[{"status":"public","type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:12491","author":[{"first_name":"Bettina","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","full_name":"Zens, Bettina"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"date_updated":"2026-04-07T13:49:23Z","language":[{"iso":"eng"}],"citation":{"ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491"},"has_accepted_license":"1","corr_author":"1","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"file_date_updated":"2024-02-08T23:30:04Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"02","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"related_material":{"record":[{"id":"8586","status":"public","relation":"part_of_dissertation"}]},"page":"187","file":[{"embargo":"2024-02-07","relation":"main_file","checksum":"069d87f025e0799bf9e3c375664264f2","file_size":23082464,"date_updated":"2024-02-08T23:30:04Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","content_type":"application/pdf","creator":"bzens","file_id":"12527","access_level":"open_access","date_created":"2023-02-07T13:07:38Z"},{"creator":"bzens","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12528","access_level":"closed","date_created":"2023-02-07T13:09:05Z","relation":"source_file","checksum":"8c66ed203495d6e078ed1002a866520c","embargo_to":"open_access","file_size":106169509,"file_name":"PhDThesis_BettinaZens_2023_final.docx","date_updated":"2024-02-08T23:30:04Z"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"degree_awarded":"PhD","date_created":"2023-02-02T14:50:20Z","abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"oa":1,"year":"2023","alternative_title":["ISTA Thesis"],"date_published":"2023-02-02T00:00:00Z","ddc":["570"],"supervisor":[{"full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"publisher":"Institute of Science and Technology Austria","day":"02","_id":"12491","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","OA_place":"publisher","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"]},{"ddc":["570","577"],"_id":"13984","day":"08","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"OA_place":"publisher","title":"Individual and social immunity against viral infections in ants","degree_awarded":"PhD","abstract":[{"text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection.","lang":"eng"}],"date_created":"2023-08-08T15:33:29Z","oa":1,"date_published":"2023-08-08T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2023","has_accepted_license":"1","citation":{"ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984","apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984."},"language":[{"iso":"eng"}],"file_date_updated":"2024-10-29T23:31:04Z","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"08","acknowledged_ssus":[{"_id":"LifeSc"}],"file":[{"file_size":10416761,"embargo_to":"open_access","checksum":"55c876b73d49db15228a7f571592ec77","title":"Combined Version of original Thesis and Addendum","relation":"main_file","date_updated":"2024-10-29T23:31:04Z","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","content_type":"application/pdf","creator":"cchlebak","date_created":"2024-03-01T08:56:06Z","access_level":"open_access","file_id":"15044"},{"file_size":10797612,"checksum":"27220243d5d51c3b0d7d61c0879d7a0c","embargo":"2024-08-08","relation":"main_file","date_updated":"2024-08-09T22:30:03Z","file_name":"Thesis_AnnaFranschitz_202308.pdf","creator":"afransch","content_type":"application/pdf","date_created":"2023-08-08T18:01:28Z","access_level":"open_access","file_id":"13986"},{"file_id":"13987","date_created":"2023-08-08T18:02:25Z","access_level":"closed","creator":"afransch","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_AnnaFranschitz_202308.docx","date_updated":"2024-08-09T22:30:03Z","embargo_to":"open_access","checksum":"40abf7ccca14a3893f72dc7fb88585d6","relation":"source_file","file_size":2619085},{"file_size":85956,"relation":"main_file","title":"Addendum","embargo":"2024-08-08","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","date_updated":"2024-10-29T23:31:04Z","file_name":"Addendum_AnnaFranschitz202402.pdf","description":"Minor modifications and clarifications - Feb 2024","creator":"cchlebak","content_type":"application/pdf","access_level":"open_access","date_created":"2024-03-01T08:37:15Z","file_id":"15042"},{"creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"15043","access_level":"closed","date_created":"2024-03-01T08:39:20Z","title":"Addendum - source file","relation":"source_file","embargo_to":"open_access","checksum":"66745aa01f960f17472c024875c049ed","file_size":11818,"file_name":"Addendum_AnnaFranschitz202402.docx","date_updated":"2024-08-09T22:30:03Z"}],"page":"89","publication_identifier":{"isbn":["978-3-99078-034-3"],"issn":["2663-337X"]},"status":"public","doi":"10.15479/at:ista:13984","publication_status":"published","oa_version":"Published Version","type":"dissertation","article_processing_charge":"No","author":[{"last_name":"Franschitz","full_name":"Franschitz, Anna","id":"480826C8-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"date_updated":"2026-04-07T13:51:29Z","department":[{"_id":"GradSch"},{"_id":"SyCr"}]},{"OA_place":"publisher","title":"Mechanochemical pattern formation across biological scales","ec_funded":1,"ddc":["530"],"_id":"12964","day":"17","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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","short":"CC BY-NC-SA (4.0)"},"oa":1,"date_published":"2023-05-17T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2023","degree_awarded":"PhD","date_created":"2023-05-15T14:52:36Z","abstract":[{"lang":"eng","text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability."}],"month":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8602"}]},"page":"146","file":[{"file_size":40414730,"relation":"main_file","embargo":"2024-05-17","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","file_name":"thesis_boocock.pdf","date_updated":"2024-05-18T22:30:03Z","content_type":"application/pdf","creator":"dboocock","access_level":"open_access","date_created":"2023-05-17T13:39:54Z","file_id":"12988"},{"file_size":34338567,"embargo_to":"open_access","checksum":"581a2313ffeb40fe77e8a122a25a7795","relation":"source_file","file_name":"thesis_boocock.zip","date_updated":"2024-05-18T22:30:03Z","content_type":"application/zip","creator":"dboocock","date_created":"2023-05-17T13:39:53Z","access_level":"closed","file_id":"12989"}],"publication_identifier":{"isbn":["978-3-99078-032-9"],"issn":["2663-337X"]},"has_accepted_license":"1","citation":{"ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964"},"language":[{"iso":"eng"}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"file_date_updated":"2024-05-18T22:30:03Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","corr_author":"1","author":[{"orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R","last_name":"Boocock","full_name":"Boocock, Daniel R"}],"article_processing_charge":"No","date_updated":"2026-04-07T13:52:57Z","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"status":"public","doi":"10.15479/at:ista:12964","publication_status":"published","oa_version":"Published Version","type":"dissertation"},{"has_accepted_license":"1","citation":{"mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.","apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891"},"language":[{"iso":"eng"}],"project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239"}],"file_date_updated":"2024-05-06T22:30:03Z","corr_author":"1","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"page":"190","file":[{"checksum":"59b0303dc483f40a96a610a90aab7ee9","relation":"main_file","embargo":"2024-05-05","file_size":31434230,"file_name":"Thesis_Schauer_final.pdf","date_updated":"2024-05-06T22:30:03Z","creator":"aschauer","content_type":"application/pdf","file_id":"12907","date_created":"2023-05-05T13:01:14Z","access_level":"open_access"},{"embargo_to":"open_access","checksum":"25f54e12479b6adaabd129a20568e6c1","relation":"source_file","file_size":43809109,"file_name":"Thesis_Schauer_final.docx","date_updated":"2024-05-06T22:30:03Z","creator":"aschauer","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12908","date_created":"2023-05-05T13:04:15Z","access_level":"closed"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7888"},{"id":"8966","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"status":"public","doi":"10.15479/at:ista:12891","publication_status":"published","oa_version":"Published Version","type":"dissertation","author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra"}],"article_processing_charge":"No","date_updated":"2025-06-12T06:56:58Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"ddc":["570"],"_id":"12891","day":"05","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","ec_funded":1,"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context."}],"date_created":"2023-05-05T08:48:20Z","oa":1,"date_published":"2023-05-05T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2023"},{"abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"date_created":"2023-10-12T14:13:25Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"year":"2023","date_published":"2023-10-12T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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","short":"CC BY-NC-SA (4.0)"},"day":"12","supervisor":[{"last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"}],"publisher":"Institute of Science and Technology Austria","_id":"14422","ddc":["610"],"title":"Synapseek: Meta-learning synaptic plasticity rules","ec_funded":1,"OA_place":"publisher","oa_version":"Published Version","type":"dissertation","doi":"10.15479/at:ista:14422","publication_status":"published","status":"public","department":[{"_id":"GradSch"},{"_id":"TiVo"}],"date_updated":"2026-04-07T13:53:13Z","author":[{"first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J","last_name":"Confavreux"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"file_date_updated":"2024-10-13T22:30:04Z","corr_author":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.","apa":"Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422","mla":"Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422.","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023."},"publication_identifier":{"issn":["2663-337X"]},"page":"148","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9633"}]},"file":[{"file_id":"14424","access_level":"open_access","date_created":"2023-10-12T14:53:50Z","creator":"cchlebak","content_type":"application/pdf","file_name":"Confavreux_Thesis_2A.pdf","date_updated":"2024-10-13T22:30:04Z","relation":"main_file","embargo":"2024-10-12","checksum":"7f636555eae7803323df287672fd13ed","file_size":30599717},{"date_created":"2023-10-18T07:38:34Z","access_level":"closed","file_id":"14440","creator":"cchlebak","content_type":"application/x-zip-compressed","file_name":"Confavreux Thesis.zip","date_updated":"2024-10-13T22:30:04Z","file_size":68406739,"embargo_to":"open_access","checksum":"725e85946db92290a4583a0de9779e1b","relation":"source_file"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"10"},{"_id":"14656","day":"29","publisher":"Society for Neuroscience","ddc":["570"],"pmid":1,"publication":"The Journal of Neuroscience","volume":43,"article_type":"original","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","ec_funded":1,"date_created":"2023-12-10T23:00:58Z","abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"intvolume":" 43","quality_controlled":"1","date_published":"2023-11-29T00:00:00Z","issue":"48","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"scopus_import":"1","file_date_updated":"2024-06-02T22:30:03Z","project":[{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"has_accepted_license":"1","citation":{"chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156."},"language":[{"iso":"eng"}],"external_id":{"pmid":["37758476"],"isi":["001148071000005"]},"acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","page":"8140-8156","related_material":{"record":[{"id":"10077","status":"public","relation":"earlier_version"}]},"file":[{"file_size":2280632,"checksum":"e2503c8f84be1050e28f64320f1d5bd2","embargo":"2024-06-01","relation":"main_file","date_updated":"2024-06-02T22:30:03Z","file_name":"2023_JourNeuroscience_Nardin.pdf","content_type":"application/pdf","creator":"dernst","date_created":"2023-12-11T11:30:37Z","access_level":"open_access","file_id":"14674"}],"publication_identifier":{"eissn":["1529-2401"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"11","doi":"10.1523/JNEUROSCI.0194-23.2023","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","date_updated":"2025-09-09T13:37:51Z","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"author":[{"orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Nardin","full_name":"Nardin, Michele"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina","last_name":"Savin"}],"article_processing_charge":"Yes (in subscription journal)"},{"publication_identifier":{"issn":["2663-337X"]},"page":"115","file":[{"file_id":"12814","access_level":"open_access","date_created":"2023-04-07T06:16:06Z","creator":"cchlebak","content_type":"application/pdf","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_updated":"2024-04-08T22:30:03Z","relation":"main_file","embargo":"2024-04-07","checksum":"35b5997d2b0acb461f9d33d073da0df5","file_size":9881969},{"date_created":"2023-04-07T06:17:11Z","access_level":"closed","file_id":"12815","content_type":"application/pdf","creator":"cchlebak","date_updated":"2024-04-08T22:30:03Z","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","file_size":44201583,"embargo_to":"open_access","checksum":"81198f63c294890f6d58e8b29782efdc","relation":"source_file"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","date_created":"2023-04-07T06:18:05Z","access_level":"closed","file_id":"12816","file_size":84731244,"embargo_to":"open_access","checksum":"0317bf7f457bb585f99d453ffa69eb53","relation":"source_file","date_updated":"2024-04-08T22:30:03Z","file_name":"Thesis_CatarinaAlcarva_final.docx"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"month":"04","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","file_date_updated":"2024-04-08T22:30:03Z","project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"citation":{"chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023."},"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"RySh"}],"date_updated":"2026-04-07T13:53:28Z","article_processing_charge":"No","author":[{"id":"3A96634C-F248-11E8-B48F-1D18A9856A87","first_name":"Catarina","last_name":"Alcarva","full_name":"Alcarva, Catarina"}],"type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:12809","status":"public","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","OA_place":"publisher","supervisor":[{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"}],"publisher":"Institute of Science and Technology Austria","day":"06","_id":"12809","ddc":["570"],"year":"2023","alternative_title":["ISTA Thesis"],"date_published":"2023-04-06T00:00:00Z","oa":1,"date_created":"2023-04-06T07:54:09Z","abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"degree_awarded":"PhD"},{"day":"12","publisher":"National Academy of Sciences","_id":"13201","pmid":1,"ddc":["570"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","article_type":"original","volume":120,"quality_controlled":"1","date_created":"2023-07-09T22:01:12Z","intvolume":" 120","abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"issue":"25","year":"2023","date_published":"2023-06-12T00:00:00Z","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"file_date_updated":"2023-12-13T23:30:03Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","language":[{"iso":"eng"}],"article_number":"e2221313120","has_accepted_license":"1","citation":{"apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(25). doi:10.1073/pnas.2221313120","ieee":"Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25. National Academy of Sciences, 2023.","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120."},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"external_id":{"isi":["001030689600003"],"pmid":["37307446"]},"acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), Hainan Provincial Natural Science Foundation of China (323CXTD379), Chinese Universities Scientific Fund (2023TC019), Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, and China Postdoctoral Science Foundation (BH2020259460).","file":[{"content_type":"application/pdf","creator":"alisjak","access_level":"open_access","date_created":"2023-07-10T08:48:40Z","file_id":"13204","file_size":5244581,"embargo":"2023-12-12","relation":"main_file","checksum":"d800e06252eaefba28531fa9440f23f0","file_name":"2023_PNAS_Wang.pdf","date_updated":"2023-12-13T23:30:03Z"}],"month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","doi":"10.1073/pnas.2221313120","publication_status":"published","status":"public","isi":1,"department":[{"_id":"JiFr"}],"date_updated":"2023-12-13T23:30:04Z","author":[{"first_name":"Yalu","last_name":"Wang","full_name":"Wang, Yalu"},{"last_name":"Yuan","full_name":"Yuan, Zhi","first_name":"Zhi"},{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"last_name":"Xiao","full_name":"Xiao, Huixin","first_name":"Huixin"},{"first_name":"Lu","last_name":"Wan","full_name":"Wan, Lu"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li"},{"first_name":"Yan","full_name":"Guo, Yan","last_name":"Guo"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"last_name":"Zhang","full_name":"Zhang, Jing","first_name":"Jing"}],"article_processing_charge":"No"},{"has_accepted_license":"1","citation":{"ama":"Sack S. Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.","apa":"Sack, S. (2023). Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","mla":"Sack, Stefan. Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.","ista":"Sack S. 2023. Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","ieee":"S. Sack, “Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","short":"S. Sack, Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023."},"language":[{"iso":"eng"}],"project":[{"name":"IMB PhD Nomination Fellowship - Stefan Sack","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"file_date_updated":"2024-11-30T23:30:03Z","corr_author":"1","month":"11","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"PhD_Thesis.pdf","date_updated":"2024-11-30T23:30:03Z","checksum":"068fd3570506ec42b2faa390de784bc4","relation":"main_file","embargo":"2024-11-30","file_size":11947523,"file_id":"14635","date_created":"2023-11-30T15:53:10Z","access_level":"open_access","content_type":"application/pdf","creator":"ssack"},{"date_created":"2023-11-30T15:54:11Z","access_level":"closed","file_id":"14636","content_type":"application/zip","creator":"ssack","date_updated":"2024-11-30T23:30:03Z","file_name":"PhD Thesis (1).zip","file_size":18422964,"embargo_to":"open_access","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","relation":"source_file"}],"page":"142","related_material":{"record":[{"id":"13125","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11471"},{"id":"9760","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"status":"public","doi":"10.15479/at:ista:14622","publication_status":"published","oa_version":"Published Version","type":"dissertation","article_processing_charge":"No","author":[{"first_name":"Stefan","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan","last_name":"Sack"}],"date_updated":"2026-04-07T13:53:47Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"ddc":["530"],"_id":"14622","day":"30","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","title":"Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems","ec_funded":1,"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum\r\ncomputation due to their moderate hardware requirements and resilience to noise. Our\r\nprimary focus lies on two particular types of VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE), utilized for finding ground states of quantum many-body systems.\r\nIn the first part of the thesis, we examine the issue of effective parameter initialization for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA often leads to\r\nconvergence in local minima with sub-optimal performance. To mitigate this issue, we propose\r\nan initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization leads to the same performance as the best of an exponentially\r\nscaling number of random initializations.\r\nThe second study introduces Transition States (TS), stationary points with a single direction\r\nof descent, as a tool for systematically exploring the QAOA optimization landscape. This\r\nleads us to propose a novel greedy parameter initialization strategy that guarantees for the\r\nenergy to decrease with increasing number of circuit layers.\r\nIn the third section, we extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations of qubits. This chapter provides theoretical insights and practical strategies for\r\nleveraging the increased computational power of qudits in the context of quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients that obstruct efficient parameter optimization. This novel approach relies\r\non defining a notion of weak barren plateaus based on the entropies of local reduced density\r\nmatrices and showcases how these can be efficiently quantified using shadow tomography.\r\nTo illustrate the approach we employ the strategy in the VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization and throughout the optimization.\r\nTaken together, this thesis greatly enhances our understanding of parameter initialization and\r\noptimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method to address the challenge of barren plateaus using the VQE. These\r\ninsights are instrumental in advancing the field of near-term quantum computation."}],"date_created":"2023-11-28T10:58:13Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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","short":"CC BY-NC-SA (4.0)"},"oa":1,"date_published":"2023-11-30T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2023"},{"isi":1,"status":"public","publication_status":"published","doi":"10.1103/physreva.107.062404","type":"journal_article","oa_version":"Published Version","author":[{"last_name":"Sack","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan"},{"last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"first_name":"Richard","last_name":"Kueng","full_name":"Kueng, Richard"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"article_processing_charge":"No","date_updated":"2026-05-13T22:30:23Z","department":[{"_id":"MaSe"}],"citation":{"chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/physreva.107.062404.","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404.","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404."},"has_accepted_license":"1","article_number":"062404","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","project":[{"grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"file_date_updated":"2023-06-13T07:28:36Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"13131","success":1,"access_level":"open_access","date_created":"2023-06-13T07:28:36Z","relation":"main_file","checksum":"0d71423888eeccaa60d8f41197f26306","file_size":2524611,"file_name":"2023_PhysRevA_Sack.pdf","date_updated":"2023-06-13T07:28:36Z"}],"related_material":{"record":[{"id":"17208","status":"public","relation":"dissertation_contains"},{"id":"14622","status":"public","relation":"dissertation_contains"}]},"external_id":{"arxiv":["2209.01159"],"isi":["001016927100012"]},"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"date_created":"2023-06-07T06:57:32Z","intvolume":" 107","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2023-06-02T00:00:00Z","year":"2023","issue":"6","ddc":["530"],"_id":"13125","publisher":"American Physical Society","arxiv":1,"day":"02","volume":107,"ec_funded":1,"title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","article_type":"original","publication":"Physical Review A"},{"date_published":"2023-11-01T00:00:00Z","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"intvolume":" 19","date_created":"2023-08-11T07:41:17Z","abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"quality_controlled":"1","publication":"Nature Physics","keyword":["General Physics and Astronomy"],"volume":19,"title":"Superconductivity from a melted insulator in Josephson junction arrays","article_type":"original","ec_funded":1,"_id":"14032","day":"01","publisher":"Springer Nature","ddc":["530"],"date_updated":"2026-05-13T22:30:26Z","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"author":[{"first_name":"Soham","orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay"},{"full_name":"Senior, Jorden L","last_name":"Senior","first_name":"Jorden L","orcid":"0000-0002-0672-9295","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime"},{"first_name":"Denise","orcid":"0000-0003-1144-2763","id":"4D495994-AE37-11E9-AC72-31CAE5697425","last_name":"Puglia","full_name":"Puglia, Denise"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"}],"article_processing_charge":"Yes (in subscription journal)","doi":"10.1038/s41567-023-02161-w","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"isi":["001054563800006"]},"page":"1630-1635","file":[{"file_id":"14899","date_created":"2024-01-29T11:25:38Z","access_level":"open_access","success":1,"content_type":"application/pdf","creator":"dernst","date_updated":"2024-01-29T11:25:38Z","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","checksum":"1fc86d71bfbf836e221c1e925343adc5","relation":"main_file","file_size":1977706}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17881"}]},"acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","scopus_import":"1","project":[{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"file_date_updated":"2024-01-29T11:25:38Z","corr_author":"1","has_accepted_license":"1","citation":{"chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02161-w","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635. doi:10.1038/s41567-023-02161-w","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:10.1038/s41567-023-02161-w.","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","ieee":"S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023.","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635."},"language":[{"iso":"eng"}]},{"oa_version":"Published Version","type":"journal_article","doi":"10.1093/evlett/qrac004","publication_status":"published","status":"public","isi":1,"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"date_updated":"2026-05-13T22:30:29Z","author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"article_processing_charge":"Yes (via OA deal)","project":[{"grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"file_date_updated":"2023-08-16T11:43:33Z","corr_author":"1","scopus_import":"1","language":[{"iso":"eng"}],"article_number":"qrac004","has_accepted_license":"1","citation":{"apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004."},"publication_identifier":{"issn":["2056-3744"]},"external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18531"}]},"acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","file":[{"file_id":"14068","success":1,"access_level":"open_access","date_created":"2023-08-16T11:43:33Z","content_type":"application/pdf","creator":"dernst","file_name":"2023_EvLetters_Mrnjavac.pdf","date_updated":"2023-08-16T11:43:33Z","relation":"main_file","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_size":2592189}],"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_created":"2023-02-06T13:59:12Z","abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"intvolume":" 7","issue":"1","year":"2023","date_published":"2023-02-01T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"day":"01","publisher":"Oxford University Press","_id":"12521","pmid":1,"ddc":["570"],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"publication":"Evolution Letters","article_type":"original","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","ec_funded":1,"volume":7},{"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"day":"20","_id":"14697","ddc":["570"],"ec_funded":1,"title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","OA_place":"publisher","date_created":"2023-12-18T19:14:28Z","abstract":[{"lang":"eng","text":"During my Ph.D. research, I managed a series of projects, each focused on the\r\nmechanisms underlying cell migration. My work involved an in-depth examination of\r\nthe complex strategies employed by neutrophils, with a specific focus on their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient perception. However, it\r\nis essential to acknowledge that not all projects yielded successful results, as some\r\nideas were discontinued and are archived for future reference within this thesis.\r\nMy main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source\r\ntype – linear or point-like. By combining single-cell tracking in 3D environments with\r\nproxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential gradients from point sources. In addition, neutrophils\r\nexhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over\r\ntime and employed a \"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic \"tumbles\" for efficient navigation.\r\nThe project extended to the possibility of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings, pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences\r\nin migratory efficacy were detected across pore sizes and device heights, quantifying\r\ngradient manipulation effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\" (LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through extensive experimentation with multiple\r\nparameters, we attempted to trigger responses from neutrophils. Despite these efforts\r\nand collaboration, the project failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line. Despite their existence, their migratory behavior was largely\r\nunexplored due to potential limitations. Through differentiation protocol refinements we\r\nenhanced their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils. Despite this, the improved migration potential of these cells pointed toward\r\ntheir utility for in vitro murine neutrophil migration studies."}],"degree_awarded":"PhD","year":"2023","alternative_title":["ISTA Thesis"],"date_published":"2023-12-20T00:00:00Z","oa":1,"corr_author":"1","file_date_updated":"2024-12-20T23:30:04Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"language":[{"iso":"eng"}],"citation":{"ama":"Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697","apa":"Stopp, J. A. (2023). Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697","chicago":"Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.","short":"J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","ista":"Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","ieee":"J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","mla":"Stopp, Julian A. Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697."},"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-038-1"]},"page":"226","file":[{"creator":"jstopp","content_type":"application/pdf","access_level":"open_access","date_created":"2023-12-20T09:35:34Z","file_id":"14699","file_size":51585778,"relation":"main_file","embargo":"2024-12-20","checksum":"457927165d5d556305d3086f6b83e5c7","file_name":"Thesis.pdf","date_updated":"2024-12-20T23:30:04Z"},{"file_id":"14700","access_level":"closed","date_created":"2023-12-20T09:35:35Z","creator":"jstopp","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis.docx","date_updated":"2024-12-20T23:30:04Z","relation":"source_file","embargo_to":"open_access","checksum":"e8d26449ac461f5e8478a62c9507506f","file_size":69625950}],"related_material":{"record":[{"id":"14360","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12272"},{"status":"public","relation":"part_of_dissertation","id":"14274"},{"relation":"part_of_dissertation","status":"public","id":"6328"},{"id":"7885","status":"public","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:14697","status":"public","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"date_updated":"2026-04-07T13:57:40Z","article_processing_charge":"No","author":[{"first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","full_name":"Stopp, Julian A"}]},{"quality_controlled":"1","intvolume":" 8","date_created":"2023-09-06T08:07:51Z","abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"year":"2023","issue":"87","date_published":"2023-09-01T00:00:00Z","oa":1,"publisher":"American Association for the Advancement of Science","day":"01","_id":"14274","pmid":1,"publication":"Science Immunology","keyword":["General Medicine","Immunology"],"ec_funded":1,"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","article_type":"original","volume":8,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1126/sciimmunol.adc9584","status":"public","isi":1,"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"date_updated":"2026-05-13T22:30:30Z","article_processing_charge":"No","author":[{"last_name":"Alanko","full_name":"Alanko, Jonna H","first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061"},{"last_name":"Ucar","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","first_name":"Nikola","last_name":"Canigova","full_name":"Canigova, Nikola"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","last_name":"Stopp","full_name":"Stopp, Julian A"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan","last_name":"Schwarz"},{"full_name":"Merrin, Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"}],"corr_author":"1","project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","grant_number":"W01250-B20"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"scopus_import":"1","language":[{"iso":"eng"}],"citation":{"apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584."},"article_number":"adc9584","publication_identifier":{"issn":["2470-9468"]},"acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","related_material":{"record":[{"id":"14279","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"19745"},{"status":"public","relation":"dissertation_contains","id":"14697"}]},"external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 14","date_created":"2023-09-24T22:01:10Z","abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2023-09-13T00:00:00Z","year":"2023","ddc":["570"],"pmid":1,"_id":"14360","publisher":"Springer Nature","day":"13","volume":14,"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","article_type":"original","publication":"Nature Communications","isi":1,"status":"public","publication_status":"published","doi":"10.1038/s41467-023-41173-1","type":"journal_article","oa_version":"Published Version","author":[{"first_name":"Ewa","last_name":"Sitarska","full_name":"Sitarska, Ewa"},{"first_name":"Silvia Dias","last_name":"Almeida","full_name":"Almeida, Silvia Dias"},{"full_name":"Beckwith, Marianne Sandvold","last_name":"Beckwith","first_name":"Marianne Sandvold"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","last_name":"Stopp","full_name":"Stopp, Julian A"},{"last_name":"Czuchnowski","full_name":"Czuchnowski, Jakub","first_name":"Jakub"},{"full_name":"Siggel, Marc","last_name":"Siggel","first_name":"Marc"},{"first_name":"Rita","full_name":"Roessner, Rita","last_name":"Roessner"},{"first_name":"Aline","full_name":"Tschanz, Aline","last_name":"Tschanz"},{"last_name":"Ejsing","full_name":"Ejsing, Christer","first_name":"Christer"},{"full_name":"Schwab, Yannick","last_name":"Schwab","first_name":"Yannick"},{"last_name":"Kosinski","full_name":"Kosinski, Jan","first_name":"Jan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"},{"first_name":"Anna","last_name":"Kreshuk","full_name":"Kreshuk, Anna"},{"full_name":"Erzberger, Anna","last_name":"Erzberger","first_name":"Anna"},{"last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba","first_name":"Alba"}],"article_processing_charge":"Yes (via OA deal)","date_updated":"2026-05-13T22:30:30Z","department":[{"_id":"MiSi"}],"citation":{"mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications, vol. 14, 5644, Springer Nature, 2023, doi:10.1038/s41467-023-41173-1.","ieee":"E. Sitarska et al., “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 2023;14. doi:10.1038/s41467-023-41173-1","chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41173-1.","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41173-1"},"has_accepted_license":"1","article_number":"5644","language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2023-09-25T08:22:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14697"}]},"file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2023-09-25T08:22:58Z","success":1,"access_level":"open_access","file_id":"14365","file_size":2725421,"checksum":"ad670e3b3c64fc585675948370f6b149","relation":"main_file","file_name":"2023_NatureComm_Sitarska.pdf","date_updated":"2023-09-25T08:22:58Z"}],"external_id":{"pmid":["37704612"],"isi":["001087583700008"]},"publication_identifier":{"eissn":["2041-1723"]}},{"type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:14280","status":"public","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"date_updated":"2026-04-07T14:06:05Z","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","full_name":"Radler, Philipp","last_name":"Radler"}],"article_processing_charge":"No","corr_author":"1","file_date_updated":"2024-10-05T22:30:03Z","project":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163"},{"grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"citation":{"short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280"},"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"file":[{"date_updated":"2024-10-05T22:30:03Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","relation":"source_file","checksum":"87eef11fbc5c7df0826f12a3a629b444","embargo_to":"open_access","file_size":114932847,"file_id":"14390","access_level":"closed","date_created":"2023-10-04T10:11:53Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"pradler"},{"content_type":"application/pdf","creator":"pradler","access_level":"open_access","date_created":"2023-10-04T10:11:21Z","file_id":"14391","file_size":37838778,"embargo":"2024-10-04","relation":"main_file","checksum":"3253e099b7126469d941fd9419d68b4f","date_updated":"2024-10-05T22:30:03Z","file_name":"PhD Thesis_Philipp Radler_20231004.pdf"}],"page":"156","related_material":{"record":[{"id":"10934","status":"public","relation":"research_data"},{"id":"11373","relation":"part_of_dissertation","status":"public"},{"id":"7387","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"date_created":"2023-09-06T10:58:25Z","degree_awarded":"PhD","year":"2023","alternative_title":["ISTA Thesis"],"date_published":"2023-09-25T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"}],"publisher":"Institute of Science and Technology Austria","day":"25","_id":"14280","ddc":["572"],"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"ec_funded":1,"title":"Spatiotemporal signaling during assembly of the bacterial divisome","OA_place":"publisher"},{"corr_author":"1","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus"}],"file_date_updated":"2023-10-04T11:40:51Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., & Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience. Springer Nature, 2023. https://doi.org/10.1038/s41593-023-01280-0.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023, pp. 606–14, doi:10.1038/s41593-023-01280-0."},"has_accepted_license":"1","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"related_material":{"record":[{"id":"12370","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"18574"}]},"page":"606-614","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"14395","access_level":"open_access","success":1,"date_created":"2023-10-04T11:40:51Z","relation":"main_file","checksum":"a33d91e398e548f34003170e10988368","file_size":6144866,"date_updated":"2023-10-04T11:40:51Z","file_name":"2023_NatureNeuroscience_Gupta.pdf"}],"acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","external_id":{"pmid":["36959418"],"isi":["000955258300002"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41593-023-01280-0","status":"public","isi":1,"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"date_updated":"2026-05-13T22:30:35Z","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Divyansh","orcid":"0000-0001-7400-6665","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Divyansh","last_name":"Gupta"},{"full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F"},{"orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87","first_name":"Anton L","full_name":"Sumser, Anton L","last_name":"Sumser"},{"full_name":"Symonova, Olga","last_name":"Symonova","first_name":"Olga","orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Svaton","full_name":"Svaton, Jan","orcid":"0000-0002-6198-2939","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","first_name":"Jan"},{"last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","day":"01","_id":"12349","pmid":1,"ddc":["570"],"publication":"Nature Neuroscience","ec_funded":1,"article_type":"original","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","volume":26,"quality_controlled":"1","date_created":"2023-01-23T14:14:19Z","abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.","lang":"eng"}],"intvolume":" 26","year":"2023","date_published":"2023-04-01T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"date_published":"2023-01-26T00:00:00Z","year":"2023","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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","short":"CC BY-NC-SA (4.0)"},"oa":1,"abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. "}],"date_created":"2023-01-25T12:45:18Z","title":"Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields","ec_funded":1,"_id":"12370","day":"26","publisher":"Institute of Science and Technology Austria","ddc":["571"],"contributor":[{"last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","contributor_type":"researcher"},{"last_name":"Mlynarski","contributor_type":"researcher","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Svaton","first_name":"Jan","contributor_type":"researcher","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2"}],"date_updated":"2026-05-13T22:30:35Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"article_processing_charge":"No","author":[{"last_name":"Gupta","full_name":"Gupta, 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L., & Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370","mla":"Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12370.","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023)."}},{"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"day":"05","_id":"12800","ddc":["576"],"year":"2023","alternative_title":["ISTA Master's Thesis"],"date_published":"2023-04-05T00:00:00Z","oa":1,"date_created":"2023-04-04T18:57:11Z","abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"degree_awarded":"MS","publication_identifier":{"issn":["2791-4585"]},"page":"21","file":[{"date_updated":"2023-06-02T22:30:04Z","file_name":"Dispersaldata.xlsx","relation":"supplementary_material","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","embargo_to":"open_access","file_size":52795,"file_id":"12805","access_level":"closed","date_created":"2023-04-06T06:09:40Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","creator":"mjulseth"},{"file_size":787239,"relation":"supplementary_material","embargo":"2023-06-01","checksum":"5a13b6d204371572e249f03795bc0d04","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_updated":"2023-06-02T22:30:04Z","creator":"mjulseth","content_type":"application/vnd.wolfram.nb","access_level":"open_access","date_created":"2023-04-06T06:11:27Z","file_id":"12806"},{"creator":"mjulseth","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12812","access_level":"closed","date_created":"2023-04-06T08:26:12Z","relation":"source_file","checksum":"c3ec842839ed1e66bf2618ae33047df8","embargo_to":"open_access","file_size":1061763,"file_name":"ThesisMaraJulseth_04_23.docx","date_updated":"2023-06-02T22:30:04Z"},{"date_created":"2023-04-06T08:26:37Z","access_level":"open_access","file_id":"12813","creator":"mjulseth","content_type":"application/pdf","file_name":"ThesisMaraJulseth_04_23.pdf","date_updated":"2023-06-02T22:30:04Z","file_size":1741364,"checksum":"3132cc998fbe3ae2a3a83c2a69367f37","relation":"main_file","embargo":"2023-06-01"}],"month":"04","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","file_date_updated":"2023-06-02T22:30:04Z","language":[{"iso":"eng"}],"citation":{"short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800."},"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_updated":"2026-04-07T14:01:51Z","article_processing_charge":"No","author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara","full_name":"Julseth, Mara","last_name":"Julseth"}],"type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:12800","status":"public"},{"status":"public","oa_version":"Published Version","type":"dissertation","doi":"10.15479/at:ista:12781","publication_status":"published","article_processing_charge":"No","author":[{"last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089","first_name":"Vladyslav"}],"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"date_updated":"2026-04-07T14:10:40Z","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781"},"project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines","grant_number":"101020697"}],"file_date_updated":"2024-04-22T22:30:06Z","corr_author":"1","month":"03","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"page":"127","file":[{"checksum":"5ebb6345cb4119f93460c81310265a6d","relation":"main_file","embargo":"2024-04-20","file_size":6071553,"date_updated":"2024-04-22T22:30:06Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","creator":"vkravchu","content_type":"application/pdf","file_id":"12852","date_created":"2023-04-19T14:33:41Z","access_level":"open_access"},{"date_updated":"2024-04-22T22:30:06Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","file_size":19468766,"relation":"source_file","embargo":"2024-04-20","checksum":"c12055c48411d030d2afa51de2166221","access_level":"open_access","date_created":"2023-04-19T14:33:52Z","file_id":"12853","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"vkravchu"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12138"}]},"degree_awarded":"PhD","date_created":"2023-03-31T12:24:42Z","abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"oa":1,"alternative_title":["ISTA Thesis"],"year":"2023","date_published":"2023-03-23T00:00:00Z","ddc":["570","572"],"day":"23","supervisor":[{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"publisher":"Institute of Science and Technology Austria","_id":"12781","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","ec_funded":1,"OA_place":"publisher"}]