"2025","acknowledgement":"Plant Facility,\r\nProtein Service Facility","_id":"20364","status":"public","oa_version":"Published Version"},{"date_created":"2025-05-30T09:14:58Z","article_processing_charge":"No","project":[{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"13136","relation":"part_of_dissertation"},{"status":"public","id":"17148","relation":"part_of_dissertation"},{"status":"public","id":"18601","relation":"part_of_dissertation"},{"id":"18807","relation":"part_of_dissertation","status":"public"}]},"page":"129","department":[{"_id":"AnKi"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"05","publication_identifier":{"issn":["2663-337X"]},"title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","oa":1,"doi":"10.15479/AT-ISTA-19763","type":"dissertation","corr_author":"1","author":[{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093","first_name":"Stefanie"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"file":[{"file_name":"Thesis_Lehr_PDFA.pdf","file_size":42879974,"embargo":"2025-11-30","date_created":"2025-05-30T09:10:22Z","file_id":"19764","content_type":"application/pdf","date_updated":"2025-11-30T23:30:02Z","creator":"cchlebak","checksum":"8cd7fe3ca990adbcafdece119aa0973d","access_level":"open_access","relation":"main_file"},{"file_name":"Thesis_Lehr_emptyPages.docx","file_size":18731094,"date_created":"2025-05-30T09:31:15Z","embargo_to":"open_access","file_id":"19765","date_updated":"2025-11-30T23:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","checksum":"0c87dd5fc803450a47b20736b5f86a2f","access_level":"closed","relation":"source_file"}],"status":"public","_id":"19763","oa_version":"Published Version","day":"29","supervisor":[{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"}],"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.","year":"2025","citation":{"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>.","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>.","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>","ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025.","ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria.","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>"},"publisher":"Institute of Science and Technology Austria","ddc":["570"],"has_accepted_license":"1","date_published":"2025-05-29T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-19763","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-20T08:57:07Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2025-11-30T23:30:02Z","abstract":[{"text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation.","lang":"eng"}]},{"doi":"10.15479/AT-ISTA-20694","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"oa":1,"title":"Using genealogies to study the genomic basis of species divergence","corr_author":"1","author":[{"first_name":"Arka","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"}],"date_created":"2025-11-25T13:19:11Z","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12159"},{"status":"public","id":"20190","relation":"part_of_dissertation"},{"status":"public","id":"14796","relation":"part_of_dissertation"}]},"project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"},{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_status":"published","page":"268","month":"11","fulldoi":"https://doi.org/10.15479/AT-ISTA-20694","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["576","578"],"has_accepted_license":"1","date_published":"2025-11-25T00:00:00Z","OA_place":"publisher","date_updated":"2026-10-21T08:23:54Z","alternative_title":["ISTA Thesis"],"file_date_updated":"2026-03-01T23:30:03Z","abstract":[{"lang":"eng","text":"Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"creator":"apal","date_updated":"2026-03-01T23:30:03Z","content_type":"application/pdf","relation":"main_file","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","access_level":"open_access","file_size":42723135,"embargo":"2026-03-01","date_created":"2025-12-01T13:53:36Z","file_name":"2025_Pal_Arka_Thesis.pdf","file_id":"20721"},{"checksum":"166d832b08d0434ce407f8f3cb930fe5","access_level":"closed","relation":"source_file","creator":"apal","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-03-01T23:30:03Z","embargo_to":"open_access","file_id":"20722","file_size":60632116,"date_created":"2025-12-01T13:53:39Z","file_name":"2025_Pal_Arka_Thesis.docx"}],"oa_version":"Published Version","_id":"20694","status":"public","citation":{"short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025.","mla":"Pal, Arka. <i>Using Genealogies to Study the Genomic Basis of Species Divergence</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>.","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.","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>","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria.","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>"},"year":"2025","publisher":"Institute of Science and Technology Austria","day":"25","supervisor":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}]}]