[{"citation":{"chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>"},"doi":"10.15479/at:ista:9397","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"_id":"9397","oa_version":"Published Version","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2022-05-21T22:30:04Z","day":"18","date_updated":"2026-04-08T07:12:51Z","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev","first_name":"Karla"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"date_created":"2021-05-17T12:31:30Z","publisher":"Institute of Science and Technology Austria","ddc":["571"],"month":"05","corr_author":"1","status":"public","degree_awarded":"PhD","type":"dissertation","oa":1,"page":"101","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-05-18T00:00:00Z","article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"file_id":"9398","date_updated":"2022-05-21T22:30:04Z","embargo_to":"open_access","checksum":"7f98532f5324a0b2f3fa8de2967baa19","creator":"khuljev","file_name":"KHuljev_Thesis_corrections.docx","relation":"source_file","date_created":"2021-05-17T12:29:12Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":47799741},{"access_level":"open_access","content_type":"application/pdf","file_size":16542131,"file_name":"new_KHuljev_Thesis_corrections.pdf","creator":"khuljev","checksum":"bf512f8a1e572a543778fc4b227c01ba","date_created":"2021-05-18T14:50:28Z","relation":"main_file","date_updated":"2022-05-21T22:30:04Z","embargo":"2022-05-20","file_id":"9401"}]},{"supervisor":[{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","date_created":"2021-07-27T13:40:30Z","abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"M-Shop"}],"status":"public","ddc":["532"],"corr_author":"1","month":"07","degree_awarded":"PhD","type":"dissertation","oa":1,"page":"118","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-07-29T00:00:00Z","article_processing_charge":"No","year":"2021","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"publication_status":"published","file":[{"date_created":"2021-07-28T13:32:02Z","relation":"source_file","creator":"nagrawal","checksum":"77436be3563a90435024307b1b5ee7e8","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","file_size":22859658,"access_level":"closed","content_type":"application/x-zip-compressed","file_id":"9744","embargo_to":"open_access","date_updated":"2022-07-29T22:30:05Z"},{"file_id":"9745","embargo":"2022-07-28","date_updated":"2022-07-29T22:30:05Z","creator":"nagrawal","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","checksum":"72a891d7daba85445c29b868c22575ed","relation":"main_file","date_created":"2021-07-28T13:32:05Z","content_type":"application/pdf","access_level":"open_access","file_size":18658048}],"citation":{"apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/at:ista:9728","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"_id":"9728","oa_version":"Published Version","OA_place":"publisher","related_material":{"record":[{"relation":"part_of_dissertation","id":"6189","status":"public"}]},"file_date_updated":"2022-07-29T22:30:05Z","publication_identifier":{"issn":["2663-337X"]},"day":"29","date_updated":"2026-04-16T08:43:20Z","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","full_name":"Agrawal, Nishchal","first_name":"Nishchal","last_name":"Agrawal"}]},{"oa_version":"Published Version","_id":"9992","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"citation":{"mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.15479/at:ista:9992","project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer"}],"date_updated":"2026-04-08T07:11:47Z","title":"Wound healing in the Arabidopsis root meristem","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"6943","relation":"part_of_dissertation"},{"status":"public","id":"8002","relation":"part_of_dissertation"},{"status":"public","id":"6351","relation":"part_of_dissertation"}]},"file_date_updated":"2021-09-15T22:30:26Z","day":"13","OA_place":"publisher","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"corr_author":"1","month":"09","status":"public","ddc":["575"],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"date_created":"2021-09-09T07:37:20Z","has_accepted_license":"1","abstract":[{"text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. ","lang":"eng"}],"language":[{"iso":"eng"}],"supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"file":[{"date_created":"2021-09-09T07:29:48Z","relation":"source_file","checksum":"c763064adaa720e16066c1a4f9682bbb","creator":"lhoermaye","file_name":"Thesis_vupload.docx","file_size":25179004,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"9993","embargo_to":"open_access","date_updated":"2021-09-15T22:30:26Z"},{"relation":"main_file","date_created":"2021-09-09T14:25:08Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","file_name":"Thesis_vfinal_pdfa.pdf","creator":"lhoermaye","file_size":6246900,"content_type":"application/pdf","access_level":"open_access","embargo":"2021-09-09","file_id":"9996","date_updated":"2021-09-15T22:30:26Z"}],"article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-09-13T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"168","oa":1,"ec_funded":1,"type":"dissertation"},{"oa":1,"type":"dissertation","page":"111","date_published":"2021-07-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"9624","embargo_to":"open_access","date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:48:54Z","relation":"source_file","file_name":"PhDThesis_SCM.docx","creator":"scaballe","checksum":"e039225a47ef32666d59bf35ddd30ecf","file_size":131946790,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"embargo":"2022-07-01","file_id":"9625","date_updated":"2022-07-02T22:30:06Z","file_name":"PhDThesis_SCM.pdf","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","creator":"scaballe","relation":"main_file","date_created":"2021-07-01T14:46:25Z","content_type":"application/pdf","access_level":"open_access","file_size":17094958}],"publication_status":"published","year":"2021","article_processing_charge":"No","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_created":"2021-07-01T14:50:17Z","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"ddc":["570"],"status":"public","corr_author":"1","month":"07","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","OA_place":"publisher","publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"9006","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9750"}]},"file_date_updated":"2022-07-02T22:30:06Z","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","date_updated":"2026-07-06T12:45:39Z","author":[{"orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia"}],"citation":{"chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>"},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.15479/at:ista:9623","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"oa_version":"Published Version","_id":"9623"},{"OA_place":"publisher","file_date_updated":"2022-12-20T23:30:05Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"10316","relation":"part_of_dissertation"}]},"day":"18","date_updated":"2026-07-06T12:48:19Z","title":"Pathogenic Escherichia coli hijack the host immune response","author":[{"first_name":"Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"}],"citation":{"ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>."},"doi":"10.15479/at:ista:10307","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"oa_version":"Published Version","_id":"10307","oa":1,"type":"dissertation","page":"73","date_published":"2021-11-18T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_updated":"2022-12-20T23:30:05Z","file_id":"10308","embargo":"2022-11-18","access_level":"open_access","content_type":"application/pdf","file_size":13266088,"file_name":"ThesisTomasekKathrin.pdf","checksum":"b39c9e0ef18d0484d537a67551effd02","creator":"ktomasek","date_created":"2021-11-18T15:07:31Z","relation":"main_file"},{"file_size":7539509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","date_created":"2021-11-18T15:07:46Z","file_name":"ThesisTomasekKathrin.docx","creator":"ktomasek","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","embargo_to":"open_access","date_updated":"2022-12-20T23:30:05Z","file_id":"10309"}],"article_processing_charge":"No","year":"2021","publication_status":"published","supervisor":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response.","lang":"eng"}],"date_created":"2021-11-18T15:05:06Z","has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"status":"public","corr_author":"1","month":"11","ddc":["570"],"degree_awarded":"PhD"},{"intvolume":"        56","language":[{"iso":"eng"}],"publisher":"Elsevier","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.","lang":"eng"}],"pmid":1,"date_created":"2021-01-17T23:01:10Z","ddc":["570"],"publication":"Developmental Cell","month":"01","status":"public","corr_author":"1","issue":"2","oa":1,"type":"journal_article","isi":1,"page":"P213-226","date_published":"2021-01-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2021","article_processing_charge":"No","doi":"10.1016/j.devcel.2020.12.002","citation":{"chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” <i>Developmental Cell</i>, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>.","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. <i>Developmental Cell</i>. 2021;56(2):P213-226. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>","apa":"Shamipour, S., Caballero Mancebo, S., &#38; Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226."},"volume":56,"scopus_import":"1","department":[{"_id":"CaHe"}],"quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"_id":"9006","external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"day":"25","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","article_type":"original","related_material":{"record":[{"status":"public","id":"9623","relation":"dissertation_contains"}]},"title":"Cytoplasm's got moves","date_updated":"2026-09-02T22:30:26Z","author":[{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"first_name":"Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"}]},{"type":"preprint","ec_funded":1,"oa":1,"related_material":{"record":[{"relation":"later_version","id":"11843","status":"public"},{"id":"10307","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-09-02T22:30:27Z","date_published":"2021-10-18T00:00:00Z","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","year":"2021","article_processing_charge":"No","publication_status":"draft","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","first_name":"Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","first_name":"Alexander F"},{"first_name":"Ivana","last_name":"Glatzová","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","full_name":"Glatzová, Ivana"},{"full_name":"Lukesch, Michael S.","first_name":"Michael S.","last_name":"Lukesch"},{"first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-4561-241X","last_name":"Sixt"}],"language":[{"iso":"eng"}],"project":[{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911","call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>bioRxiv</i>. .","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>."},"doi":"10.1101/2021.10.18.464770","abstract":[{"text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.","lang":"eng"}],"department":[{"_id":"CaGu"},{"_id":"MiSi"}],"date_created":"2021-11-19T12:24:16Z","das_tickbox":"1","_id":"10316","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1","open_access":"1"}],"oa_version":"Preprint","status":"public","publication":"bioRxiv","month":"10","corr_author":"1"},{"date_published":"2021-09-29T00:00:00Z","date_updated":"2026-09-02T22:30:26Z","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina","first_name":"Cristina","last_name":"Savin"}],"article_processing_charge":"No","year":"2021","publication_status":"draft","oa":1,"type":"preprint","ec_funded":1,"acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","related_material":{"record":[{"id":"11932","relation":"dissertation_contains","status":"public"},{"status":"public","id":"14656","relation":"later_version"}]},"day":"29","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"month":"09","publication":"bioRxiv","status":"public","oa_version":"Preprint","das_tickbox":"1","_id":"10077","doi":"10.1101/2021.09.28.460602","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. .","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>."},"language":[{"iso":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"date_created":"2021-10-04T06:23:34Z","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}]},{"page":"5345-58","oa":1,"type":"journal_article","isi":1,"file":[{"checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","creator":"dernst","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","relation":"main_file","date_created":"2022-05-06T09:47:18Z","content_type":"application/pdf","access_level":"open_access","file_size":1008594,"file_id":"11352","success":1,"date_updated":"2022-05-06T09:47:18Z"}],"publication_status":"published","year":"2021","article_processing_charge":"No","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"date_published":"2021-06-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","pmid":1,"date_created":"2021-10-21T07:49:12Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"intvolume":"       138","language":[{"iso":"eng"}],"issue":"12","publication":"Molecular Biology and Evolution","ddc":["610"],"corr_author":"1","month":"06","status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"das_tickbox":"1","day":"19","file_date_updated":"2022-05-06T09:47:18Z","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","related_material":{"record":[{"status":"public","id":"19386","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"article_type":"original","external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"author":[{"full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"},{"first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L","first_name":"Marion A L","orcid":"0000-0002-8101-2518","last_name":"Picard"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","date_updated":"2026-09-02T22:30:28Z","volume":138,"department":[{"_id":"BeVi"}],"scopus_import":"1","citation":{"chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press, pp. 5345–58, 2021.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press, 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/molbev/msab178","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","quality_controlled":"1","_id":"10167"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2021","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"page":"1106–1112","publication":"Nature Materials","corr_author":"1","status":"public","month":"08","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"issue":"8","language":[{"iso":"eng"}],"intvolume":"        20","abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"date_created":"2020-12-02T10:50:47Z","pmid":1,"publisher":"Springer Nature","title":"A singlet triplet hole spin qubit in planar Ge","date_updated":"2026-09-02T22:30:43Z","author":[{"first_name":"Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hofmann","first_name":"Andrea C","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"full_name":"Mutter, Philipp M.","last_name":"Mutter","first_name":"Philipp M."},{"last_name":"Tavani","first_name":"Giulio","full_name":"Tavani, Giulio"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","full_name":"Crippa, Alessandro","first_name":"Alessandro","orcid":"0000-0002-2968-611X","last_name":"Crippa"},{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi"},{"last_name":"Martins","orcid":"0000-0003-2668-2401","first_name":"Frederico","full_name":"Martins, Frederico","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E"},{"first_name":"Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez"},{"first_name":"Maksim","last_name":"Borovkov","full_name":"Borovkov, Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2011.13755"],"pmid":["34083775"],"isi":["000657596400001"]},"day":"01","related_material":{"record":[{"id":"9323","relation":"research_data","status":"public"},{"status":"public","id":"10058","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/quantum-computing-with-holes/","relation":"press_release","description":"News on IST Homepage"}]},"publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"article_type":"original","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","arxiv":1,"_id":"8909","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2011.13755","open_access":"1"}],"project":[{"call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>.","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","ieee":"D. Jirovec <i>et al.</i>, “A singlet triplet hole spin qubit in planar Ge,” <i>Nature Materials</i>, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. 2021;20(8):1106–1112. doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>"},"doi":"10.1038/s41563-021-01022-2","scopus_import":"1","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"volume":20},{"page":"151","oa":1,"type":"dissertation","file":[{"date_created":"2021-09-30T14:29:14Z","relation":"source_file","file_name":"PHD_Thesis_Jirovec_Source.zip","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","creator":"djirovec","file_size":32397600,"access_level":"closed","content_type":"application/x-zip-compressed","file_id":"10061","embargo_to":"open_access","date_updated":"2022-12-20T23:30:07Z"},{"file_size":26910829,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-05T07:56:49Z","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_name":"PHD_Thesis_pdfa2b_1.pdf","creator":"djirovec","date_updated":"2022-12-20T23:30:07Z","embargo":"2022-10-06","file_id":"10087"}],"publication_status":"published","year":"2021","keyword":["qubits","quantum computing","holes"],"article_processing_charge":"No","date_published":"2021-10-05T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","date_created":"2021-09-30T07:53:49Z","abstract":[{"text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term.  The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.","lang":"eng"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"degree_awarded":"PhD","status":"public","corr_author":"1","month":"10","ddc":["621","539"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"day":"05","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","file_date_updated":"2022-12-20T23:30:07Z","related_material":{"record":[{"id":"10066","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10065"},{"status":"public","id":"8831","relation":"part_of_dissertation"},{"status":"public","id":"8909","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5816","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","author":[{"first_name":"Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","date_updated":"2026-04-08T07:12:19Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/at:ista:10058","citation":{"ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","mla":"Jirovec, Daniel. <i>Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10058\">10.15479/at:ista:10058</a>.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10058\">10.15479/at:ista:10058</a>","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","apa":"Jirovec, D. (2021). <i>Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10058\">https://doi.org/10.15479/at:ista:10058</a>","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10058\">https://doi.org/10.15479/at:ista:10058</a>.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021."},"project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"}],"oa_version":"Published Version","_id":"10058"},{"title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","article_number":"2107.12975","date_published":"2021-07-27T00:00:00Z","date_updated":"2026-09-02T22:30:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Severin, B.","last_name":"Severin","first_name":"B."},{"first_name":"D. T.","last_name":"Lennon","full_name":"Lennon, D. T."},{"last_name":"Camenzind","first_name":"L. C.","full_name":"Camenzind, L. C."},{"first_name":"F.","last_name":"Vigneau","full_name":"Vigneau, F."},{"full_name":"Fedele, F.","last_name":"Fedele","first_name":"F."},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","first_name":"Daniel"},{"first_name":"A.","last_name":"Ballabio","full_name":"Ballabio, A."},{"last_name":"Chrastina","first_name":"D.","full_name":"Chrastina, D."},{"last_name":"Isella","first_name":"G.","full_name":"Isella, G."},{"first_name":"M. de","last_name":"Kruijf","full_name":"Kruijf, M. de"},{"full_name":"Carballido, M. J.","first_name":"M. J.","last_name":"Carballido"},{"last_name":"Svab","first_name":"S.","full_name":"Svab, S."},{"full_name":"Kuhlmann, A. V.","first_name":"A. V.","last_name":"Kuhlmann"},{"full_name":"Braakman, F. R.","first_name":"F. R.","last_name":"Braakman"},{"last_name":"Geyer","first_name":"S.","full_name":"Geyer, S."},{"full_name":"Froning, F. N. M.","last_name":"Froning","first_name":"F. N. M."},{"first_name":"H.","last_name":"Moon","full_name":"Moon, H."},{"full_name":"Osborne, M. A.","last_name":"Osborne","first_name":"M. A."},{"full_name":"Sejdinovic, D.","last_name":"Sejdinovic","first_name":"D."},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"},{"full_name":"Zumbühl, D. M.","first_name":"D. M.","last_name":"Zumbühl"},{"full_name":"Briggs, G. A. D.","last_name":"Briggs","first_name":"G. A. D."},{"full_name":"Ares, N.","first_name":"N.","last_name":"Ares"}],"publication_status":"draft","year":"2021","article_processing_charge":"No","oa":1,"external_id":{"arxiv":["2107.12975"]},"type":"preprint","arxiv":1,"day":"27","related_material":{"record":[{"status":"public","relation":"later_version","id":"17389"},{"id":"10058","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations.","status":"public","month":"07","publication":"arXiv","oa_version":"Preprint","acknowledged_ssus":[{"_id":"NanoFab"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12975","open_access":"1"}],"_id":"10066","citation":{"ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975.","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2107.12975\">https://doi.org/10.48550/arXiv.2107.12975</a>","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2107.12975\">10.48550/arXiv.2107.12975</a>","ieee":"B. Severin <i>et al.</i>, “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” <i>arXiv</i>. .","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>ArXiv</i>, 2107.12975, doi:<a href=\"https://doi.org/10.48550/arXiv.2107.12975\">10.48550/arXiv.2107.12975</a>.","short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.).","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2107.12975\">https://doi.org/10.48550/arXiv.2107.12975</a>."},"doi":"10.48550/arXiv.2107.12975","project":[{"call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"language":[{"iso":"eng"}],"date_created":"2021-10-01T12:40:22Z","abstract":[{"lang":"eng","text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning."}],"department":[{"_id":"GeKa"}]},{"oa_version":"Published Version","quality_controlled":"1","_id":"8931","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.plantsci.2020.110750","citation":{"ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>."},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"volume":303,"scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"Bio"}],"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","date_updated":"2026-09-02T22:30:45Z","author":[{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"full_name":"Brunoud, Géraldine","first_name":"Géraldine","last_name":"Brunoud"},{"orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi"},{"first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","full_name":"Michalko, Jaroslav","last_name":"Michalko","first_name":"Jaroslav"},{"first_name":"Zlata","last_name":"Pavlovicova","full_name":"Pavlovicova, Zlata"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","first_name":"Inge"},{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"first_name":"Jakub","last_name":"Hajny","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"first_name":"Milada","last_name":"Čovanová","full_name":"Čovanová, Milada"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","first_name":"Lukas"},{"first_name":"Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"day":"01","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","id":"11626","status":"public"},{"status":"public","id":"10083","relation":"dissertation_contains"}]},"file_date_updated":"2021-02-04T07:49:25Z","publication_identifier":{"issn":["0168-9452"]},"month":"02","status":"public","corr_author":"1","ddc":["580"],"publication":"Plant Science","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":"       303","language":[{"iso":"eng"}],"publisher":"Elsevier","date_created":"2020-12-09T14:48:28Z","abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"pmid":1,"has_accepted_license":"1","date_published":"2021-02-01T00:00:00Z","article_number":"110750","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"file_id":"9083","date_updated":"2021-02-04T07:49:25Z","date_created":"2021-02-04T07:49:25Z","relation":"main_file","creator":"dernst","file_name":"2021_PlantScience_Gelova.pdf","checksum":"a7f2562bdca62d67dfa88e271b62a629","file_size":12563728,"access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"year":"2021","oa":1,"ec_funded":1,"type":"journal_article","isi":1},{"issue":"2","month":"06","status":"public","corr_author":"1","ddc":["580"],"publication":"Plant Physiology","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"date_created":"2021-03-26T12:08:38Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. "}],"pmid":1,"publisher":"Oxford University Press","language":[{"iso":"eng"}],"intvolume":"       186","publication_status":"published","year":"2021","article_processing_charge":"Yes (in subscription journal)","file":[{"file_name":"2021_PlantPhysio_Narasimhan.pdf","creator":"cziletti","checksum":"532bb9469d3b665907f06df8c383eade","relation":"main_file","date_created":"2021-11-11T15:07:51Z","content_type":"application/pdf","access_level":"open_access","file_size":2289127,"success":1,"file_id":"10273","date_updated":"2021-11-11T15:07:51Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-06-01T00:00:00Z","page":"1122–1142","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"_id":"9287","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","department":[{"_id":"JiFr"}],"volume":186,"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"citation":{"ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. 2021;186(2):1122–1142. doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>.","ieee":"M. Narasimhan <i>et al.</i>, “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” <i>Plant Physiology</i>, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/plphys/kiab134","author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","first_name":"Madhumitha"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"first_name":"Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin"},{"full_name":"Himschoot, E","first_name":"E","last_name":"Himschoot"},{"full_name":"Wang, R","first_name":"R","last_name":"Wang"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"first_name":"J","last_name":"Sánchez-Simarro","full_name":"Sánchez-Simarro, J"},{"last_name":"Aniento","first_name":"F","full_name":"Aniento, F"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","date_updated":"2026-09-02T22:30:45Z","day":"01","article_type":"original","related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"10083"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1093/plphys/kiab380"}]},"file_date_updated":"2021-11-11T15:07:51Z","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","external_id":{"pmid":["33734402"],"isi":["000671555900031"]}},{"_id":"10083","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"citation":{"ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>","apa":"Li, L. (2021). <i>Rapid cell growth regulation in Arabidopsis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","mla":"Li, Lanxin. <i>Rapid Cell Growth Regulation in Arabidopsis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.15479/at:ista:10083","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin"}],"title":"Rapid cell growth regulation in Arabidopsis","date_updated":"2026-04-16T12:20:41Z","day":"06","file_date_updated":"2022-12-20T23:30:03Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"442","status":"public"},{"id":"6627","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8931","relation":"part_of_dissertation"},{"status":"public","id":"8986","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10095"},{"status":"public","id":"8283","relation":"part_of_dissertation"},{"id":"9287","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10015","relation":"part_of_dissertation"}]},"OA_place":"publisher","degree_awarded":"PhD","status":"public","corr_author":"1","month":"10","ddc":["575"],"date_created":"2021-10-04T13:33:10Z","abstract":[{"text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that  vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. ","lang":"eng"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"language":[{"iso":"eng"}],"publication_status":"published","year":"2021","article_processing_charge":"No","file":[{"date_updated":"2022-12-20T23:30:03Z","file_id":"10138","embargo":"2022-10-14","file_size":8616142,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-14T08:00:07Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","creator":"cchlebak","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10"},{"file_size":15058499,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","date_created":"2021-10-14T08:00:13Z","checksum":"f23ed258ca894f6aabf58b0c128bf242","creator":"cchlebak","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","embargo_to":"open_access","date_updated":"2022-12-20T23:30:03Z","file_id":"10139"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-10-06T00:00:00Z","ec_funded":1,"type":"dissertation","oa":1},{"title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","date_updated":"2026-09-02T22:30:45Z","author":[{"full_name":"Nikonorova, N","last_name":"Nikonorova","first_name":"N"},{"last_name":"Murphy","first_name":"E","full_name":"Murphy, E"},{"first_name":"CF","last_name":"Fonseca de Lima","full_name":"Fonseca de Lima, CF"},{"full_name":"Zhu, S","first_name":"S","last_name":"Zhu"},{"first_name":"B","last_name":"van de Cotte","full_name":"van de Cotte, B"},{"full_name":"Vu, LD","last_name":"Vu","first_name":"LD"},{"full_name":"Balcerowicz, D","first_name":"D","last_name":"Balcerowicz"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin"},{"first_name":"X","last_name":"Kong","full_name":"Kong, X"},{"full_name":"De Rop, G","first_name":"G","last_name":"De Rop"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Vissenberg","first_name":"K","full_name":"Vissenberg, K"},{"last_name":"Morris","first_name":"PC","full_name":"Morris, PC"},{"first_name":"Z","last_name":"Ding","full_name":"Ding, Z"},{"last_name":"De Smet","first_name":"I","full_name":"De Smet, I"}],"external_id":{"pmid":["34359847"],"isi":["000676604700001"]},"day":"02","article_type":"original","acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","publication_identifier":{"issn":["2073-4409"]},"file_date_updated":"2021-09-16T09:07:06Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10083"}]},"oa_version":"Published Version","quality_controlled":"1","_id":"10015","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. 2021;10. doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>","ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665.","mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>, vol. 10, 1665, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>.","ieee":"N. Nikonorova <i>et al.</i>, “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” <i>Cells</i>, vol. 10. MDPI, 2021.","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).","chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>."},"doi":"10.3390/cells10071665","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"volume":10,"department":[{"_id":"JiFr"}],"scopus_import":"1","date_published":"2021-07-02T00:00:00Z","article_number":"1665 ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2021-09-16T09:07:06Z","relation":"main_file","file_name":"2021_Cells_Nikonorova.pdf","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","creator":"cchlebak","file_size":2667848,"access_level":"open_access","content_type":"application/pdf","file_id":"10021","success":1,"date_updated":"2021-09-16T09:07:06Z"}],"publication_status":"published","article_processing_charge":"Yes","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"year":"2021","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","month":"07","publication":"Cells","status":"public","ddc":["575"],"intvolume":"        10","language":[{"iso":"eng"}],"publisher":"MDPI","pmid":1,"date_created":"2021-09-14T11:36:20Z","abstract":[{"text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip.","lang":"eng"}],"has_accepted_license":"1","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"]},{"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.21203/rs.3.rs-266395/v3","citation":{"short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. ."},"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"_id":"10095","oa_version":"Preprint","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"day":"09","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","related_material":{"record":[{"id":"10223","relation":"later_version","status":"public"},{"status":"public","id":"10083","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["2693-5015"]},"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","date_updated":"2026-09-02T22:30:45Z","author":[{"first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"full_name":"Ren, Hong","last_name":"Ren","first_name":"Hong"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Sergey","last_name":"Shabala","full_name":"Shabala, Sergey"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Kinoshita, Toshinori","first_name":"Toshinori","last_name":"Kinoshita"},{"full_name":"Gray, William M.","last_name":"Gray","first_name":"William M."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"date_created":"2021-10-06T08:56:22Z","publication":"Research Square","month":"09","corr_author":"1","status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"ec_funded":1,"type":"preprint","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"266395","date_published":"2021-09-09T00:00:00Z","publication_status":"draft","year":"2021","article_processing_charge":"No"},{"page":"171","oa":1,"type":"dissertation","ec_funded":1,"file":[{"creator":"lschmid","file_name":"submission_new.zip","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","date_created":"2021-11-18T12:41:46Z","relation":"source_file","access_level":"closed","content_type":"application/zip","file_size":29703124,"file_id":"10305","date_updated":"2022-12-20T23:30:08Z","embargo_to":"open_access"},{"date_updated":"2022-12-20T23:30:08Z","embargo":"2022-10-18","file_id":"10306","content_type":"application/pdf","access_level":"open_access","file_size":8320985,"file_name":"thesis_new_upload.pdf","creator":"lschmid","checksum":"d940af042e94660c6b6a7b4f0b184d47","relation":"main_file","date_created":"2021-11-18T12:59:15Z"}],"article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-11-17T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","date_created":"2021-11-15T17:12:57Z","abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"language":[{"iso":"eng"}],"supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"}],"degree_awarded":"PhD","ddc":["519","576"],"month":"11","status":"public","corr_author":"1","related_material":{"record":[{"status":"public","id":"9997","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9402","status":"public"},{"id":"2","relation":"part_of_dissertation","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2022-12-20T23:30:08Z","day":"17","OA_place":"publisher","author":[{"full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329"}],"date_updated":"2026-04-08T07:11:20Z","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"doi":"10.15479/at:ista:10293","citation":{"short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>.","apa":"Schmid, L. (2021). <i>Evolution of cooperation via (in)direct reciprocity under imperfect information</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","mla":"Schmid, Laura. <i>Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>."},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","_id":"10293"},{"external_id":{"isi":["000692406400018"],"pmid":["34465830"]},"file_date_updated":"2021-09-13T10:31:21Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10293"}]},"publication_identifier":{"eissn":["2045-2322"]},"article_type":"original","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","day":"31","date_updated":"2026-09-02T22:30:46Z","title":"The evolution of indirect reciprocity under action and assessment generosity","author":[{"full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329"},{"full_name":"Shati, Pouya","last_name":"Shati","first_name":"Pouya"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"citation":{"mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>.","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","apa":"Schmid, L., Shati, P., Hilbe, C., &#38; Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41598-021-96932-1","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"volume":11,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"oa_version":"Published Version","quality_controlled":"1","_id":"9997","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"date_published":"2021-08-31T00:00:00Z","article_number":"17443","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":2424943,"file_name":"2021_ScientificReports_Schmid.pdf","checksum":"19df8816cf958b272b85841565c73182","creator":"cchlebak","date_created":"2021-09-13T10:31:21Z","relation":"main_file","date_updated":"2021-09-13T10:31:21Z","file_id":"10006","success":1}],"keyword":["Multidisciplinary"],"year":"2021","article_processing_charge":"Yes","publication_status":"published","intvolume":"        11","language":[{"iso":"eng"}],"publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms."}],"has_accepted_license":"1","pmid":1,"date_created":"2021-09-11T16:22:02Z","publication":"Scientific Reports","ddc":["003"],"status":"public","corr_author":"1","month":"08","issue":"1"},{"oa":1,"type":"dissertation","date_published":"2021-10-13T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"creator":"cziletti","checksum":"ce7108853e6cec6224f17cd6429b51fe","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","date_created":"2021-10-27T07:45:37Z","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":28508629,"file_id":"10186","date_updated":"2022-12-20T23:30:05Z","embargo_to":"open_access"},{"date_created":"2021-10-27T07:45:57Z","relation":"main_file","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","checksum":"0d7afb846e8e31ec794de47bf44e12ef","creator":"cziletti","file_size":10623525,"access_level":"open_access","content_type":"application/pdf","file_id":"10187","embargo":"2022-10-28","date_updated":"2022-12-20T23:30:05Z"}],"year":"2021","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"date_created":"2021-10-13T13:42:48Z","abstract":[{"lang":"eng","text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects."}],"has_accepted_license":"1","month":"10","ddc":["570"],"corr_author":"1","status":"public","degree_awarded":"PhD","OA_place":"publisher","file_date_updated":"2022-12-20T23:30:05Z","publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9160"}]},"day":"13","date_updated":"2026-04-08T07:12:06Z","title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","author":[{"first_name":"Hana","last_name":"Semerádová","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semerádová, Hana"}],"doi":"10.15479/at:ista:10135","citation":{"apa":"Semerádová, H. (2021). <i>Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>","mla":"Semerádová, Hana. <i>Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>."},"project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","grant_number":"24746"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"oa_version":"Published Version","_id":"10135"}]