[{"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12132","alternative_title":["ISTA Thesis"],"day":"26","ddc":["530"],"file_date_updated":"2023-01-26T23:30:44Z","oa":1,"date_created":"2023-01-25T09:17:02Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","call_identifier":"H2020"}],"year":"2022","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"ec_funded":1,"citation":{"chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-024-4"]},"type":"dissertation","supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M"}],"_id":"12366","status":"public","date_updated":"2026-04-07T14:22:39Z","month":"09","abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"oa_version":"Published Version","has_accepted_license":"1","title":"Controllable states of superconducting Qubit ensembles","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"}],"date_published":"2022-09-26T00:00:00Z","page":"168","publication_status":"published","file":[{"file_size":56076868,"date_created":"2023-01-25T09:41:49Z","file_name":"Final_Thesis_ES_Redchenko.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"12367","embargo":"2022-12-28","checksum":"39eabb1e006b41335f17f3b29af09648","creator":"cchlebak","relation":"main_file","date_updated":"2023-01-26T23:30:44Z"}]},{"project":[{"grant_number":"24800","name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"DaSi"}],"year":"2022","corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"file_date_updated":"2023-04-21T22:30:03Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2022-04-20T08:59:07Z","degree_awarded":"PhD","ddc":["570"],"day":"20","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:11193","file":[{"access_level":"open_access","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","file_id":"11195","content_type":"application/pdf","file_size":8820951,"date_created":"2022-04-20T09:03:57Z","date_updated":"2023-04-21T22:30:03Z","relation":"main_file","checksum":"999ab16884c4522486136ebc5ae8dbff","creator":"cchlebak","embargo":"2023-04-20"},{"creator":"cchlebak","relation":"source_file","checksum":"fd92b1e38d53bdf8b458213882d41383","date_updated":"2023-04-21T22:30:03Z","embargo_to":"open_access","date_created":"2022-04-22T12:41:00Z","file_size":65864612,"content_type":"application/x-zip-compressed","access_level":"closed","file_name":"Thesis_Stephanie_Wachner_20200414.zip","file_id":"11329"}],"page":"170","publication_status":"published","author":[{"last_name":"Wachner","full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2022-04-20T00:00:00Z","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","has_accepted_license":"1","date_updated":"2026-04-07T14:24:19Z","abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"month":"04","related_material":{"record":[{"id":"10614","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"544","status":"public"}]},"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"_id":"11193","status":"public","citation":{"ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>.","mla":"Wachner, Stephanie. <i>Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","apa":"Wachner, S. (2022). <i>Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation"},{"author":[{"orcid":"0000-0001-9434-8902","last_name":"Colombo","full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","full_name":"Cubero, Ryan J"},{"full_name":"Kanari, Lida","last_name":"Kanari","first_name":"Lida"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","full_name":"Venturino, Alessandro"},{"full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","last_name":"Schulz","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scolamiero, Martina","last_name":"Scolamiero","first_name":"Martina"},{"full_name":"Agerberg, Jens","last_name":"Agerberg","first_name":"Jens"},{"first_name":"Hansruedi","full_name":"Mathys, Hansruedi","last_name":"Mathys"},{"first_name":"Li-Huei","full_name":"Tsai, Li-Huei","last_name":"Tsai"},{"first_name":"Wojciech","full_name":"Chachólski, Wojciech","last_name":"Chachólski"},{"last_name":"Hess","full_name":"Hess, Kathryn","first_name":"Kathryn"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Siegert, Sandra"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"date_published":"2022-10-01T00:00:00Z","title":"A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes","file":[{"success":1,"relation":"main_file","checksum":"28431146873096f52e0107b534f178c9","creator":"dernst","date_updated":"2023-01-30T08:06:56Z","file_size":23789835,"date_created":"2023-01-30T08:06:56Z","content_type":"application/pdf","file_name":"2022_NatureNeuroscience_Colombo.pdf","access_level":"open_access","file_id":"12437"}],"publication":"Nature Neuroscience","pmid":1,"quality_controlled":"1","page":"1379-1393","publication_status":"published","_id":"12244","status":"public","citation":{"ama":"Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. 2022;25(10):1379-1393. doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>","apa":"Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero, M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>","ista":"Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 25(10), 1379–1393.","short":"G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero, J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature Neuroscience 25 (2022) 1379–1393.","mla":"Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>.","ieee":"G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022.","chicago":"Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>."},"article_processing_charge":"No","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","issue":"10","date_updated":"2026-08-31T22:30:09Z","abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology."}],"month":"10","volume":25,"related_material":{"record":[{"id":"12378","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/","relation":"press_release"}]},"keyword":["General Neuroscience"],"article_type":"original","corr_author":"1","external_id":{"pmid":["36180790"],"isi":["000862214700001"]},"language":[{"iso":"eng"}],"file_date_updated":"2023-01-30T08:06:56Z","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2023-01-16T09:53:07Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"SaSi"}],"intvolume":"        25","year":"2022","ec_funded":1,"day":"01","publisher":"Springer Nature","doi":"10.1038/s41593-022-01167-6","scopus_import":"1","ddc":["570"],"acknowledgement":"We thank the scientific service units at ISTA, in particular M. Schunn’s team at the preclinical facility, and especially our colony manager S. Haslinger, for excellent support. We are also grateful to the ISTA Imaging & Optics Facility, and in particular C. Sommer for helping with the data file conversions. We thank R. Erhart from the ISTA Scientific Computing Unit for improving the script performance. We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert group for constant feedback on the project and on the manuscript. This research was supported by the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript."},{"publication":"Developmental Cell","pmid":1,"quality_controlled":"1","page":"47-62.e9","publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"author":[{"first_name":"Florian","last_name":"Gaertner","full_name":"Gaertner, Florian"},{"full_name":"Dos Reis Rodrigues, Patricia","orcid":"0000-0003-1681-508X","last_name":"Dos Reis Rodrigues","first_name":"Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"full_name":"Hons, Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348","first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Aguilera","full_name":"Aguilera, Juan","first_name":"Juan"},{"full_name":"Riedl, Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"orcid":"0000-0003-1671-393X","last_name":"Tasciyan","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"},{"first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","last_name":"Zheden","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"}],"date_published":"2022-01-10T00:00:00Z","title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version","isi":1,"date_updated":"2026-08-31T22:30:11Z","issue":"1","month":"01","abstract":[{"lang":"eng","text":"When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes."}],"volume":57,"related_material":{"record":[{"status":"public","id":"20149","relation":"dissertation_contains"},{"id":"12726","status":"public","relation":"dissertation_contains"},{"id":"14530","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"12401"}]},"article_type":"original","_id":"10703","status":"public","citation":{"ista":"Gaertner F, Dos Reis Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9.","short":"F. Gaertner, P. Dos Reis Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9.","mla":"Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>, vol. 57, no. 1, Cell Press, 2022, p. 47–62.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>.","chicago":"Gaertner, Florian, Patricia Dos Reis Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>.","ieee":"F. Gaertner <i>et al.</i>, “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” <i>Developmental Cell</i>, vol. 57, no. 1. Cell Press, p. 47–62.e9, 2022.","ama":"Gaertner F, Dos Reis Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. 2022;57(1):47-62.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>","apa":"Gaertner, F., Dos Reis Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>"},"article_processing_charge":"No","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"type":"journal_article","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497","open_access":"1"}],"project":[{"grant_number":"747687","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"year":"2022","intvolume":"        57","ec_funded":1,"corr_author":"1","external_id":{"isi":["000768933800005"],"pmid":["34919802"]},"language":[{"iso":"eng"}],"oa":1,"date_created":"2022-01-30T23:01:33Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","ddc":["570"],"day":"10","publisher":"Cell Press","doi":"10.1016/j.devcel.2021.11.024"},{"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2023-01-25T14:27:43Z","file_date_updated":"2023-04-12T22:30:03Z","oa":1,"language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","ec_funded":1,"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"year":"2022","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"doi":"10.15479/at:ista:12378","publisher":"Institute of Science and Technology Austria","day":"11","alternative_title":["ISTA Thesis"],"ddc":["570"],"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"author":[{"full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-11-11T00:00:00Z","publication_status":"published","page":"142","file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12379","file_name":"Gloria_Colombo_Thesis.docx","file_size":23890382,"date_created":"2023-01-25T14:31:32Z","embargo_to":"open_access","date_updated":"2023-04-12T22:30:03Z","creator":"cchlebak","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","relation":"source_file"},{"access_level":"open_access","file_name":"Gloria_Colombo_Thesis.pdf","file_id":"12380","content_type":"application/pdf","file_size":13802421,"date_created":"2023-01-25T14:31:36Z","embargo":"2023-04-11","date_updated":"2023-04-12T22:30:03Z","relation":"main_file","creator":"cchlebak","checksum":"8af4319c18b516e8758e9a6cb02b103b"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","citation":{"ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>"},"article_processing_charge":"No","status":"public","_id":"12378","supervisor":[{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"12244","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2026-04-07T14:29:41Z","month":"11","abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"year":"2022","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2022-05-16T16:49:18Z","file_date_updated":"2023-05-20T22:30:03Z","oa":1,"ddc":["576"],"alternative_title":["ISTA Thesis"],"day":"18","doi":"10.15479/at:ista:11388","publisher":"Institute of Science and Technology Austria","file":[{"file_size":8247240,"date_created":"2022-05-19T13:03:13Z","file_id":"11398","access_level":"open_access","content_type":"application/pdf","file_name":"thesis_sb_final_pdfa.pdf","embargo":"2023-05-19","creator":"sbelohla","relation":"main_file","checksum":"4d75e6a619df7e8a9d6e840aee182380","date_updated":"2023-05-20T22:30:03Z"},{"file_name":"thesis_sb_final.zip","content_type":"application/x-zip-compressed","file_id":"11399","access_level":"closed","date_created":"2022-05-19T13:07:47Z","file_size":7094,"embargo_to":"open_access","date_updated":"2023-05-20T22:30:03Z","creator":"sbelohla","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","relation":"source_file"}],"page":"98","publication_status":"published","author":[{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","last_name":"Belohlavy","first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-05-18T00:00:00Z","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"part_of_dissertation","id":"6713","status":"public"}]},"date_updated":"2026-04-07T14:29:57Z","month":"05","abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"_id":"11388","status":"public","publication_identifier":{"isbn":["978-3-99078-018-3"]},"type":"dissertation","citation":{"chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>"},"article_processing_charge":"No"},{"doi":"10.15479/at:ista:12401","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"day":"22","ddc":["610"],"date_created":"2023-01-26T11:55:16Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"file_date_updated":"2023-12-21T23:30:03Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"year":"2022","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","citation":{"mla":"Tasciyan, Saren. <i>Role of Microenvironment Heterogeneity in Cancer Cell Invasion</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>.","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>.","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022.","apa":"Tasciyan, S. (2022). <i>Role of microenvironment heterogeneity in cancer cell invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>"},"_id":"12401","supervisor":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"status":"public","related_material":{"record":[{"status":"public","id":"7885","relation":"part_of_dissertation"},{"id":"10703","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"679","status":"public"},{"status":"public","id":"9429","relation":"part_of_dissertation"}]},"abstract":[{"text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening.","lang":"eng"}],"month":"12","date_updated":"2026-04-14T09:07:14Z","has_accepted_license":"1","oa_version":"Published Version","title":"Role of microenvironment heterogeneity in cancer cell invasion","date_published":"2022-12-22T00:00:00Z","author":[{"full_name":"Tasciyan, Saren","last_name":"Tasciyan","orcid":"0000-0003-1671-393X","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"}],"page":"105","publication_status":"published","file":[{"embargo":"2023-12-20","date_updated":"2023-12-21T23:30:03Z","relation":"main_file","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","creator":"cchlebak","content_type":"application/pdf","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","access_level":"open_access","file_id":"12402","date_created":"2023-01-26T11:58:14Z","file_size":42059787},{"date_updated":"2023-12-21T23:30:03Z","creator":"cchlebak","relation":"source_file","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","embargo_to":"open_access","access_level":"closed","file_id":"12403","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","content_type":"application/x-zip-compressed","date_created":"2023-01-26T12:00:10Z","file_size":261256696}]},{"date_updated":"2026-08-31T22:30:12Z","month":"04","abstract":[{"lang":"eng","text":"FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments.  Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. "}],"related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.6400639","relation":"software","description":"A custom written code (FRAPdiff) to quantify the Off binding rate and Diffusion coefficient of membrane bound proteins. Written by Christoph Sommer."}],"record":[{"relation":"used_in_publication","id":"11373","status":"public"},{"relation":"used_in_publication","id":"14280","status":"public"}]},"keyword":["Bacterial cell division","in vitro reconstitution","FtsZ","FtsN","FtsA"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Submitted Version","has_accepted_license":"1","citation":{"ama":"Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>","apa":"Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>","short":"P. Radler, (2022).","ista":"Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>.","ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022.","chicago":"Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>.","mla":"Radler, Philipp. <i>In Vitro Reconstitution of Escherichia Coli Divisome Activation</i>. 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Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","ddc":["572"],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:10934","contributor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","contributor_type":"supervisor"},{"contributor_type":"researcher","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"contributor_type":"researcher","last_name":"Caldas","first_name":"Paulo"},{"contributor_type":"researcher","last_name":"Michalik","first_name":"David","id":"B9577E20-AA38-11E9-AC9A-0930E6697425"},{"contributor_type":"researcher","last_name":"Baranova","first_name":"Natalia"}],"day":"05","project":[{"call_identifier":"H2020","grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"year":"2022","ec_funded":1,"file_date_updated":"2022-04-22T10:15:19Z","oa":1,"date_created":"2022-03-31T11:32:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1"},{"intvolume":"        13","year":"2022","department":[{"_id":"MaLo"}],"project":[{"name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"679239"},{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"ec_funded":1,"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000795171100037"]},"oa":1,"file_date_updated":"2022-05-13T09:10:51Z","date_created":"2022-05-13T09:06:28Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","ddc":["570"],"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","day":"12","publisher":"Springer Nature","doi":"10.1038/s41467-022-30301-y","publication":"Nature Communications","file":[{"date_updated":"2022-05-13T09:10:51Z","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","file_id":"11374","content_type":"application/pdf","file_name":"2022_NatureCommunications_Radler.pdf","date_created":"2022-05-13T09:10:51Z","file_size":6945191}],"quality_controlled":"1","publication_status":"published","article_number":"2635","date_published":"2022-05-12T00:00:00Z","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler","full_name":"Radler, Philipp"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S."},{"first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","last_name":"Dos Santos Caldas"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"id":"B9577E20-AA38-11E9-AC9A-0930E6697425","first_name":"David","last_name":"Michalik","full_name":"Michalik, David"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"title":"In vitro reconstitution of Escherichia coli divisome activation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"month":"05","abstract":[{"lang":"eng","text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ."}],"volume":13,"date_updated":"2026-08-31T22:30:12Z","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-34485-1","relation":"erratum"}],"record":[{"status":"public","id":"10934","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"14280"}]},"status":"public","_id":"11373","article_processing_charge":"No","citation":{"apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635."},"type":"journal_article","publication_identifier":{"issn":["2041-1723"]}},{"year":"2022","department":[{"_id":"DaSi"}],"intvolume":"       221","language":[{"iso":"eng"}],"external_id":{"isi":["000932770500001"],"pmid":["35984332"]},"oa":1,"file_date_updated":"2023-02-21T23:30:39Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-09-11T22:01:54Z","scopus_import":"1","acknowledgement":"This work was supported by JSPS KAKENHI GRANT #18K062291, and the Takeda Science Foundation to J.Y. Toshima, as well as JSPS KAKENHI GRANT #19K065710, the Uehara Memorial Foundation, and Life Science Foundation of JAPAN to J. Toshima.","ddc":["570"],"day":"19","publisher":"Rockefeller University Press","doi":"10.1083/jcb.202112138","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2022_JCB_Enshoji.pdf","file_id":"12321","file_size":7816875,"date_created":"2023-01-20T09:32:53Z","embargo":"2023-02-20","date_updated":"2023-02-21T23:30:39Z","creator":"dernst","relation":"main_file","checksum":"f2e581e66b5cdab9df81b56e850b3eaa"}],"publication":"Journal of Cell Biology","quality_controlled":"1","pmid":1,"publication_status":"published","date_published":"2022-08-19T00:00:00Z","article_number":"e202112138","author":[{"full_name":"Enshoji, Mariko","last_name":"Enshoji","first_name":"Mariko"},{"first_name":"Yoshiko","full_name":"Miyano, Yoshiko","last_name":"Miyano"},{"last_name":"Yoshida","full_name":"Yoshida, Nao","first_name":"Nao"},{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"full_name":"Watanabe, Minami","last_name":"Watanabe","first_name":"Minami"},{"full_name":"Kunihiro, Mayumi","last_name":"Kunihiro","first_name":"Mayumi"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"first_name":"Junko Y.","full_name":"Toshima, Junko Y.","last_name":"Toshima"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"title":"Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","month":"08","volume":221,"abstract":[{"text":"Endocytosis is a multistep process involving the sequential recruitment and action of numerous proteins. This process can be divided into two phases: an early phase, in which sites of endocytosis are formed, and a late phase in which clathrin-coated vesicles are formed and internalized into the cytosol, but how these phases link to each other remains unclear. In this study, we demonstrate that anchoring the yeast Eps15-like protein Pan1p to the peroxisome triggers most of the events occurring during the late phase at the peroxisome. At this ectopic location, Pan1p recruits most proteins that function in the late phases—including actin nucleation promoting factors—and then initiates actin polymerization. Pan1p also recruited Prk1 kinase and actin depolymerizing factors, thereby triggering disassembly immediately after actin assembly and inducing dissociation of endocytic proteins from the peroxisome. These observations suggest that Pan1p is a key regulator for initiating, processing, and completing the late phase of endocytosis.","lang":"eng"}],"issue":"10","date_updated":"2023-08-03T13:49:07Z","article_type":"original","_id":"12080","status":"public","article_processing_charge":"No","citation":{"ama":"Enshoji M, Miyano Y, Yoshida N, et al. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. 2022;221(10). doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>","apa":"Enshoji, M., Miyano, Y., Yoshida, N., Nagano, M., Watanabe, M., Kunihiro, M., … Toshima, J. (2022). Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>","ista":"Enshoji M, Miyano Y, Yoshida N, Nagano M, Watanabe M, Kunihiro M, Siekhaus DE, Toshima JY, Toshima J. 2022. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. Journal of Cell Biology. 221(10), e202112138.","short":"M. Enshoji, Y. Miyano, N. Yoshida, M. Nagano, M. Watanabe, M. Kunihiro, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Biology 221 (2022).","mla":"Enshoji, Mariko, et al. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>, vol. 221, no. 10, e202112138, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>.","ieee":"M. Enshoji <i>et al.</i>, “Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway,” <i>Journal of Cell Biology</i>, vol. 221, no. 10. Rockefeller University Press, 2022.","chicago":"Enshoji, Mariko, Yoshiko Miyano, Nao Yoshida, Makoto Nagano, Minami Watanabe, Mayumi Kunihiro, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>."},"type":"journal_article","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]}},{"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","date_created":"2022-07-26T11:01:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2022-08-08T22:30:04Z","date_published":"2022-08-05T00:00:00Z","corr_author":"1","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"}],"year":"2022","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file":[{"date_updated":"2022-08-08T22:30:04Z","relation":"main_file","creator":"melkrewi","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","embargo":"2022-08-07","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","content_type":"application/x-zip-compressed","access_level":"open_access","file_name":"Data.zip","file_id":"11655","date_created":"2022-07-26T12:37:52Z","title":"Supplementary Datasets","file_size":2209382998}],"type":"research_data","doi":"10.15479/AT:ISTA:11653","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","short":"M.N. Elkrewi, (2022).","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022."},"_id":"11653","status":"public","day":"05","contributor":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K","last_name":"Bett"},{"last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Luca","last_name":"Sax"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"first_name":"Francisco","last_name":"Hontoria "},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"related_material":{"record":[{"id":"12248","status":"public","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"month":"08","date_updated":"2025-04-15T08:34:17Z","ddc":["570"],"has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"day":"22","publisher":"Springer Nature","doi":"10.1038/s41586-022-05199-7","scopus_import":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance with collecting cryo-EM data and A. Charnagalov for the assistance with protein purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also supported by the Medical Research Council (UK).","ddc":["572"],"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000854788200001"],"pmid":["36104567"]},"oa":1,"file_date_updated":"2023-05-30T17:07:05Z","date_created":"2023-01-12T12:04:33Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","intvolume":"       609","department":[{"_id":"LeSa"}],"project":[{"grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"name":"Structure and mechanism of respiratory chain molecular machines","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","grant_number":"101020697"}],"ec_funded":1,"status":"public","_id":"12138","article_processing_charge":"No","citation":{"ista":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928), 808–814.","short":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A. Sazanov, Nature 609 (2022) 808–814.","mla":"Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14, doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>.","ieee":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” <i>Nature</i>, vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.","chicago":"Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason, Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>.","ama":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. A universal coupling mechanism of respiratory complex I. <i>Nature</i>. 2022;609(7928):808-814. doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>","apa":"Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z., &#38; Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex I. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>"},"type":"journal_article","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"has_accepted_license":"1","isi":1,"oa_version":"Submitted Version","abstract":[{"text":"Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.","lang":"eng"}],"month":"09","volume":609,"date_updated":"2026-08-31T22:30:13Z","issue":"7928","article_type":"original","keyword":["Multidisciplinary"],"related_material":{"record":[{"relation":"dissertation_contains","id":"12781","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41586-022-05457-8","relation":"erratum"},{"url":"https://ista.ac.at/en/news/proton-dominos-kick-off-life/","relation":"press_release","description":"News on ISTA website"}]},"date_published":"2022-09-22T00:00:00Z","author":[{"full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","last_name":"Kravchuk","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Petrova, Olga","last_name":"Petrova","first_name":"Olga","id":"5D8C9660-5D49-11EA-8188-567B3DDC885E"},{"first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen","last_name":"Kampjut","orcid":"0000-0002-6018-3422"},{"full_name":"Wojciechowska-Bason, Anna","last_name":"Wojciechowska-Bason","first_name":"Anna"},{"first_name":"Zara","full_name":"Breese, Zara","last_name":"Breese"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"title":"A universal coupling mechanism of respiratory complex I","file":[{"date_updated":"2023-05-30T17:05:31Z","success":1,"relation":"main_file","creator":"lsazanov","checksum":"d42a93e24f59e883ef0b5429832391d0","content_type":"application/pdf","file_id":"13104","access_level":"open_access","file_name":"EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf","file_size":1425655,"date_created":"2023-05-30T17:05:31Z"},{"creator":"lsazanov","success":1,"relation":"main_file","checksum":"5422bc0a73b3daadafa262c7ea6deae3","date_updated":"2023-05-30T17:07:05Z","date_created":"2023-05-30T17:07:05Z","file_size":9842513,"access_level":"open_access","file_name":"EcCxI_manuscript_rev3_SI_All_opt_upd.pdf","content_type":"application/pdf","file_id":"13105"}],"publication":"Nature","quality_controlled":"1","pmid":1,"page":"808-814","publication_status":"published"},{"has_accepted_license":"1","oa_version":"Published Version","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"keyword":["Cell Biology"],"article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14697"}]},"volume":221,"month":"07","abstract":[{"lang":"eng","text":"Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant."}],"issue":"8","date_updated":"2026-08-31T22:30:15Z","_id":"12272","status":"public","type":"journal_article","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"article_processing_charge":"No","citation":{"ama":"Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. 2022;221(8). doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>","apa":"Stopp, J. A., &#38; Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>","short":"J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).","ista":"Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127.","chicago":"Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>.","ieee":"J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” <i>Journal of Cell Biology</i>, vol. 221, no. 8. Rockefeller University Press, 2022.","mla":"Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>."},"quality_controlled":"1","pmid":1,"publication":"Journal of Cell Biology","file":[{"date_updated":"2023-01-30T10:39:34Z","checksum":"6b1620743669679b48b9389bb40f5a11","success":1,"creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2022_JourCellBiology_Stopp.pdf","file_id":"12451","access_level":"open_access","date_created":"2023-01-30T10:39:34Z","file_size":969969}],"publication_status":"published","date_published":"2022-07-20T00:00:00Z","article_number":"e202206127","author":[{"full_name":"Stopp, Julian A","last_name":"Stopp","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"title":"Plan your trip before you leave: The neutrophils’ search-and-run journey","ddc":["570"],"scopus_import":"1","day":"20","doi":"10.1083/jcb.202206127","publisher":"Rockefeller University Press","intvolume":"       221","department":[{"_id":"MiSi"}],"year":"2022","language":[{"iso":"eng"}],"external_id":{"isi":["000874717200001"],"pmid":["35856919"]},"corr_author":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2023-01-16T10:01:08Z","oa":1,"file_date_updated":"2023-01-30T10:39:34Z"},{"title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","date_published":"2022-04-01T00:00:00Z","author":[{"first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko"},{"full_name":"Kungurtsev, Vyacheslav","last_name":"Kungurtsev","first_name":"Vyacheslav"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"page":"1-55","publication_status":"published","quality_controlled":"1","file":[{"date_updated":"2022-05-30T08:22:55Z","relation":"main_file","checksum":"d4ff5d1affb34848b5c5e4002483fc62","success":1,"creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","file_id":"11422","file_name":"21-1365.pdf","file_size":1521701,"date_created":"2022-05-30T08:22:55Z"}],"publication":"Journal of Machine Learning Research","type":"journal_article","publication_identifier":{"eissn":["1533-7928"],"issn":["1532-4435"]},"article_processing_charge":"No","citation":{"ieee":"A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.","chicago":"Shevchenko, Alexander, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2022.","mla":"Shevchenko, Alexander, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55.","ista":"Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55.","apa":"Shevchenko, A., Kungurtsev, V., &#38; Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","ama":"Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. 2022;23(130):1-55."},"status":"public","_id":"11420","article_type":"original","related_material":{"link":[{"relation":"other","url":"https://www.jmlr.org/papers/v23/21-1365.html"}],"record":[{"id":"17465","status":"public","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory."}],"volume":23,"month":"04","issue":"130","date_updated":"2026-08-31T22:30:17Z","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2022-05-29T22:01:54Z","oa":1,"file_date_updated":"2022-05-30T08:22:55Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2111.02278"]},"corr_author":"1","year":"2022","intvolume":"        23","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"arxiv":1,"publisher":"Journal of Machine Learning Research","day":"01","acknowledgement":"We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n","ddc":["000"],"scopus_import":"1"},{"file":[{"embargo_to":"open_access","content_type":"application/zip","file_id":"11935","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","access_level":"closed","date_created":"2022-08-19T16:31:34Z","file_size":13515457,"date_updated":"2023-06-20T22:30:04Z","relation":"source_file","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","creator":"mnardin"},{"embargo":"2023-06-19","date_updated":"2023-06-20T22:30:04Z","relation":"main_file","checksum":"0ec94035ea35a47a9f589ed168e60b48","creator":"mnardin","content_type":"application/pdf","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","file_id":"11941","access_level":"open_access","date_created":"2022-08-22T09:43:50Z","file_size":9906458}],"publication_status":"published","page":"136","author":[{"full_name":"Nardin, Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-08-19T00:00:00Z","title":"On the encoding, transfer, and consolidation of spatial memories","oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"6194","status":"public"},{"relation":"part_of_dissertation","id":"10077","status":"public"}]},"date_updated":"2026-07-06T12:47:25Z","abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"month":"08","_id":"11932","status":"public","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","citation":{"mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>"},"article_processing_charge":"No","ec_funded":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"year":"2022","language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","date_created":"2022-08-19T08:52:30Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2023-06-20T22:30:04Z","oa":1,"acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","ddc":["573"],"day":"19","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:11932","publisher":"Institute of Science and Technology Austria"},{"publication_status":"published","file":[{"file_name":"2022_Genetics_Elkrewi.pdf","file_id":"12440","content_type":"application/pdf","access_level":"open_access","file_size":1347136,"date_created":"2023-01-30T08:59:58Z","date_updated":"2023-01-30T08:59:58Z","relation":"main_file","checksum":"f79ff5383e882ea3f95f3da47a78029d","creator":"dernst","success":1}],"publication":"Genetics","quality_controlled":"1","pmid":1,"title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","article_number":"iyac123","date_published":"2022-10-01T00:00:00Z","author":[{"orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","first_name":"Uladzislava","last_name":"Khauratovich","full_name":"Khauratovich, Uladzislava"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","full_name":"Toups, Melissa A"},{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K","last_name":"Bett"},{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"full_name":"Sax, Luca","last_name":"Sax","first_name":"Luca","id":"701c5602-97d8-11ed-96b5-b52773c70189"},{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Francisco","last_name":"Hontoria","full_name":"Hontoria, Francisco"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"volume":222,"month":"10","date_updated":"2026-08-31T22:30:30Z","issue":"2","keyword":["Genetics"],"article_type":"original","related_material":{"record":[{"status":"public","id":"11653","relation":"research_data"},{"status":"public","id":"19386","relation":"dissertation_contains"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"article_processing_charge":"No","citation":{"ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>"},"type":"journal_article","publication_identifier":{"issn":["1943-2631"]},"_id":"12248","status":"public","year":"2022","department":[{"_id":"BeVi"}],"intvolume":"       222","project":[{"call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"ec_funded":1,"oa":1,"file_date_updated":"2023-01-30T08:59:58Z","date_created":"2023-01-16T09:56:10Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["35977389"],"isi":["000850270300001"]},"scopus_import":"1","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","ddc":["570"],"publisher":"Oxford University Press","doi":"10.1093/genetics/iyac123","day":"01"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","date_updated":"2026-08-31T22:30:31Z","issue":"1968","abstract":[{"lang":"eng","text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination."}],"month":"02","volume":289,"related_material":{"record":[{"relation":"dissertation_contains","id":"19386","status":"public"},{"status":"public","id":"17119","relation":"dissertation_contains"}]},"article_type":"original","status":"public","_id":"10767","citation":{"ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>.","chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>"},"article_processing_charge":"No","publication_identifier":{"eissn":["1471-2954"]},"type":"journal_article","file":[{"file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","access_level":"open_access","file_id":"10779","content_type":"application/pdf","date_created":"2022-02-21T08:17:38Z","file_size":2366976,"date_updated":"2022-02-21T08:17:38Z","success":1,"relation":"main_file","creator":"dernst","checksum":"27042a3706ae52a919fed1ac114bf7bb"}],"publication":"Proceedings of the Royal Society B: Biological Sciences","pmid":1,"quality_controlled":"1","page":"20211985","publication_status":"published","author":[{"full_name":"Kelemen, Réka K","last_name":"Kelemen","orcid":"0000-0002-8489-9281","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"first_name":"Anna K.","full_name":"Lindholm, Anna K.","last_name":"Lindholm"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"date_published":"2022-02-09T00:00:00Z","title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","scopus_import":"1","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","ddc":["570"],"day":"09","publisher":"The Royal Society","doi":"10.1098/rspb.2021.1985","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020"}],"department":[{"_id":"BeVi"}],"year":"2022","intvolume":"       289","ec_funded":1,"corr_author":"1","external_id":{"pmid":["35135349"],"isi":["000752812800012"]},"language":[{"iso":"eng"}],"file_date_updated":"2022-02-21T08:17:38Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-02-20T23:01:31Z"},{"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["35277488"],"isi":["000767892300013"],"arxiv":["2107.08303"]},"oa":1,"file_date_updated":"2022-03-28T08:02:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-03-27T22:01:45Z","department":[{"_id":"JoFi"}],"intvolume":"        13","year":"2022","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020"},{"name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","grant_number":"899354"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","call_identifier":"H2020"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"ec_funded":1,"day":"11","publisher":"Springer Nature","arxiv":1,"doi":"10.1038/s41467-022-28924-2","scopus_import":"1","acknowledgement":"The authors thank S. Wald and F. Diorico for their help with optical filtering, O. Hosten\r\nand M. Aspelmeyer for equipment, H.G.L. Schwefel for materials and discussions, L.\r\nDrmic and P. Zielinski for software support, and the MIBA workshop at IST Austria for\r\nmachining the microwave cavity. This work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG QUNNECT) and the European\r\nUnion’s Horizon 2020 research and innovation program under grant agreement no.\r\n899354 (FETopen SuperQuLAN). W.H. is the recipient of an ISTplus postdoctoral fellowship\r\nwith funding from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the\r\nrecipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F.\r\nacknowledges support from the Austrian Science Fund (FWF) through BeyondC (F7105)\r\nand the European Union’s Horizon 2020 research and innovation programs under grant\r\nagreement no. 862644 (FETopen QUARTET).","ddc":["530"],"article_number":"1276","date_published":"2022-03-11T00:00:00Z","author":[{"last_name":"Sahu","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"},{"first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J","last_name":"Hease","orcid":"0000-0001-9868-2166"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M"},{"first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267","last_name":"Qiu"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"title":"Quantum-enabled operation of a microwave-optical interface","publication":"Nature Communications","file":[{"date_updated":"2022-03-28T08:02:12Z","success":1,"relation":"main_file","checksum":"7c5176db7b8e2ed18a4e0c5aca70a72c","creator":"dernst","file_name":"2022_NatureCommunications_Sahu.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"10929","file_size":1167492,"date_created":"2022-03-28T08:02:12Z"}],"quality_controlled":"1","pmid":1,"publication_status":"published","_id":"10924","status":"public","article_processing_charge":"No","citation":{"mla":"Sahu, Rishabh, et al. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>, vol. 13, 1276, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>.","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Quantum-enabled operation of a microwave-optical interface,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>.","ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 13, 1276.","short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, Nature Communications 13 (2022).","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., &#38; Fink, J. M. (2022). Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>","ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>"},"type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","month":"03","abstract":[{"text":"Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only 0.16+0.02−0.01 microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with 0.41+0.02−0.02), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago.","lang":"eng"}],"volume":13,"date_updated":"2026-08-31T22:30:36Z","article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13175"},{"id":"12900","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"18871","status":"public"}]}},{"title":"Pathogen-mediated sexual selection and immunization in ant colonies","date_published":"2022-02-07T00:00:00Z","author":[{"first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","last_name":"Metzler"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"publication_status":"published","file":[{"date_created":"2022-02-04T15:36:12Z","file_size":6757886,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10728","access_level":"closed","file_name":"Thesis_Sina_Metzler.docx","embargo_to":"open_access","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","relation":"source_file","creator":"smetzler","date_updated":"2023-02-03T23:30:03Z"},{"date_updated":"2023-02-03T23:30:03Z","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","creator":"smetzler","relation":"main_file","embargo":"2023-02-02","content_type":"application/pdf","access_level":"open_access","file_id":"10730","file_name":"Thesis_Sina_Metzler_A2.pdf","file_size":6314921,"date_created":"2022-02-04T15:36:43Z"},{"checksum":"dedd14b7be7a75d63018dbfc68dd8113","relation":"main_file","creator":"smetzler","date_updated":"2023-02-04T23:30:03Z","embargo":"2023-02-02","date_created":"2022-02-07T10:35:02Z","file_size":6882557,"access_level":"open_access","file_name":"Thesis_Sina_Metzler_print.pdf","file_id":"10742","content_type":"application/pdf"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","citation":{"ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>","apa":"Metzler, S. (2022). <i>Pathogen-mediated sexual selection and immunization in ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","mla":"Metzler, Sina. <i>Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>."},"_id":"10727","status":"public","supervisor":[{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"abstract":[{"lang":"eng","text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history."}],"month":"02","date_updated":"2026-04-07T14:30:18Z","has_accepted_license":"1","oa_version":"Published Version","date_created":"2022-02-04T15:45:12Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"file_date_updated":"2023-02-04T23:30:03Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"SyCr"}],"year":"2022","project":[{"name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771402"}],"doi":"10.15479/AT:ISTA:10727","publisher":"Institute of Science and Technology Austria","day":"07","alternative_title":["ISTA Thesis"],"ddc":["570"]},{"intvolume":"        13","department":[{"_id":"HeEd"}],"year":"2022","project":[{"name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF"}],"oa":1,"file_date_updated":"2022-12-20T23:30:08Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-11-02T09:28:55Z","language":[{"iso":"eng"}],"external_id":{"isi":["000712198000001"]},"scopus_import":"1","ddc":["000"],"acknowledgement":"The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","publisher":"Springer Nature","doi":"10.1007/s12652-021-03569-z","day":"01","publication_status":"published","page":"2621–2635","file":[{"embargo":"2022-11-12","relation":"main_file","checksum":"0a8961416a9bb2be5a1cebda65468bcf","creator":"fkarimip","date_updated":"2022-12-20T23:30:08Z","file_size":1634958,"date_created":"2021-11-12T19:38:05Z","access_level":"open_access","content_type":"application/pdf","file_id":"10279","file_name":"A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf"}],"publication":"Journal of Ambient Intelligence and Humanized Computing","quality_controlled":"1","title":"A context-aware dimension reduction framework for trajectory and health signal analyses","date_published":"2022-05-01T00:00:00Z","author":[{"first_name":"Samira","full_name":"Goudarzi, Samira","last_name":"Goudarzi"},{"last_name":"Sharif","full_name":"Sharif, Mohammad","first_name":"Mohammad"},{"full_name":"Karimipour, Farid","orcid":"0000-0001-6746-4174","last_name":"Karimipour","first_name":"Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425"}],"month":"05","abstract":[{"text":"It is practical to collect a huge amount of movement data and environmental context information along with the health signals of individuals because there is the emergence of new generations of positioning and tracking technologies and rapid advancements of health sensors. The study of the relations between these datasets and their sequence similarity analysis is of interest to many applications such as health monitoring and recommender systems. However, entering all movement parameters and health signals can lead to the complexity of the problem and an increase in its computational load. In this situation, dimension reduction techniques can be used to avoid consideration of simultaneous dependent parameters in the process of similarity measurement of the trajectories. The present study provides a framework, named CaDRAW, to use spatial–temporal data and movement parameters along with independent context information in the process of measuring the similarity of trajectories. In this regard, the omission of dependent movement characteristic signals is conducted by using an unsupervised feature selection dimension reduction technique. To evaluate the effectiveness of the proposed framework, it was applied to a real contextualized movement and related health signal datasets of individuals. The results indicated the capability of the proposed framework in measuring the similarity and in decreasing the characteristic signals in such a way that the similarity results -before and after reduction of dependent characteristic signals- have small differences. The mean differences between the obtained results before and after reducing the dimension were 0.029 and 0.023 for the round path, respectively.","lang":"eng"}],"volume":13,"date_updated":"2025-04-15T07:16:55Z","article_type":"original","keyword":["general computer science"],"has_accepted_license":"1","isi":1,"oa_version":"Submitted Version","article_processing_charge":"No","citation":{"mla":"Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>.","chicago":"Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>.","ieee":"S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction framework for trajectory and health signal analyses,” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13. Springer Nature, pp. 2621–2635, 2022.","ista":"Goudarzi S, Sharif M, Karimipour F. 2022. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 13, 2621–2635.","short":"S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635.","apa":"Goudarzi, S., Sharif, M., &#38; Karimipour, F. (2022). A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>","ama":"Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. 2022;13:2621–2635. doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>"},"type":"journal_article","publication_identifier":{"issn":["1868-5137"],"eissn":["1868-5145"]},"_id":"10208","status":"public"}]