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We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","year":"2021","volume":16,"date_created":"2021-05-30T22:01:24Z","date_updated":"2023-08-10T22:30:51Z","author":[{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","first_name":"Yuji","last_name":"Okamoto","full_name":"Okamoto, Yuji"},{"orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina","full_name":"Borges Merjane, Carolina"},{"first_name":"Victor M","last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"last_name":"Suter","first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"2947–2967","article_type":"original","citation":{"ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967."},"publication":"Nature Protocols","date_published":"2021-06-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system."}],"intvolume":" 16","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","status":"public","ddc":["570"],"_id":"9438","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"VandaeletalAuthorVersion2021.pdf","access_level":"open_access","content_type":"application/pdf","file_size":38574802,"creator":"cziletti","relation":"main_file","file_id":"9639","embargo":"2021-12-01","date_created":"2021-07-08T12:27:55Z","date_updated":"2021-12-02T23:30:05Z","checksum":"7eb580abd8893cdb0b410cf41bc8c263"}],"oa_version":"Submitted Version"},{"has_accepted_license":"1","article_processing_charge":"No","day":"13","date_published":"2021-09-13T00:00:00Z","page":"168","citation":{"mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021."},"abstract":[{"lang":"eng","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. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"source_file","file_id":"9993","checksum":"c763064adaa720e16066c1a4f9682bbb","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T07:29:48Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_vupload.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25179004,"creator":"lhoermaye"},{"file_size":6246900,"content_type":"application/pdf","creator":"lhoermaye","access_level":"open_access","file_name":"Thesis_vfinal_pdfa.pdf","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T14:25:08Z","relation":"main_file","embargo":"2021-09-09","file_id":"9996"}],"oa_version":"Published Version","status":"public","title":"Wound healing in the Arabidopsis root meristem","ddc":["575"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9992","publication_identifier":{"issn":["2663-337X"]},"month":"09","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/at:ista:9992","project":[{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"ec_funded":1,"file_date_updated":"2021-09-15T22:30:26Z","date_updated":"2023-09-07T13:38:33Z","date_created":"2021-09-09T07:37:20Z","related_material":{"record":[{"id":"6351","status":"public","relation":"part_of_dissertation"},{"id":"6943","status":"public","relation":"part_of_dissertation"},{"id":"8002","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","year":"2021"},{"day":"16","has_accepted_license":"1","article_processing_charge":"No","keyword":["general medicine"],"scopus_import":"1","date_published":"2021-12-16T00:00:00Z","article_type":"original","page":"830-842","publication":"Nature Computational Science","citation":{"apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1."},"abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"issue":"12","type":"journal_article","oa_version":"Submitted Version","file":[{"file_name":"Guzmanetal2021.pdf","access_level":"open_access","creator":"patrickd","file_size":1699466,"content_type":"application/pdf","embargo":"2022-06-17","file_id":"11430","relation":"main_file","date_created":"2022-06-02T12:51:07Z","date_updated":"2022-06-18T22:30:03Z","checksum":"9fec5b667909ef52be96d502e4f8c2ae"},{"relation":"supplementary_material","embargo":"2022-06-17","file_id":"11431","title":"Supplementary Material","date_updated":"2022-06-18T22:30:03Z","date_created":"2022-06-02T12:53:47Z","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","file_name":"Guzmanetal2021Suppl.pdf","access_level":"open_access","file_size":3005651,"content_type":"application/pdf","creator":"patrickd"}],"ddc":["610"],"status":"public","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","intvolume":" 1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10816","month":"12","publication_identifier":{"issn":["2662-8457"]},"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1038/s43588-021-00157-1","quality_controlled":"1","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/647800","open_access":"1"}],"oa":1,"file_date_updated":"2022-06-18T22:30:03Z","ec_funded":1,"date_updated":"2023-08-10T22:30:10Z","date_created":"2022-03-04T08:32:36Z","volume":1,"author":[{"first_name":"José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois"},{"orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia "},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin","full_name":"Zhang, Xiaomin"},{"full_name":"Suter, Benjamin","last_name":"Suter","first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/spot-the-difference/","relation":"press_release"}],"record":[{"id":"10110","status":"public","relation":"software"}]},"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Springer Nature","acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","year":"2021"},{"date_published":"2021-12-16T00:00:00Z","doi":"10.15479/AT:ISTA:10110","oa":1,"tmp":{"short":"GPL 3.0","name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html"},"citation":{"ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. https://doi.org/10.15479/AT:ISTA:10110","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.","mla":"Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021)."},"has_accepted_license":"1","month":"12","day":"16","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/spot-the-difference/"}],"record":[{"id":"10816","status":"public","relation":"used_for_analysis_in"}]},"author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","first_name":"José","last_name":"Guzmán","full_name":"Guzmán, José"},{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"last_name":"Espinoza Martinez","first_name":"Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia "},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Suter, Benjamin","last_name":"Suter","first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"file":[{"date_updated":"2021-10-08T08:46:04Z","date_created":"2021-10-08T08:46:04Z","checksum":"f92f8931cad0aa7e411c1715337bf408","success":1,"relation":"main_file","file_id":"10114","content_type":"application/x-zip-compressed","file_size":332990101,"creator":"cchlebak","file_name":"patternseparation-main (1).zip","access_level":"open_access"}],"date_created":"2021-10-08T06:44:22Z","date_updated":"2024-03-28T23:30:11Z","_id":"10110","year":"2021","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"IST Austria","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","ddc":["005"],"status":"public","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"file_date_updated":"2021-10-08T08:46:04Z","license":"https://opensource.org/licenses/GPL-3.0","type":"software"},{"day":"29","month":"09","article_processing_charge":"No","date_published":"2021-09-29T00:00:00Z","doi":"10.1101/2021.09.28.460602","language":[{"iso":"eng"}],"publication":"bioRxiv","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.","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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602."},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"}],"abstract":[{"lang":"eng","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."}],"ec_funded":1,"type":"preprint","author":[{"last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina"}],"related_material":{"record":[{"id":"11932","status":"public","relation":"dissertation_contains"}]},"date_created":"2021-10-04T06:23:34Z","date_updated":"2024-03-28T23:30:16Z","oa_version":"Preprint","year":"2021","_id":"10077","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.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","publication_status":"submitted","status":"public","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"publisher":"Cold Spring Harbor Laboratory"},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"StFr"}],"year":"2021","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","pmid":1,"date_created":"2021-03-16T11:12:20Z","date_updated":"2023-09-05T15:34:44Z","volume":13,"author":[{"full_name":"Petit, Yann K.","first_name":"Yann K.","last_name":"Petit"},{"first_name":"Eléonore","last_name":"Mourad","full_name":"Mourad, Eléonore"},{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"first_name":"Christian","last_name":"Leypold","full_name":"Leypold, Christian"},{"full_name":"Windischbacher, Andreas","last_name":"Windischbacher","first_name":"Andreas"},{"full_name":"Mijailovic, Daniel","first_name":"Daniel","last_name":"Mijailovic"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"first_name":"Sergey M.","last_name":"Borisov","full_name":"Borisov, Sergey M."},{"full_name":"Zojer, Egbert","first_name":"Egbert","last_name":"Zojer"},{"full_name":"Brutti, Sergio","last_name":"Brutti","first_name":"Sergio"},{"last_name":"Fontaine","first_name":"Olivier","full_name":"Fontaine, Olivier"},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"file_date_updated":"2021-09-16T22:30:03Z","quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41557-021-00643-z","month":"03","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"status":"public","title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","ddc":["540"],"intvolume":" 13","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9250","file":[{"file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1811448,"creator":"dernst","relation":"main_file","file_id":"9276","embargo":"2021-09-15","date_created":"2021-03-22T11:46:00Z","date_updated":"2021-09-16T22:30:03Z","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.","lang":"eng"}],"issue":"5","article_type":"original","page":"465-471","publication":"Nature Chemistry","citation":{"apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-021-00643-z","ieee":"Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 2021;13(5):465-471. doi:10.1038/s41557-021-00643-z","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z."},"date_published":"2021-03-15T00:00:00Z","keyword":["General Chemistry","General Chemical Engineering"],"scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No"},{"month":"07","publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.15479/at:ista:9623","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"file_date_updated":"2022-07-02T22:30:06Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"author":[{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","first_name":"Silvia","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9750"},{"id":"9006","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-07T13:33:27Z","date_created":"2021-07-01T14:50:17Z","has_accepted_license":"1","article_processing_charge":"No","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. https://doi.org/10.15479/at:ista:9623.","mla":"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, doi:10.15479/at:ista:9623.","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.","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.","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.","apa":"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. https://doi.org/10.15479/at:ista:9623","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623"},"page":"111","date_published":"2021-07-01T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9623","status":"public","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","ddc":["570"],"oa_version":"Published Version","file":[{"relation":"source_file","file_id":"9624","date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:48:54Z","checksum":"e039225a47ef32666d59bf35ddd30ecf","embargo_to":"open_access","file_name":"PhDThesis_SCM.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":131946790,"creator":"scaballe"},{"relation":"main_file","file_id":"9625","embargo":"2022-07-01","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","date_created":"2021-07-01T14:46:25Z","date_updated":"2022-07-02T22:30:06Z","access_level":"open_access","file_name":"PhDThesis_SCM.pdf","file_size":17094958,"content_type":"application/pdf","creator":"scaballe"}]},{"isi":1,"quality_controlled":"1","external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2020.12.002","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"month":"01","publisher":"Elsevier","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2021","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.","volume":56,"date_updated":"2024-03-28T23:30:19Z","date_created":"2021-01-17T23:01:10Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9623"}]},"author":[{"first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","first_name":"Silvia","last_name":"Caballero Mancebo"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"page":"P213-226","article_type":"original","citation":{"ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002","apa":"Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002."},"publication":"Developmental Cell","date_published":"2021-01-25T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"25","intvolume":" 56","status":"public","title":"Cytoplasm's got moves","_id":"9006","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","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."}]},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"doi":"10.1038/s41467-021-23123-x","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy"},{"name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000658769900010"]},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"05","volume":12,"date_created":"2021-05-28T11:49:46Z","date_updated":"2024-03-28T23:30:23Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7800"},{"relation":"dissertation_contains","status":"public","id":"12401"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}]},"author":[{"first_name":"Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin"},{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Lena A"},{"full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"full_name":"Tasciyan, Saren","last_name":"Tasciyan","first_name":"Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer"},{"full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph"},{"first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"id":"D23090A2-9057-11EA-883A-A8396FC7A38F","last_name":"Dobler","first_name":"Zoe","full_name":"Dobler, Zoe"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"publisher":"Springer Nature","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","year":"2021","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file_date_updated":"2021-05-28T12:39:43Z","article_number":"3058","date_published":"2021-05-24T00:00:00Z","article_type":"original","citation":{"chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x"},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"24","keyword":["General Biochemistry","Genetics and Molecular Biology"],"file":[{"creator":"kschuh","content_type":"application/pdf","file_size":9358599,"access_level":"open_access","file_name":"2021_NatureCommunications_Morandell.pdf","success":1,"checksum":"337e0f7959c35ec959984cacdcb472ba","date_updated":"2021-05-28T12:39:43Z","date_created":"2021-05-28T12:39:43Z","file_id":"9430","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 12","status":"public","ddc":["572"],"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","_id":"9429","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs."}],"type":"journal_article"},{"oa_version":"Published Version","file":[{"embargo_to":"open_access","file_name":"PHD_Thesis_Jirovec_Source.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":32397600,"creator":"djirovec","relation":"source_file","file_id":"10061","date_updated":"2022-12-20T23:30:07Z","date_created":"2021-09-30T14:29:14Z","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5"},{"file_id":"10087","embargo":"2022-10-06","relation":"main_file","checksum":"5fbe08d4f66d1153e04c47971538fae8","date_created":"2021-10-05T07:56:49Z","date_updated":"2022-12-20T23:30:07Z","access_level":"open_access","file_name":"PHD_Thesis_pdfa2b_1.pdf","creator":"djirovec","file_size":26910829,"content_type":"application/pdf"}],"_id":"10058","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["621","539"],"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","status":"public","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"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2021-10-05T00:00:00Z","citation":{"short":"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. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria."},"page":"151","day":"05","article_processing_charge":"No","has_accepted_license":"1","keyword":["qubits","quantum computing","holes"],"author":[{"first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"}],"related_material":{"record":[{"id":"8831","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10065"},{"id":"10066","status":"public","relation":"part_of_dissertation"},{"id":"8909","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"5816"}]},"date_created":"2021-09-30T07:53:49Z","date_updated":"2023-09-08T11:41:08Z","year":"2021","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"file_date_updated":"2022-12-20T23:30:07Z","doi":"10.15479/at:ista:10058","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"supervisor":[{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"month":"10","publication_identifier":{"issn":["2663-337X"]}},{"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.","year":"2021","publisher":"Springer Nature","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"publication_status":"published","related_material":{"record":[{"id":"9323","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10058"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}]},"author":[{"first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"},{"full_name":"Hofmann, Andrea C","first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"last_name":"Mutter","first_name":"Philipp M.","full_name":"Mutter, Philipp M."},{"full_name":"Tavani, Giulio","last_name":"Tavani","first_name":"Giulio"},{"full_name":"Botifoll, Marc","first_name":"Marc","last_name":"Botifoll"},{"full_name":"Crippa, Alessandro","first_name":"Alessandro","last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","orcid":"0000-0002-2968-611X"},{"full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","first_name":"Oliver","full_name":"Sagi, Oliver"},{"orcid":"0000-0003-2668-2401","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","last_name":"Martins","first_name":"Frederico","full_name":"Martins, Frederico"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714"},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Borovkov","first_name":"Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","full_name":"Borovkov, Maksim"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"volume":20,"date_created":"2020-12-02T10:50:47Z","date_updated":"2024-03-28T23:30:27Z","ec_funded":1,"external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"]},"main_file_link":[{"url":"https://arxiv.org/abs/2011.13755","open_access":"1"}],"oa":1,"project":[{"grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41563-021-01022-2","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"month":"08","_id":"8909","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","title":"A singlet triplet hole spin qubit in planar Ge","status":"public","oa_version":"Preprint","type":"journal_article","issue":"8","abstract":[{"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.","lang":"eng"}],"citation":{"ieee":"D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,” Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","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. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2","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.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2","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.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2.","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.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2."},"publication":"Nature Materials","page":"1106–1112","article_type":"original","date_published":"2021-08-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","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"}],"title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","status":"public","ddc":["571"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9397","file":[{"date_updated":"2022-05-21T22:30:04Z","date_created":"2021-05-17T12:29:12Z","checksum":"7f98532f5324a0b2f3fa8de2967baa19","file_id":"9398","relation":"source_file","creator":"khuljev","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":47799741,"file_name":"KHuljev_Thesis_corrections.docx","embargo_to":"open_access","access_level":"closed"},{"date_created":"2021-05-18T14:50:28Z","date_updated":"2022-05-21T22:30:04Z","checksum":"bf512f8a1e572a543778fc4b227c01ba","file_id":"9401","embargo":"2022-05-20","relation":"main_file","creator":"khuljev","file_size":16542131,"content_type":"application/pdf","file_name":"new_KHuljev_Thesis_corrections.pdf","access_level":"open_access"}],"oa_version":"Published Version","day":"18","has_accepted_license":"1","article_processing_charge":"No","page":"101","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. https://doi.org/10.15479/at:ista:9397.","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","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.","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). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","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.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397"},"date_published":"2021-05-18T00:00:00Z","file_date_updated":"2022-05-21T22:30:04Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"year":"2021","date_updated":"2023-09-07T13:32:32Z","date_created":"2021-05-17T12:31:30Z","author":[{"last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla"}],"month":"05","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9397"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10058"}]},"author":[{"full_name":"Severin, B.","first_name":"B.","last_name":"Severin"},{"full_name":"Lennon, D. T.","first_name":"D. T.","last_name":"Lennon"},{"full_name":"Camenzind, L. C.","first_name":"L. C.","last_name":"Camenzind"},{"first_name":"F.","last_name":"Vigneau","full_name":"Vigneau, F."},{"full_name":"Fedele, F.","last_name":"Fedele","first_name":"F."},{"full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","first_name":"Daniel","last_name":"Jirovec"},{"first_name":"A.","last_name":"Ballabio","full_name":"Ballabio, A."},{"full_name":"Chrastina, D.","first_name":"D.","last_name":"Chrastina"},{"full_name":"Isella, G.","last_name":"Isella","first_name":"G."},{"first_name":"M. de","last_name":"Kruijf","full_name":"Kruijf, M. de"},{"last_name":"Carballido","first_name":"M. J.","full_name":"Carballido, M. J."},{"first_name":"S.","last_name":"Svab","full_name":"Svab, S."},{"full_name":"Kuhlmann, A. V.","first_name":"A. V.","last_name":"Kuhlmann"},{"last_name":"Braakman","first_name":"F. R.","full_name":"Braakman, F. R."},{"last_name":"Geyer","first_name":"S.","full_name":"Geyer, S."},{"first_name":"F. N. M.","last_name":"Froning","full_name":"Froning, F. N. M."},{"last_name":"Moon","first_name":"H.","full_name":"Moon, H."},{"last_name":"Osborne","first_name":"M. A.","full_name":"Osborne, M. A."},{"first_name":"D.","last_name":"Sejdinovic","full_name":"Sejdinovic, D."},{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"},{"last_name":"Zumbühl","first_name":"D. M.","full_name":"Zumbühl, D. M."},{"full_name":"Briggs, G. A. D.","last_name":"Briggs","first_name":"G. A. D."},{"full_name":"Ares, N.","first_name":"N.","last_name":"Ares"}],"oa_version":"Preprint","date_updated":"2024-03-28T23:30:27Z","date_created":"2021-10-01T12:40:22Z","year":"2021","_id":"10066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","department":[{"_id":"GeKa"}],"status":"public","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","publication_status":"submitted","abstract":[{"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.","lang":"eng"}],"type":"preprint","article_number":"2107.12975","date_published":"2021-07-27T00:00:00Z","doi":"10.48550/arXiv.2107.12975","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"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. arXiv. https://doi.org/10.48550/arXiv.2107.12975","ieee":"B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” arXiv. .","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. doi:10.48550/arXiv.2107.12975","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.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.12975.","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, 2107.12975, doi:10.48550/arXiv.2107.12975.","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.)."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.12975"}],"external_id":{"arxiv":["2107.12975"]},"publication":"arXiv","project":[{"grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF"}],"article_processing_charge":"No","month":"07","day":"27"},{"scopus_import":"1","day":"29","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"eLife","citation":{"ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274."},"date_published":"2021-04-29T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation."}],"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","status":"public","ddc":["570"],"intvolume":" 10","_id":"9437","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"6ebcb79999f889766f7cd79ee134ad28","date_updated":"2021-05-31T09:43:09Z","date_created":"2021-05-31T09:43:09Z","file_id":"9440","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":8174719,"access_level":"open_access","file_name":"2021_eLife_Bhandari.pdf"}],"oa_version":"Published Version","month":"04","publication_identifier":{"eissn":["2050-084X"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000651761700001"]},"language":[{"iso":"eng"}],"doi":"10.7554/ELIFE.68274","article_number":"e68274","file_date_updated":"2021-05-31T09:43:09Z","ec_funded":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"},{"_id":"PeJo"}],"acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","year":"2021","date_updated":"2024-03-28T23:30:31Z","date_created":"2021-05-30T22:01:23Z","volume":10,"author":[{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","first_name":"Pradeep","last_name":"Bhandari","full_name":"Bhandari, Pradeep"},{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"full_name":"Fernández-Fernández, Diego","last_name":"Fernández-Fernández","first_name":"Diego"},{"full_name":"Fritzius, Thorsten","first_name":"Thorsten","last_name":"Fritzius"},{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst","full_name":"Kleindienst, David"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C","last_name":"Önal","full_name":"Önal, Hüseyin C"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire"},{"last_name":"Gassmann","first_name":"Martin","full_name":"Gassmann, Martin"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"full_name":"Kulik, Akos","last_name":"Kulik","first_name":"Akos"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}],"link":[{"url":"https://doi.org/10.1101/2020.04.16.045112","relation":"earlier_version"}]}},{"month":"06","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9562","oa":1,"file_date_updated":"2022-07-02T22:30:04Z","date_updated":"2023-09-11T12:55:53Z","date_created":"2021-06-17T14:10:47Z","author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David","full_name":"Kleindienst, David"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9756"},{"id":"9437","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8532"},{"relation":"part_of_dissertation","status":"public","id":"612"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"year":"2021","day":"01","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-06-01T00:00:00Z","page":"124","citation":{"chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562"},"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"main_file","embargo":"2022-07-01","file_id":"9563","checksum":"659df5518db495f679cb1df9e9bd1d94","date_created":"2021-06-17T14:03:14Z","date_updated":"2022-07-02T22:30:04Z","access_level":"open_access","file_name":"Thesis.pdf","content_type":"application/pdf","file_size":77299142,"creator":"dkleindienst"},{"creator":"dkleindienst","file_size":369804895,"content_type":"application/zip","file_name":"Thesis_source.zip","embargo_to":"open_access","access_level":"closed","date_created":"2021-06-17T14:04:30Z","date_updated":"2022-07-02T22:30:04Z","checksum":"3bcf63a2b19e5b6663be051bea332748","file_id":"9564","relation":"source_file"}],"oa_version":"Published Version","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","ddc":["570"],"status":"public","_id":"9562","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"9756","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 169","ddc":["573"],"status":"public","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","oa_version":"None","type":"book_chapter","alternative_title":["Neuromethods"],"abstract":[{"text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms.","lang":"eng"}],"citation":{"ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain (Vol. 169, pp. 267–283). New York: Humana. https://doi.org/10.1007/978-1-0716-1522-5_19","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the Brain, vol. 169, New York: Humana, 2021, pp. 267–283.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection in the Brain, 169:267–83. Neuromethods. New York: Humana, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” Receptor and Ion Channel Detection in the Brain, vol. 169, Humana, 2021, pp. 267–83, doi:10.1007/978-1-0716-1522-5_19.","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283."},"publication":" Receptor and Ion Channel Detection in the Brain","page":"267-283","date_published":"2021-07-27T00:00:00Z","series_title":"Neuromethods","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"article_processing_charge":"No","has_accepted_license":"1","day":"27","year":"2021","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"publisher":"Humana","publication_status":"published","related_material":{"record":[{"id":"9562","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Harada, Harumi","last_name":"Harada","first_name":"Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"volume":169,"date_updated":"2024-03-28T23:30:31Z","date_created":"2021-07-30T09:34:56Z","place":"New York","ec_funded":1,"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020"}],"quality_controlled":"1","doi":"10.1007/978-1-0716-1522-5_19","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"month":"07"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-01-01T00:00:00Z","citation":{"short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria."},"page":"278","abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"checksum":"d1b9db3725aed34dadd81274aeb9426c","date_updated":"2021-12-23T23:30:04Z","date_created":"2020-12-22T20:08:44Z","relation":"main_file","embargo":"2021-12-22","file_id":"8969","content_type":"application/pdf","file_size":5251507,"creator":"akafshda","access_level":"open_access","file_name":"Thesis-pdfa.pdf"},{"checksum":"1661df7b393e6866d2460eba3c905130","date_created":"2020-12-22T20:08:50Z","date_updated":"2021-03-04T23:30:04Z","relation":"source_file","file_id":"8970","file_size":10636756,"content_type":"application/zip","creator":"akafshda","access_level":"closed","embargo_to":"open_access","file_name":"source.zip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8934","status":"public","ddc":["005"],"title":"Parameterized and algebro-geometric advances in static program analysis","month":"01","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8934","degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"file_date_updated":"2021-12-23T23:30:04Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","author":[{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1386"},{"relation":"part_of_dissertation","status":"public","id":"1437"},{"status":"public","relation":"part_of_dissertation","id":"311"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6380"},{"id":"639","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"66"},{"id":"6780","relation":"part_of_dissertation","status":"public"},{"id":"6918","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7810"},{"id":"6175","status":"public","relation":"part_of_dissertation"},{"id":"6378","relation":"part_of_dissertation","status":"public"},{"id":"6490","status":"public","relation":"part_of_dissertation"},{"id":"7014","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8089"},{"status":"public","relation":"part_of_dissertation","id":"8728"},{"status":"public","relation":"part_of_dissertation","id":"7158"},{"status":"public","relation":"part_of_dissertation","id":"5977"},{"id":"6009","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6340"},{"id":"949","relation":"part_of_dissertation","status":"public"}]},"date_created":"2020-12-10T12:17:07Z","date_updated":"2023-09-22T10:03:21Z","year":"2021","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria"},{"_id":"10307","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Pathogenic Escherichia coli hijack the host immune response","oa_version":"Published Version","file":[{"creator":"ktomasek","file_size":13266088,"content_type":"application/pdf","access_level":"open_access","file_name":"ThesisTomasekKathrin.pdf","checksum":"b39c9e0ef18d0484d537a67551effd02","date_created":"2021-11-18T15:07:31Z","date_updated":"2022-12-20T23:30:05Z","file_id":"10308","embargo":"2022-11-18","relation":"main_file"},{"file_id":"10309","relation":"source_file","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:46Z","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_name":"ThesisTomasekKathrin.docx","embargo_to":"open_access","access_level":"closed","creator":"ktomasek","file_size":7539509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","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."}],"citation":{"ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307."},"page":"73","date_published":"2021-11-18T00:00:00Z","day":"18","has_accepted_license":"1","article_processing_charge":"No","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"author":[{"orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin"}],"related_material":{"record":[{"id":"10316","relation":"part_of_dissertation","status":"public"}]},"date_created":"2021-11-18T15:05:06Z","date_updated":"2023-09-07T13:34:38Z","file_date_updated":"2022-12-20T23:30:05Z","oa":1,"doi":"10.15479/at:ista:10307","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["2663-337X"]}},{"article_processing_charge":"No","day":"18","month":"10","date_published":"2021-10-18T00:00:00Z","doi":"10.1101/2021.10.18.464770","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"citation":{"mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770.","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. bioRxiv. doi:10.1101/2021.10.18.464770","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, 10.1101/2021.10.18.464770.","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,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770"},"publication":"bioRxiv","project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin"}],"ec_funded":1,"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"}],"type":"preprint","related_material":{"record":[{"status":"public","relation":"later_version","id":"11843"},{"id":"10307","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Tomasek","first_name":"Kathrin","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","first_name":"Ivana","last_name":"Glatzová","full_name":"Glatzová, Ivana"},{"last_name":"Lukesch","first_name":"Michael S.","full_name":"Lukesch, Michael S."},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Michael K","last_name":"Sixt"}],"oa_version":"Preprint","date_updated":"2024-03-28T23:30:35Z","date_created":"2021-11-19T12:24:16Z","_id":"10316","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2021","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.","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"publisher":"Cold Spring Harbor Laboratory","publication_status":"submitted","status":"public","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14"},{"year":"2021","acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","pmid":1,"publication_status":"published","publisher":"Embo Press","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"author":[{"first_name":"Krisztina","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina"},{"last_name":"Marconi","first_name":"Marco","full_name":"Marconi, Marco"},{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"last_name":"O’Brien","first_name":"Jose","full_name":"O’Brien, Jose"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","first_name":"Rashed","last_name":"Abualia","full_name":"Abualia, Rashed"},{"last_name":"Antonielli","first_name":"Livio","full_name":"Antonielli, Livio"},{"full_name":"Montesinos López, Juan C","last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Yuzhou"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","first_name":"Candela","full_name":"Cuesta, Candela"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina"},{"first_name":"Eleonore","last_name":"Bouguyon","full_name":"Bouguyon, Eleonore"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gutiérrez, Rodrigo A.","first_name":"Rodrigo A.","last_name":"Gutiérrez"},{"full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","first_name":"Krzysztof T"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}]},"date_updated":"2024-03-28T23:30:39Z","date_created":"2021-01-17T23:01:12Z","volume":40,"article_number":"e106862","file_date_updated":"2021-02-11T12:28:29Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"},{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"doi":"10.15252/embj.2020106862","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9010","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","ddc":["580"],"status":"public","intvolume":" 40","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_Embo_Otvos.pdf","creator":"dernst","file_size":2358617,"content_type":"application/pdf","file_id":"9110","relation":"main_file","success":1,"checksum":"dc55c900f3b061d6c2790b8813d759a3","date_updated":"2021-02-11T12:28:29Z","date_created":"2021-02-11T12:28:29Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments."}],"issue":"3","publication":"EMBO Journal","citation":{"mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862, Embo Press, 2021, doi:10.15252/embj.2020106862.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2020106862.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3). doi:10.15252/embj.2020106862","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","ieee":"K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo Press, 2021.","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862"},"article_type":"original","date_published":"2021-02-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9913","status":"public","title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","ddc":["580"],"intvolume":" 22","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":3144854,"content_type":"application/pdf","file_name":"2021_EmboR_Vega.pdf","access_level":"open_access","date_updated":"2021-10-05T13:36:42Z","date_created":"2021-10-05T13:36:42Z","success":1,"checksum":"750de03dc3b715c37090126c1548ba13","file_id":"10090","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate."}],"issue":"9","publication":"EMBO Reports","citation":{"ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813","ieee":"A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813."},"article_type":"original","date_published":"2021-09-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"Yes","has_accepted_license":"1","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"publisher":"Wiley","author":[{"first_name":"Andrea","last_name":"Vega","full_name":"Vega, Andrea"},{"full_name":"Fredes, Isabel","first_name":"Isabel","last_name":"Fredes"},{"full_name":"O’Brien, José","last_name":"O’Brien","first_name":"José"},{"last_name":"Shen","first_name":"Zhouxin","full_name":"Shen, Zhouxin"},{"first_name":"Krisztina","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina"},{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"full_name":"Briggs, Steven P.","last_name":"Briggs","first_name":"Steven P."},{"full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez","first_name":"Rodrigo A."}],"related_material":{"record":[{"id":"10303","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:40Z","date_created":"2021-08-15T22:01:30Z","volume":22,"article_number":"e51813","file_date_updated":"2021-10-05T13:36:42Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000681754200001"],"pmid":["34357701 "]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.15252/embr.202051813","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]}},{"month":"11","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10303","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2022-12-20T23:30:06Z","date_created":"2021-11-18T11:20:59Z","date_updated":"2023-09-19T14:42:45Z","author":[{"full_name":"Abualia, Rashed","first_name":"Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"id":"9913","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"47"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","year":"2021","day":"22","has_accepted_license":"1","article_processing_charge":"No","date_published":"2021-11-22T00:00:00Z","page":"139","citation":{"apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303."},"abstract":[{"text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"creator":"rabualia","file_size":28005730,"content_type":"application/pdf","access_level":"open_access","file_name":"AbualiaPhDthesisfinalv3.pdf","checksum":"dea38b98aa4da1cea03dcd0f10862818","date_created":"2021-11-22T14:48:21Z","date_updated":"2022-12-20T23:30:06Z","embargo":"2022-11-23","file_id":"10331","relation":"main_file"},{"relation":"source_file","file_id":"10332","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","date_created":"2021-11-22T14:48:34Z","date_updated":"2022-12-20T23:30:06Z","access_level":"closed","embargo_to":"open_access","file_name":"AbualiaPhDthesisfinalv3.docx","file_size":62841883,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"rabualia"}],"status":"public","ddc":["580","581"],"title":"Role of hormones in nitrate regulated growth","_id":"10303","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"file_date_updated":"2022-09-03T22:30:04Z","author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8569"},{"id":"960","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-22T09:58:30Z","date_created":"2021-08-29T12:36:50Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:9962","degree_awarded":"PhD","supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"abstract":[{"text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_size":10629190,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ahansen","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Hansen.docx","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","date_created":"2021-08-30T09:17:39Z","date_updated":"2022-09-03T22:30:04Z","relation":"source_file","file_id":"9971"},{"relation":"main_file","file_id":"9972","embargo":"2022-09-02","date_updated":"2022-09-03T22:30:04Z","date_created":"2021-08-30T09:29:44Z","checksum":"204fa40321a1c6289b68c473634c4bf3","file_name":"Thesis_Hansen_PDFA-1a.pdf","access_level":"open_access","file_size":13457469,"content_type":"application/pdf","creator":"ahansen"}],"oa_version":"Published Version","_id":"9962","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","status":"public","ddc":["570"],"day":"02","has_accepted_license":"1","article_processing_charge":"No","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"date_published":"2021-09-02T00:00:00Z","citation":{"apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962."},"page":"182"},{"file":[{"checksum":"316ed42ea1b42b0f1a3025bb476266fc","date_created":"2021-09-20T09:27:43Z","date_updated":"2021-12-02T23:30:03Z","embargo":"2021-12-01","file_id":"10026","relation":"main_file","creator":"patrickd","content_type":"application/pdf","file_size":10028836,"access_level":"open_access","file_name":"RevisedQMBSreview.pdf"}],"oa_version":"Preprint","intvolume":" 17","title":"Quantum many-body scars and weak breaking of ergodicity","status":"public","ddc":["539"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9428","issue":"6","abstract":[{"text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology.","lang":"eng"}],"type":"journal_article","date_published":"2021-06-01T00:00:00Z","page":"675–685","article_type":"review","citation":{"ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2."},"publication":"Nature Physics","article_processing_charge":"No","has_accepted_license":"1","day":"01","volume":17,"date_updated":"2023-10-18T08:20:59Z","date_created":"2021-05-28T09:03:50Z","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"}],"department":[{"_id":"MaSe"}],"publisher":"Nature Research","publication_status":"published","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","year":"2021","ec_funded":1,"file_date_updated":"2021-12-02T23:30:03Z","language":[{"iso":"eng"}],"doi":"10.1038/s41567-021-01230-2","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"oa":1,"publication_identifier":{"eissn":["1745-2481"]},"month":"06"},{"department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"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.","year":"2021","volume":303,"date_updated":"2024-03-28T23:30:44Z","date_created":"2020-12-09T14:48:28Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana","last_name":"Gelová"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"last_name":"Brunoud","first_name":"Géraldine","full_name":"Brunoud, Géraldine"},{"orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","first_name":"Xixi","full_name":"Zhang, Xixi"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous"},{"full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"full_name":"Michalko, Jaroslav","last_name":"Michalko","first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova","first_name":"Zlata"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","full_name":"Verstraeten, Inge"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Čovanová, Milada","first_name":"Milada","last_name":"Čovanová"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"last_name":"Hörmayer","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"article_number":"110750","ec_funded":1,"file_date_updated":"2021-02-04T07:49:25Z","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","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","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1016/j.plantsci.2020.110750","publication_identifier":{"issn":["0168-9452"]},"month":"02","intvolume":" 303","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","ddc":["580"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8931","oa_version":"Published Version","file":[{"creator":"dernst","file_size":12563728,"content_type":"application/pdf","file_name":"2021_PlantScience_Gelova.pdf","access_level":"open_access","date_created":"2021-02-04T07:49:25Z","date_updated":"2021-02-04T07:49:25Z","success":1,"checksum":"a7f2562bdca62d67dfa88e271b62a629","file_id":"9083","relation":"main_file"}],"type":"journal_article","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."}],"article_type":"original","citation":{"mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750.","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.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750.","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750","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.","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. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750","ieee":"Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021."},"publication":"Plant Science","date_published":"2021-02-01T00:00:00Z","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01"},{"type":"journal_article","issue":"2","abstract":[{"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. ","lang":"eng"}],"_id":"9287","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 186","title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","ddc":["580"],"status":"public","oa_version":"Published Version","file":[{"success":1,"checksum":"532bb9469d3b665907f06df8c383eade","date_updated":"2021-11-11T15:07:51Z","date_created":"2021-11-11T15:07:51Z","file_id":"10273","relation":"main_file","creator":"cziletti","file_size":2289127,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_PlantPhysio_Narasimhan.pdf"}],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","citation":{"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. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiab134","ieee":"M. Narasimhan et al., “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” Plant Physiology, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","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. Plant Physiology. 2021;186(2):1122–1142. doi:10.1093/plphys/kiab134","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.” Plant Physiology. Oxford University Press, 2021. https://doi.org/10.1093/plphys/kiab134.","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.","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:10.1093/plphys/kiab134."},"publication":"Plant Physiology","page":"1122–1142","article_type":"original","date_published":"2021-06-01T00:00:00Z","ec_funded":1,"file_date_updated":"2021-11-11T15:07:51Z","pmid":1,"year":"2021","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. ","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"link":[{"url":"10.1093/plphys/kiab380","relation":"erratum"}],"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","first_name":"Madhumitha"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","first_name":"Lesia","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin"},{"last_name":"Himschoot","first_name":"E","full_name":"Himschoot, E"},{"full_name":"Wang, R","first_name":"R","last_name":"Wang"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"first_name":"J","last_name":"Sánchez-Simarro","full_name":"Sánchez-Simarro, J"},{"full_name":"Aniento, F","last_name":"Aniento","first_name":"F"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"volume":186,"date_updated":"2024-03-28T23:30:44Z","date_created":"2021-03-26T12:08:38Z","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000671555900031"],"pmid":["33734402"]},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","doi":"10.1093/plphys/kiab134","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}]},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"doi":"10.15479/at:ista:10083","degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2663-337X"]},"year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"442"},{"id":"8931","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9287"},{"relation":"part_of_dissertation","status":"public","id":"8283"},{"relation":"part_of_dissertation","status":"public","id":"8986"},{"id":"6627","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10095"},{"id":"10015","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-10-31T19:30:02Z","date_created":"2021-10-04T13:33:10Z","file_date_updated":"2022-12-20T23:30:03Z","ec_funded":1,"citation":{"chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.","mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","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.","apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083"},"date_published":"2021-10-06T00:00:00Z","day":"06","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10083","title":"Rapid cell growth regulation in Arabidopsis","ddc":["575"],"status":"public","file":[{"file_size":8616142,"content_type":"application/pdf","creator":"cchlebak","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","access_level":"open_access","date_updated":"2022-12-20T23:30:03Z","date_created":"2021-10-14T08:00:07Z","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","relation":"main_file","file_id":"10138","embargo":"2022-10-14"},{"creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":15058499,"access_level":"closed","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","embargo_to":"open_access","checksum":"f23ed258ca894f6aabf58b0c128bf242","date_created":"2021-10-14T08:00:13Z","date_updated":"2022-12-20T23:30:03Z","file_id":"10139","relation":"source_file"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"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"}]},{"citation":{"mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells, vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665.","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.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071665.","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. Cells. 2021;10. doi:10.3390/cells10071665","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.","ieee":"N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” Cells, vol. 10. MDPI, 2021.","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. Cells. MDPI. https://doi.org/10.3390/cells10071665"},"publication":"Cells","article_type":"original","date_published":"2021-07-02T00:00:00Z","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"article_processing_charge":"Yes","has_accepted_license":"1","day":"02","_id":"10015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10","ddc":["575"],"status":"public","title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","file":[{"access_level":"open_access","file_name":"2021_Cells_Nikonorova.pdf","creator":"cchlebak","file_size":2667848,"content_type":"application/pdf","file_id":"10021","relation":"main_file","success":1,"checksum":"2a9f534b9c2200e72e2cde95afaf4eed","date_updated":"2021-09-16T09:07:06Z","date_created":"2021-09-16T09:07:06Z"}],"oa_version":"Published Version","type":"journal_article","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"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"}],"external_id":{"isi":["000676604700001"],"pmid":["34359847"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"quality_controlled":"1","isi":1,"doi":"10.3390/cells10071665","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2073-4409"]},"month":"07","pmid":1,"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).","year":"2021","publisher":"MDPI","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Nikonorova, N","first_name":"N","last_name":"Nikonorova"},{"full_name":"Murphy, E","first_name":"E","last_name":"Murphy"},{"last_name":"Fonseca de Lima","first_name":"CF","full_name":"Fonseca de Lima, CF"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"full_name":"van de Cotte, B","last_name":"van de Cotte","first_name":"B"},{"full_name":"Vu, LD","last_name":"Vu","first_name":"LD"},{"full_name":"Balcerowicz, D","last_name":"Balcerowicz","first_name":"D"},{"first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"last_name":"Kong","first_name":"X","full_name":"Kong, X"},{"last_name":"De Rop","first_name":"G","full_name":"De Rop, G"},{"full_name":"Beeckman, T","first_name":"T","last_name":"Beeckman"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vissenberg, K","first_name":"K","last_name":"Vissenberg"},{"first_name":"PC","last_name":"Morris","full_name":"Morris, PC"},{"full_name":"Ding, Z","first_name":"Z","last_name":"Ding"},{"full_name":"De Smet, I","last_name":"De Smet","first_name":"I"}],"volume":10,"date_created":"2021-09-14T11:36:20Z","date_updated":"2024-03-28T23:30:44Z","article_number":"1665 ","ec_funded":1,"file_date_updated":"2021-09-16T09:07:06Z"},{"article_number":"266395","ec_funded":1,"year":"2021","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.","publication_status":"accepted","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","first_name":"Lesia","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"full_name":"Shabala, Lana","last_name":"Shabala","first_name":"Lana"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Shabala","first_name":"Sergey","full_name":"Shabala, Sergey"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"full_name":"Kinoshita, Toshinori","first_name":"Toshinori","last_name":"Kinoshita"},{"full_name":"Gray, William M.","first_name":"William M.","last_name":"Gray"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"10223"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"date_created":"2021-10-06T08:56:22Z","date_updated":"2024-03-28T23:30:44Z","month":"09","publication_identifier":{"issn":["2693-5015"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"_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"}],"doi":"10.21203/rs.3.rs-266395/v3","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"type":"preprint","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."}],"_id":"10095","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","status":"public","oa_version":"Preprint","day":"09","article_processing_charge":"No","publication":"Research Square","citation":{"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.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.","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.).","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3.","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. .","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. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3","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. Research Square. doi:10.21203/rs.3.rs-266395/v3"},"date_published":"2021-09-09T00:00:00Z"},{"ec_funded":1,"file_date_updated":"2022-12-20T23:30:08Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9997"},{"id":"2","status":"public","relation":"part_of_dissertation"},{"id":"9402","status":"public","relation":"part_of_dissertation"}]},"author":[{"orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura","full_name":"Schmid, Laura"}],"date_created":"2021-11-15T17:12:57Z","date_updated":"2023-11-07T08:28:29Z","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"11","doi":"10.15479/at:ista:10293","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"degree_awarded":"PhD","oa":1,"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"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."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"closed","file_name":"submission_new.zip","embargo_to":"open_access","creator":"lschmid","content_type":"application/zip","file_size":29703124,"file_id":"10305","relation":"source_file","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","date_updated":"2022-12-20T23:30:08Z","date_created":"2021-11-18T12:41:46Z"},{"creator":"lschmid","content_type":"application/pdf","file_size":8320985,"file_name":"thesis_new_upload.pdf","access_level":"open_access","date_created":"2021-11-18T12:59:15Z","date_updated":"2022-12-20T23:30:08Z","checksum":"d940af042e94660c6b6a7b4f0b184d47","file_id":"10306","embargo":"2022-10-18","relation":"main_file"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10293","ddc":["519","576"],"status":"public","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","article_processing_charge":"No","has_accepted_license":"1","day":"17","date_published":"2021-11-17T00:00:00Z","citation":{"ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293.","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293."},"page":"171"},{"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."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":2424943,"content_type":"application/pdf","file_name":"2021_ScientificReports_Schmid.pdf","access_level":"open_access","date_created":"2021-09-13T10:31:21Z","date_updated":"2021-09-13T10:31:21Z","success":1,"checksum":"19df8816cf958b272b85841565c73182","file_id":"10006","relation":"main_file"}],"status":"public","ddc":["003"],"title":"The evolution of indirect reciprocity under action and assessment generosity","intvolume":" 11","_id":"9997","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"31","has_accepted_license":"1","article_processing_charge":"Yes","keyword":["Multidisciplinary"],"date_published":"2021-08-31T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:10.1038/s41598-021-96932-1.","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1.","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-96932-1","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","apa":"Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1","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."},"file_date_updated":"2021-09-13T10:31:21Z","ec_funded":1,"article_number":"17443","date_updated":"2024-03-28T23:30:45Z","date_created":"2021-09-11T16:22:02Z","volume":11,"author":[{"first_name":"Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura"},{"full_name":"Shati, Pouya","first_name":"Pouya","last_name":"Shati"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"related_material":{"record":[{"id":"10293","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Springer Nature","year":"2021","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).","pmid":1,"month":"08","publication_identifier":{"eissn":["2045-2322"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-021-96932-1","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34465830"],"isi":["000692406400018"]}},{"file_date_updated":"2023-11-07T08:27:23Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"year":"2021","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","pmid":1,"date_updated":"2024-03-28T23:30:45Z","date_created":"2021-05-18T16:56:57Z","volume":5,"author":[{"full_name":"Schmid, Laura","first_name":"Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/"}],"record":[{"relation":"dissertation_contains","status":"public","id":"10293"}]},"month":"05","publication_identifier":{"eissn":["2397-3374"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"oa":1,"external_id":{"isi":["000650304000002"],"pmid":["33986519"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41562-021-01114-8","type":"journal_article","abstract":[{"text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability.","lang":"eng"}],"issue":"10","status":"public","title":"A unified framework of direct and indirect reciprocity","ddc":["000"],"intvolume":" 5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9402","file":[{"content_type":"application/pdf","file_size":5232761,"creator":"dernst","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","access_level":"open_access","date_created":"2023-11-07T08:27:23Z","date_updated":"2023-11-07T08:27:23Z","checksum":"34f55e173f90dc1dab731063458ac780","success":1,"relation":"main_file","file_id":"14496"}],"oa_version":"Submitted Version","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"1292–1302","publication":"Nature Human Behaviour","citation":{"chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour. Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:10.1038/s41562-021-01114-8.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-021-01114-8","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302.","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8"},"date_published":"2021-05-13T00:00:00Z"},{"month":"07","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"language":[{"iso":"eng"}],"conference":{"name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Virtual","start_date":"2021-08-09","end_date":"2021-08-13"},"doi":"10.1145/3450626.3459800","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000674930900091"]},"file_date_updated":"2021-10-18T10:42:22Z","ec_funded":1,"article_number":"126","date_updated":"2024-03-28T23:30:47Z","date_created":"2021-08-08T22:01:26Z","volume":40,"author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"}],"related_material":{"record":[{"id":"12897","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on IST Website","url":"https://ist.ac.at/en/news/designing-with-elastic-structures/"}]},"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"year":"2021","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","day":"19","article_processing_charge":"No","has_accepted_license":"1","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"scopus_import":"1","date_published":"2021-07-19T00:00:00Z","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"ama":"Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459800","apa":"Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves. ACM Transactions on Graphics. Virtual: Association for Computing Machinery. https://doi.org/10.1145/3450626.3459800","ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459800.","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459800."},"abstract":[{"text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements.","lang":"eng"}],"issue":"4","type":"journal_article","file":[{"checksum":"7e5d08ce46b0451b3102eacd3d00f85f","success":1,"date_created":"2021-10-18T10:42:15Z","date_updated":"2021-10-18T10:42:15Z","relation":"main_file","file_id":"10150","content_type":"application/pdf","file_size":17064290,"creator":"chafner","access_level":"open_access","file_name":"elastic-curves-paper.pdf"},{"file_name":"elastic-curves-supp.pdf","access_level":"open_access","creator":"chafner","file_size":547156,"content_type":"application/pdf","file_id":"10151","relation":"supplementary_material","date_updated":"2021-10-18T10:42:22Z","date_created":"2021-10-18T10:42:22Z","checksum":"0088643478be7c01a703b5b10767348f"}],"oa_version":"Published Version","ddc":["516"],"title":"The design space of plane elastic curves","status":"public","intvolume":" 40","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9817"},{"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":28508629,"creator":"cziletti","access_level":"closed","embargo_to":"open_access","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","checksum":"ce7108853e6cec6224f17cd6429b51fe","date_created":"2021-10-27T07:45:37Z","date_updated":"2022-12-20T23:30:05Z","relation":"source_file","file_id":"10186"},{"date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:57Z","checksum":"0d7afb846e8e31ec794de47bf44e12ef","embargo":"2022-10-28","file_id":"10187","relation":"main_file","creator":"cziletti","file_size":10623525,"content_type":"application/pdf","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10135","abstract":[{"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.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-10-13T00:00:00Z","citation":{"chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","mla":"Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135.","apa":"Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","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:10.15479/at:ista:10135"},"article_processing_charge":"No","has_accepted_license":"1","day":"13","date_updated":"2024-01-25T10:53:29Z","date_created":"2021-10-13T13:42:48Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9160"}]},"author":[{"full_name":"Semerádová, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semerádová","first_name":"Hana"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","file_date_updated":"2022-12-20T23:30:05Z","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:10135","project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."}],"oa":1,"publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"month":"10"},{"page":"118","citation":{"short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","apa":"Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria."},"date_published":"2021-07-29T00:00:00Z","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"day":"29","has_accepted_license":"1","article_processing_charge":"No","ddc":["532"],"status":"public","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9728","file":[{"date_created":"2021-07-28T13:32:02Z","date_updated":"2022-07-29T22:30:05Z","checksum":"77436be3563a90435024307b1b5ee7e8","file_id":"9744","relation":"source_file","creator":"nagrawal","content_type":"application/x-zip-compressed","file_size":22859658,"file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","embargo_to":"open_access","access_level":"closed"},{"creator":"nagrawal","file_size":18658048,"content_type":"application/pdf","access_level":"open_access","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","checksum":"72a891d7daba85445c29b868c22575ed","date_updated":"2022-07-29T22:30:05Z","date_created":"2021-07-28T13:32:05Z","file_id":"9745","embargo":"2022-07-28","relation":"main_file"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","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"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9728","month":"07","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"year":"2021","date_updated":"2024-02-28T13:14:39Z","date_created":"2021-07-27T13:40:30Z","author":[{"full_name":"Agrawal, Nishchal","last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6189","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2022-07-29T22:30:05Z"},{"page":"33090-33098","article_type":"original","citation":{"ama":"Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098. doi:10.1073/pnas.2007694117","ista":"Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098.","apa":"Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117","ieee":"J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” Proceedings of the National Academy of Sciences, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.","mla":"Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117.","short":"J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098.","chicago":"Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2020-12-16T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"16","intvolume":" 117","title":"Physical mechanisms of amyloid nucleation on fluid membranes","status":"public","_id":"10336","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","type":"journal_article","issue":"52","abstract":[{"lang":"eng","text":"Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context."}],"quality_controlled":"1","external_id":{"pmid":["33328273"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2007694117","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"12","publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.","volume":117,"date_created":"2021-11-25T15:07:09Z","date_updated":"2021-11-25T15:35:58Z","author":[{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"}],"extern":"1"},{"date_published":"2020-11-27T00:00:00Z","citation":{"short":"X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias, A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić, Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science Advances 6 (2020).","mla":"Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.abc4397.","chicago":"Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone, Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.abc4397.","ama":"Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 2020;6(48). doi:10.1126/sciadv.abc4397","ieee":"X. Tian et al., “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” Science Advances, vol. 6, no. 48. American Association for the Advancement of Science, 2020.","apa":"Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J., … Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abc4397","ista":"Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 6(48), eabc4397."},"publication":"Science Advances","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"27","scopus_import":"1","keyword":["multidisciplinary"],"oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":10381298,"file_name":"2020_SciAdv_Tian.pdf","access_level":"open_access","date_created":"2021-11-26T06:50:09Z","date_updated":"2021-11-26T06:50:09Z","success":1,"checksum":"3ba2eca975930cdb0b1ce1ae876885a7","file_id":"10343","relation":"main_file"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10342","intvolume":" 6","title":"On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias","status":"public","ddc":["611"],"issue":"48","abstract":[{"text":"The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across.","lang":"eng"}],"type":"journal_article","doi":"10.1126/sciadv.abc4397","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33246953"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1"}],"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["2375-2548"]},"month":"11","author":[{"full_name":"Tian, Xiaohe","first_name":"Xiaohe","last_name":"Tian"},{"full_name":"Leite, Diana M.","last_name":"Leite","first_name":"Diana M."},{"full_name":"Scarpa, Edoardo","last_name":"Scarpa","first_name":"Edoardo"},{"full_name":"Nyberg, Sophie","first_name":"Sophie","last_name":"Nyberg"},{"first_name":"Gavin","last_name":"Fullstone","full_name":"Fullstone, Gavin"},{"full_name":"Forth, Joe","last_name":"Forth","first_name":"Joe"},{"first_name":"Diana","last_name":"Matias","full_name":"Matias, Diana"},{"full_name":"Apriceno, Azzurra","first_name":"Azzurra","last_name":"Apriceno"},{"last_name":"Poma","first_name":"Alessandro","full_name":"Poma, Alessandro"},{"full_name":"Duro-Castano, Aroa","last_name":"Duro-Castano","first_name":"Aroa"},{"first_name":"Manish","last_name":"Vuyyuru","full_name":"Vuyyuru, Manish"},{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Zhongping","last_name":"Zhang","full_name":"Zhang, Zhongping"},{"full_name":"Xiang, Pan","first_name":"Pan","last_name":"Xiang"},{"first_name":"Bin","last_name":"Fang","full_name":"Fang, Bin"},{"full_name":"Tian, Yupeng","last_name":"Tian","first_name":"Yupeng"},{"full_name":"Luo, Lei","last_name":"Luo","first_name":"Lei"},{"first_name":"Loris","last_name":"Rizzello","full_name":"Rizzello, Loris"},{"full_name":"Battaglia, Giuseppe","first_name":"Giuseppe","last_name":"Battaglia"}],"volume":6,"date_updated":"2021-11-26T07:00:24Z","date_created":"2021-11-26T06:40:28Z","pmid":1,"year":"2020","acknowledgement":"Funding: G.B. thanks the ERC for the starting grant (MEViC 278793) and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1), EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227). X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author contributions: X.T. prepared and characterized POs, performed all the fast imaging in both conventional and STED microscopy, set up the initial BBB model, encapsulated the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized POs; performed all the permeability studies, PLA assays, WB and associated data analysis, and part of the colocalization assays; and performed experiments with the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared and characterized POs and performed part of the colocalization and inhibition assays. G.F. designed, performed, and analyzed the agent-based simulations of transcytosis. J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed all fast imaging and supervised and coordinated the overall work. X.T., D.M.L., E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.","publisher":"American Association for the Advancement of Science","publication_status":"published","file_date_updated":"2021-11-26T06:50:09Z","extern":"1","article_number":"eabc4397 "},{"article_number":"228101","extern":"1","file_date_updated":"2021-11-26T07:16:49Z","publisher":"American Physical Society","publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.), the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the United Kingdom Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1).","volume":125,"date_updated":"2021-11-30T08:33:14Z","date_created":"2021-11-26T07:10:43Z","author":[{"full_name":"Forster, Joel C.","first_name":"Joel C.","last_name":"Forster"},{"full_name":"Krausser, Johannes","first_name":"Johannes","last_name":"Krausser"},{"full_name":"Vuyyuru, Manish R.","first_name":"Manish R.","last_name":"Vuyyuru"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"11","quality_controlled":"1","external_id":{"pmid":["33315453"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.125.228101","type":"journal_article","issue":"22","abstract":[{"lang":"eng","text":"In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry."}],"intvolume":" 125","status":"public","ddc":["530"],"title":"Exploring the design rules for efficient membrane-reshaping nanostructures","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10344","file":[{"checksum":"fbf2e1415e332d6add90222d60401a1d","success":1,"date_created":"2021-11-26T07:16:49Z","date_updated":"2021-11-26T07:16:49Z","relation":"main_file","file_id":"10345","file_size":844353,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2020_PhysRevLett_Forster.pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"23","article_type":"original","citation":{"chicago":"Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.228101.","short":"J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020).","mla":"Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:10.1103/physrevlett.125.228101.","apa":"Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., & Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.228101","ieee":"J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” Physical Review Letters, vol. 125, no. 22. American Physical Society, 2020.","ista":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 125(22), 228101.","ama":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 2020;125(22). doi:10.1103/physrevlett.125.228101"},"publication":"Physical Review Letters","date_published":"2020-11-23T00:00:00Z"},{"extern":"1","author":[{"full_name":"Debets, V. E.","first_name":"V. E.","last_name":"Debets"},{"full_name":"Janssen, L. M. C.","first_name":"L. M. C.","last_name":"Janssen"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"volume":16,"date_created":"2021-11-26T06:29:41Z","date_updated":"2021-11-26T07:00:33Z","pmid":1,"acknowledgement":"We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.).","year":"2020","publisher":"Royal Society of Chemistry","publication_status":"published","publication_identifier":{"issn":["1744-683X","1744-6848"]},"month":"10","doi":"10.1039/d0sm00712a","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1"}],"external_id":{"pmid":["33084724"]},"quality_controlled":"1","issue":"47","abstract":[{"lang":"eng","text":"Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes."}],"type":"journal_article","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10341","intvolume":" 16","title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes","status":"public","article_processing_charge":"No","day":"06","scopus_import":"1","keyword":["condensed matter physics","general chemistry"],"date_published":"2020-10-06T00:00:00Z","citation":{"chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter. Royal Society of Chemistry, 2020. https://doi.org/10.1039/d0sm00712a.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.","mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:10.1039/d0sm00712a.","ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” Soft Matter, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.","apa":"Debets, V. E., Janssen, L. M. C., & Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm00712a","ista":"Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 2020;16(47):10628-10639. doi:10.1039/d0sm00712a"},"publication":"Soft Matter","page":"10628-10639","article_type":"original"},{"citation":{"chicago":"Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal. Cell Press, 2020. https://doi.org/10.1016/j.bpj.2020.09.013.","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799.","mla":"Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:10.1016/j.bpj.2020.09.013.","apa":"Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., & Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. Cell Press. https://doi.org/10.1016/j.bpj.2020.09.013","ieee":"A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” Biophysical Journal, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020.","ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.","ama":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 2020;119(9):1791-1799. doi:10.1016/j.bpj.2020.09.013"},"publication":"Biophysical Journal","page":"1791-1799","article_type":"original","date_published":"2020-09-23T00:00:00Z","scopus_import":"1","keyword":["biophysics"],"article_processing_charge":"No","day":"23","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10346","intvolume":" 119","title":"Modeling fibrillogenesis of collagen-mimetic molecules","status":"public","oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"text":"One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications.","lang":"eng"}],"oa":1,"external_id":{"pmid":["33049216"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1"}],"quality_controlled":"1","doi":"10.1016/j.bpj.2020.09.013","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0006-3495"]},"month":"09","pmid":1,"year":"2020","acknowledgement":"We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu, Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.), Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).","publisher":"Cell Press","publication_status":"published","author":[{"first_name":"Anne E.","last_name":"Hafner","full_name":"Hafner, Anne E."},{"full_name":"Gyori, Noemi G.","first_name":"Noemi G.","last_name":"Gyori"},{"last_name":"Bench","first_name":"Ciaran A.","full_name":"Bench, Ciaran A."},{"first_name":"Luke K.","last_name":"Davis","full_name":"Davis, Luke K."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"}],"volume":119,"date_created":"2021-11-26T07:27:24Z","date_updated":"2021-11-26T07:45:24Z","extern":"1"},{"day":"08","article_processing_charge":"No","keyword":["general chemistry"],"scopus_import":"1","date_published":"2020-06-08T00:00:00Z","article_type":"original","page":"6236-6247","publication":"Chemical Science","citation":{"ama":"Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 2020;11(24):6236-6247. doi:10.1039/c9sc06501f","ista":"Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. 2020. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 11(24), 6236–6247.","apa":"Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., & Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c9sc06501f","ieee":"A. J. Dear et al., “Identification of on- and off-pathway oligomers in amyloid fibril formation,” Chemical Science, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020.","mla":"Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” Chemical Science, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:10.1039/c9sc06501f.","short":"A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse, T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247.","chicago":"Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” Chemical Science. Royal Society of Chemistry, 2020. https://doi.org/10.1039/c9sc06501f."},"abstract":[{"lang":"eng","text":"The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation."}],"issue":"24","type":"journal_article","oa_version":"Published Version","title":"Identification of on- and off-pathway oligomers in amyloid fibril formation","status":"public","intvolume":" 11","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10350","month":"06","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"language":[{"iso":"eng"}],"doi":"10.1039/c9sc06501f","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png"},"main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f","open_access":"1"}],"external_id":{"pmid":["32953019"]},"license":"https://creativecommons.org/licenses/by-nc/3.0/","extern":"1","date_created":"2021-11-26T09:08:19Z","date_updated":"2021-11-26T11:21:20Z","volume":11,"author":[{"first_name":"Alexander J.","last_name":"Dear","full_name":"Dear, Alexander J."},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"last_name":"Kjaergaard","first_name":"Magnus","full_name":"Kjaergaard, Magnus"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"publication_status":"published","publisher":"Royal Society of Chemistry","acknowledgement":"We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge (TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship, Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation (MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus Newman Foundation (TPJK) for financial support. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL).","year":"2020","pmid":1},{"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1126/science.aaz2532","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/774273v1"}],"external_id":{"pmid":["32764038"]},"extern":"1","volume":369,"date_created":"2021-11-26T08:21:34Z","date_updated":"2021-11-26T08:58:33Z","author":[{"full_name":"Tarrason Risa, Gabriel","first_name":"Gabriel","last_name":"Tarrason Risa"},{"last_name":"Hurtig","first_name":"Fredrik","full_name":"Hurtig, Fredrik"},{"first_name":"Sian","last_name":"Bray","full_name":"Bray, Sian"},{"first_name":"Anne E.","last_name":"Hafner","full_name":"Hafner, Anne E."},{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"full_name":"Faull, Peter","last_name":"Faull","first_name":"Peter"},{"last_name":"Davis","first_name":"Colin","full_name":"Davis, Colin"},{"full_name":"Papatziamou, Dimitra","first_name":"Dimitra","last_name":"Papatziamou"},{"last_name":"Mutavchiev","first_name":"Delyan R.","full_name":"Mutavchiev, Delyan R."},{"last_name":"Fan","first_name":"Catherine","full_name":"Fan, Catherine"},{"full_name":"Meneguello, Leticia","first_name":"Leticia","last_name":"Meneguello"},{"full_name":"Arashiro Pulschen, Andre","last_name":"Arashiro Pulschen","first_name":"Andre"},{"last_name":"Dey","first_name":"Gautam","full_name":"Dey, Gautam"},{"full_name":"Culley, Siân","last_name":"Culley","first_name":"Siân"},{"last_name":"Kilkenny","first_name":"Mairi","full_name":"Kilkenny, Mairi"},{"full_name":"Souza, Diorge P.","first_name":"Diorge P.","last_name":"Souza"},{"full_name":"Pellegrini, Luca","first_name":"Luca","last_name":"Pellegrini"},{"first_name":"Robertus A. M.","last_name":"de Bruin","full_name":"de Bruin, Robertus A. M."},{"last_name":"Henriques","first_name":"Ricardo","full_name":"Henriques, Ricardo"},{"full_name":"Snijders, Ambrosius P.","last_name":"Snijders","first_name":"Ambrosius P."},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"last_name":"Lindås","first_name":"Ann-Christin","full_name":"Lindås, Ann-Christin"},{"full_name":"Robinson, Nicholas P.","last_name":"Robinson","first_name":"Nicholas P."},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","pmid":1,"acknowledgement":"We thank the MRC LMCB at UCL for their support; the flow cytometry STP at the Francis Crick Institute for assistance, with special thanks to S. Purewal and D. Davis; C. Bertoli for mentorship\r\nand advice; J. M. Garcia-Arcos for help early on in this project; the entire Baum lab for their input throughout the project; the Albers lab for advice and reagents, with special thanks to M. Van Wolferen and S. Albers; the members of the Wellcome consortium for archaeal cytoskeleton studies for advice and comments; and J. Löwe, S. Oliferenko, M. Balasubramanian, and D. Gerlich for discussions and advice on the manuscript. N.P.R. and S.B. would like to thank N. Rzechorzek, A. Simon, and S. Anjum for discussion and advice.","year":"2020","article_processing_charge":"No","day":"07","keyword":["multidisciplinary"],"scopus_import":"1","date_published":"2020-08-07T00:00:00Z","article_type":"original","citation":{"ama":"Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 2020;369(6504). doi:10.1126/science.aaz2532","ieee":"G. Tarrason Risa et al., “The proteasome controls ESCRT-III–mediated cell division in an archaeon,” Science, vol. 369, no. 6504. American Association for the Advancement of Science, 2020.","apa":"Tarrason Risa, G., Hurtig, F., Bray, S., Hafner, A. E., Harker-Kirschneck, L., Faull, P., … Baum, B. (2020). The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaz2532","ista":"Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås A-C, Robinson NP, Baum B. 2020. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 369(6504).","short":"G. Tarrason Risa, F. Hurtig, S. Bray, A.E. Hafner, L. Harker-Kirschneck, P. Faull, C. Davis, D. Papatziamou, D.R. Mutavchiev, C. Fan, L. Meneguello, A. Arashiro Pulschen, G. Dey, S. Culley, M. Kilkenny, D.P. Souza, L. Pellegrini, R.A.M. de Bruin, R. Henriques, A.P. Snijders, A. Šarić, A.-C. Lindås, N.P. Robinson, B. Baum, Science 369 (2020).","mla":"Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” Science, vol. 369, no. 6504, American Association for the Advancement of Science, 2020, doi:10.1126/science.aaz2532.","chicago":"Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aaz2532."},"publication":"Science","issue":"6504","abstract":[{"lang":"eng","text":"Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 369","title":"The proteasome controls ESCRT-III–mediated cell division in an archaeon","status":"public","_id":"10349","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"article_type":"original","page":"24251-24257","publication":"Proceedings of the National Academy of Sciences","citation":{"ieee":"T. C. T. Michaels et al., “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” Proceedings of the National Academy of Sciences, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020.","apa":"Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio, P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2006684117","ista":"Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 117(39), 24251–24257.","ama":"Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 2020;117(39):24251-24257. doi:10.1073/pnas.2006684117","chicago":"Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller, Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006684117.","short":"T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S. Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences 117 (2020) 24251–24257.","mla":"Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:10.1073/pnas.2006684117."},"date_published":"2020-09-14T00:00:00Z","keyword":["multidisciplinary"],"scopus_import":"1","day":"14","article_processing_charge":"No","title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","status":"public","intvolume":" 117","_id":"10347","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors.","lang":"eng"}],"issue":"39","quality_controlled":"1","oa":1,"external_id":{"pmid":["32929030"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2006684117","month":"09","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","publisher":"National Academy of Sciences","acknowledgement":"We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.); the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.); Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation (T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through the ERC Grant PhysProt (Agreement 337969).","year":"2020","pmid":1,"date_updated":"2021-11-26T08:59:06Z","date_created":"2021-11-26T07:48:27Z","volume":117,"author":[{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"last_name":"Heller","first_name":"Gabriella T.","full_name":"Heller, Gabriella T."},{"first_name":"Samo","last_name":"Curk","full_name":"Curk, Samo"},{"first_name":"Paolo","last_name":"Arosio","full_name":"Arosio, Paolo"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"extern":"1"},{"month":"04","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41557-020-0452-1","quality_controlled":"1","oa":1,"external_id":{"pmid":["32303714"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.01.08.897488","open_access":"1"}],"extern":"1","date_updated":"2021-11-26T11:21:08Z","date_created":"2021-11-26T09:15:13Z","volume":12,"author":[{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"full_name":"Curk, Samo","last_name":"Curk","first_name":"Samo"},{"first_name":"Katja","last_name":"Bernfur","full_name":"Bernfur, Katja"},{"last_name":"Arosio","first_name":"Paolo","full_name":"Arosio, Paolo"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"first_name":"Alexander J.","last_name":"Dear","full_name":"Dear, Alexander J."},{"last_name":"Cohen","first_name":"Samuel I. A.","full_name":"Cohen, Samuel I. A."},{"first_name":"Christopher M.","last_name":"Dobson","full_name":"Dobson, Christopher M."},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41557-020-0468-6","relation":"erratum"}]},"publication_status":"published","publisher":"Springer Nature","acknowledgement":"We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V., C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant MAMBA (S.L., agreement no. 340890). The research that led to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969).","year":"2020","pmid":1,"day":"13","article_processing_charge":"No","keyword":["general chemical engineering","general chemistry"],"scopus_import":"1","date_published":"2020-04-13T00:00:00Z","article_type":"original","page":"445-451","publication":"Nature Chemistry","citation":{"apa":"Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G., … Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-020-0452-1","ieee":"T. C. T. Michaels et al., “Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide,” Nature Chemistry, vol. 12, no. 5. Springer Nature, pp. 445–451, 2020.","ista":"Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 12(5), 445–451.","ama":"Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 2020;12(5):445-451. doi:10.1038/s41557-020-0452-1","chicago":"Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio, Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry. Springer Nature, 2020. https://doi.org/10.1038/s41557-020-0452-1.","short":"T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J. Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Chemistry 12 (2020) 445–451.","mla":"Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry, vol. 12, no. 5, Springer Nature, 2020, pp. 445–51, doi:10.1038/s41557-020-0452-1."},"abstract":[{"lang":"eng","text":"Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases."}],"issue":"5","type":"journal_article","oa_version":"None","title":"Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide","status":"public","intvolume":" 12","_id":"10351","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"pmid":1,"acknowledgement":"The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck for careful correction of this manuscript and helpful discussions. The authors want to thank the NCCR Chemical Biology for constant support during this project. A.R. acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975, and 31003A_173087) and the European Research Council Consolidator (311536). A.Š. acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1) and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship (2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA 160728/1 [leader, Sophie Martin]).","year":"2020","publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner","first_name":"Anna-Katharina"},{"last_name":"Mercier","first_name":"Vincent","full_name":"Mercier, Vincent"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"last_name":"Moser von Filseck","first_name":"Joachim","full_name":"Moser von Filseck, Joachim"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Roux, Aurélien","first_name":"Aurélien","last_name":"Roux"}],"volume":182,"date_created":"2021-11-26T08:02:27Z","date_updated":"2021-11-26T08:58:37Z","extern":"1","oa":1,"main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296","open_access":"1"}],"external_id":{"pmid":["32814015"]},"quality_controlled":"1","doi":"10.1016/j.cell.2020.07.021","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"]},"month":"08","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10348","intvolume":" 182","status":"public","title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity."}],"citation":{"ista":"Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18.","ieee":"A.-K. Pfitzner et al., “An ESCRT-III polymerization sequence drives membrane deformation and fission,” Cell, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020.","apa":"Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., & Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.07.021","ama":"Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 2020;182(5):1140-1155.e18. doi:10.1016/j.cell.2020.07.021","chicago":"Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.07.021.","mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” Cell, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:10.1016/j.cell.2020.07.021.","short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18."},"publication":"Cell","page":"1140-1155.e18","article_type":"original","date_published":"2020-08-18T00:00:00Z","scopus_import":"1","keyword":["general biochemistry","genetics and molecular biology"],"article_processing_charge":"No","day":"18"},{"quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/571687","open_access":"1"}],"external_id":{"pmid":["32168597"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physreve.101.022420","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"month":"02","publisher":"American Physical Society","publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos (Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto) for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering and Physical Sciences Research Council (EP/L504889/1, B.W.H.).","volume":101,"date_updated":"2021-11-26T11:21:16Z","date_created":"2021-11-26T09:41:04Z","author":[{"first_name":"Luke K.","last_name":"Davis","full_name":"Davis, Luke K."},{"first_name":"Ian J.","last_name":"Ford","full_name":"Ford, Ian J."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"},{"last_name":"Hoogenboom","first_name":"Bart W.","full_name":"Hoogenboom, Bart W."}],"article_number":"022420","extern":"1","article_type":"original","citation":{"ama":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 2020;101(2). doi:10.1103/physreve.101.022420","ieee":"L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” Physical Review E, vol. 101, no. 2. American Physical Society, 2020.","apa":"Davis, L. K., Ford, I. J., Šarić, A., & Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.101.022420","ista":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 101(2), 022420.","short":"L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).","mla":"Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:10.1103/physreve.101.022420.","chicago":"Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E. American Physical Society, 2020. https://doi.org/10.1103/physreve.101.022420."},"publication":"Physical Review E","date_published":"2020-02-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"28","intvolume":" 101","title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","status":"public","_id":"10352","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events."}]},{"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.124.048102","quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/553248","open_access":"1"}],"external_id":{"pmid":["32058787"]},"oa":1,"extern":"1","article_number":"048102","volume":124,"date_created":"2021-11-26T09:57:01Z","date_updated":"2021-11-26T11:21:12Z","author":[{"full_name":"Paraschiv, Alexandru","first_name":"Alexandru","last_name":"Paraschiv"},{"full_name":"Hegde, Smitha","first_name":"Smitha","last_name":"Hegde"},{"first_name":"Raman","last_name":"Ganti","full_name":"Ganti, Raman"},{"full_name":"Pilizota, Teuta","first_name":"Teuta","last_name":"Pilizota"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"publisher":"American Physical Society","publication_status":"published","pmid":1,"acknowledgement":"We thank Samantha Miller, Bert Poolman, and the members of Šarić and Pilizota laboratories for useful discussion. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P. and A.Š.), Darwin Trust of University of Edinburgh (H.S.), Industrial Biotechnology Innovation Centre (H.S. and T.P.), BBSRC Council Crossing Biological Membrane Network (H.S. and T.P.), BBSRC/EPSRC/MRC Synthetic Biology Research Centre (T.P.), and the Royal Society (A.Š.).","year":"2020","article_processing_charge":"No","day":"31","keyword":["general physics and astronomy"],"scopus_import":"1","date_published":"2020-01-31T00:00:00Z","article_type":"original","citation":{"chicago":"Paraschiv, Alexandru, Smitha Hegde, Raman Ganti, Teuta Pilizota, and Anđela Šarić. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.124.048102.","mla":"Paraschiv, Alexandru, et al. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters, vol. 124, no. 4, 048102, American Physical Society, 2020, doi:10.1103/physrevlett.124.048102.","short":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, A. Šarić, Physical Review Letters 124 (2020).","ista":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. 2020. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 124(4), 048102.","ieee":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, and A. Šarić, “Dynamic clustering regulates activity of mechanosensitive membrane channels,” Physical Review Letters, vol. 124, no. 4. American Physical Society, 2020.","apa":"Paraschiv, A., Hegde, S., Ganti, R., Pilizota, T., & Šarić, A. (2020). Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.124.048102","ama":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 2020;124(4). doi:10.1103/physrevlett.124.048102"},"publication":"Physical Review Letters","issue":"4","abstract":[{"text":"Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 124","status":"public","title":"Dynamic clustering regulates activity of mechanosensitive membrane channels","_id":"10353","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"extern":"1","abstract":[{"lang":"eng","text":"Data storage and retrieval systems, methods, and computer-readable media utilize a cryptographically verifiable data structure that facilitates verification of a transaction in a decentralized peer-to-peer environment using multi-hop backwards and forwards links. Backward links are cryptographic hashes of past records. Forward links are cryptographic signatures of future records that are added retroactively to records once the target block has been appended to the data structure."}],"type":"patent","oa_version":"Published Version","ipc":" H04L9/3247 ; G06Q20/29 ; G06Q20/382 ; H04L9/3236","date_created":"2021-12-16T13:28:59Z","date_updated":"2021-12-21T10:04:50Z","related_material":{"link":[{"relation":"earlier_version","url":"https://patents.google.com/patent/US20180359096A1/en"}]},"author":[{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"},{"full_name":"Gasse, Linus","last_name":"Gasse","first_name":"Linus"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"}],"department":[{"_id":"ElKo"}],"applicant":["Ecole Polytechnique Federale de Lausanne"],"status":"public","title":"Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10557","year":"2020","article_processing_charge":"No","day":"03","month":"03","application_date":"2017-06-09","date_published":"2020-03-03T00:00:00Z","ipn":"10581613","citation":{"chicago":"Ford, Bryan, Linus Gasse, Eleftherios Kokoris Kogias, and Philipp Jovanovic. “Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods,” 2020.","mla":"Ford, Bryan, et al. Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods. 2020.","short":"B. Ford, L. Gasse, E. Kokoris Kogias, P. Jovanovic, (2020).","ista":"Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. 2020. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.","ieee":"B. Ford, L. Gasse, E. Kokoris Kogias, and P. Jovanovic, “Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.” 2020.","apa":"Ford, B., Gasse, L., Kokoris Kogias, E., & Jovanovic, P. (2020). Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.","ama":"Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. 2020."},"main_file_link":[{"url":"https://patents.google.com/patent/US10581613B2/en","open_access":"1"}],"publication_date":"2020-03-03","oa":1},{"keyword":["multidisciplinary"],"scopus_import":"1","day":"23","article_processing_charge":"No","article_type":"original","page":"66-70","publication":"Nature","citation":{"ista":"Polshyn H, Zhu J, Kumar MA, Zhang Y, Yang F, Tschirhart CL, Serlin M, Watanabe K, Taniguchi T, MacDonald AH, Young AF. 2020. Electrical switching of magnetic order in an orbital Chern insulator. Nature. 588(7836), 66–70.","apa":"Polshyn, H., Zhu, J., Kumar, M. A., Zhang, Y., Yang, F., Tschirhart, C. L., … Young, A. F. (2020). Electrical switching of magnetic order in an orbital Chern insulator. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2963-8","ieee":"H. Polshyn et al., “Electrical switching of magnetic order in an orbital Chern insulator,” Nature, vol. 588, no. 7836. Springer Nature, pp. 66–70, 2020.","ama":"Polshyn H, Zhu J, Kumar MA, et al. Electrical switching of magnetic order in an orbital Chern insulator. Nature. 2020;588(7836):66-70. doi:10.1038/s41586-020-2963-8","chicago":"Polshyn, Hryhoriy, J. Zhu, M. A. Kumar, Y. Zhang, F. Yang, C. L. Tschirhart, M. Serlin, et al. “Electrical Switching of Magnetic Order in an Orbital Chern Insulator.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2963-8.","mla":"Polshyn, Hryhoriy, et al. “Electrical Switching of Magnetic Order in an Orbital Chern Insulator.” Nature, vol. 588, no. 7836, Springer Nature, 2020, pp. 66–70, doi:10.1038/s41586-020-2963-8.","short":"H. Polshyn, J. Zhu, M.A. Kumar, Y. Zhang, F. Yang, C.L. Tschirhart, M. Serlin, K. Watanabe, T. Taniguchi, A.H. MacDonald, A.F. Young, Nature 588 (2020) 66–70."},"date_published":"2020-11-23T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Magnetism typically arises from the joint effect of Fermi statistics and repulsive Coulomb interactions, which favours ground states with non-zero electron spin. As a result, controlling spin magnetism with electric fields—a longstanding technological goal in spintronics and multiferroics1,2—can be achieved only indirectly. Here we experimentally demonstrate direct electric-field control of magnetic states in an orbital Chern insulator3,4,5,6, a magnetic system in which non-trivial band topology favours long-range order of orbital angular momentum but the spins are thought to remain disordered7,8,9,10,11,12,13,14. We use van der Waals heterostructures consisting of a graphene monolayer rotationally faulted with respect to a Bernal-stacked bilayer to realize narrow and topologically non-trivial valley-projected moiré minibands15,16,17. At fillings of one and three electrons per moiré unit cell within these bands, we observe quantized anomalous Hall effects18 with transverse resistance approximately equal to h/2e2 (where h is Planck’s constant and e is the charge on the electron), which is indicative of spontaneous polarization of the system into a single-valley-projected band with a Chern number equal to two. At a filling of three electrons per moiré unit cell, we find that the sign of the quantum anomalous Hall effect can be reversed via field-effect control of the chemical potential; moreover, this transition is hysteretic, which we use to demonstrate non-volatile electric-field-induced reversal of the magnetic state. A theoretical analysis19 indicates that the effect arises from the topological edge states, which drive a change in sign of the magnetization and thus a reversal in the favoured magnetic state. Voltage control of magnetic states can be used to electrically pattern non-volatile magnetic-domain structures hosting chiral edge states, with applications ranging from reconfigurable microwave circuit elements to ultralow-power magnetic memories."}],"issue":"7836","status":"public","title":"Electrical switching of magnetic order in an orbital Chern insulator","intvolume":" 588","_id":"10618","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","month":"11","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"quality_controlled":"1","oa":1,"external_id":{"arxiv":["2004.11353"],"pmid":["33230333"]},"main_file_link":[{"url":"https://arxiv.org/abs/2004.11353","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41586-020-2963-8","extern":"1","publication_status":"published","publisher":"Springer Nature","acknowledgement":"We acknowledge discussions with J. Checkelsky, S. Chen, C. Dean, M. Yankowitz, D. Reilly, I. Sodemann and M. Zaletel. Work at UCSB was primarily supported by the ARO under MURI W911NF-16-1-0361. Measurements of twisted bilayer graphene (Extended Data Fig. 8) and measurements at elevated temperatures (Extended Data Fig. 3) were supported by a SEED grant and made use of shared facilities of the UCSB MRSEC (NSF DMR 1720256), a member of the Materials Research Facilities Network (www.mrfn.org). A.F.Y. acknowledges the support of the David and Lucille Packard Foundation under award 2016-65145. A.H.M. and J.Z. were supported by the National Science Foundation through the Center for Dynamics and Control of Materials, an NSF MRSEC under Cooperative Agreement number DMR-1720595, and by the Welch Foundation under grant TBF1473. C.L.T. acknowledges support from the Hertz Foundation and from the National Science Foundation Graduate Research Fellowship Program under grant 1650114. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant Number JPMXP0112101001, JSPS KAKENHI grant numbers JP20H00354 and the CREST(JPMJCR15F3), JST.","year":"2020","pmid":1,"date_updated":"2022-01-13T14:21:04Z","date_created":"2022-01-13T14:12:17Z","volume":588,"author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy"},{"full_name":"Zhu, J.","last_name":"Zhu","first_name":"J."},{"full_name":"Kumar, M. A.","last_name":"Kumar","first_name":"M. A."},{"first_name":"Y.","last_name":"Zhang","full_name":"Zhang, Y."},{"full_name":"Yang, F.","first_name":"F.","last_name":"Yang"},{"last_name":"Tschirhart","first_name":"C. L.","full_name":"Tschirhart, C. L."},{"full_name":"Serlin, M.","last_name":"Serlin","first_name":"M."},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"last_name":"MacDonald","first_name":"A. H.","full_name":"MacDonald, A. H."},{"last_name":"Young","first_name":"A. F.","full_name":"Young, A. F."}]},{"language":[{"iso":"eng"}],"date_published":"2020-10-01T00:00:00Z","page":"55","citation":{"short":"A. Alexandradinata, N.P. Armitage, A. Baydin, W. Bi, Y. Cao, H.J. Changlani, E. Chertkov, E.H. da Silva Neto, L. Delacretaz, I. El Baggari, G.M. Ferguson, W.J. Gannon, S.A.A. Ghorashi, B.H. Goodge, O. Goulko, G. Grissonnache, A. Hallas, I.M. Hayes, Y. He, E.W. Huang, A. Kogar, D. Kumah, J.Y. Lee, A. Legros, F. Mahmood, Y. Maximenko, N. Pellatz, H. Polshyn, T. Sarkar, A. Scheie, K.L. Seyler, Z. Shi, B. Skinner, L. Steinke, K. Thirunavukkuarasu, T.V. Trevisan, M. Vogl, P.A. Volkov, Y. Wang, Y. Wang, D. Wei, K. Wei, S. Yang, X. Zhang, Y.-H. Zhang, L. Zhao, A. Zong, ArXiv (n.d.).","mla":"Alexandradinata, A., et al. “The Future of the Correlated Electron Problem.” ArXiv.","chicago":"Alexandradinata, A, N.P. Armitage, Andrey Baydin, Wenli Bi, Yue Cao, Hitesh J. Changlani, Eli Chertkov, et al. “The Future of the Correlated Electron Problem.” ArXiv, n.d.","ama":"Alexandradinata A, Armitage NP, Baydin A, et al. The future of the correlated electron problem. arXiv.","ieee":"A. Alexandradinata et al., “The future of the correlated electron problem,” arXiv. .","apa":"Alexandradinata, A., Armitage, N. P., Baydin, A., Bi, W., Cao, Y., Changlani, H. J., … Zong, A. (n.d.). The future of the correlated electron problem. arXiv.","ista":"Alexandradinata A, Armitage NP, Baydin A, Bi W, Cao Y, Changlani HJ, Chertkov E, da Silva Neto EH, Delacretaz L, El Baggari I, Ferguson GM, Gannon WJ, Ghorashi SAA, Goodge BH, Goulko O, Grissonnache G, Hallas A, Hayes IM, He Y, Huang EW, Kogar A, Kumah D, Lee JY, Legros A, Mahmood F, Maximenko Y, Pellatz N, Polshyn H, Sarkar T, Scheie A, Seyler KL, Shi Z, Skinner B, Steinke L, Thirunavukkuarasu K, Trevisan TV, Vogl M, Volkov PA, Wang Y, Wang Y, Wei D, Wei K, Yang S, Zhang X, Zhang Y-H, Zhao L, Zong A. The future of the correlated electron problem. arXiv, ."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2010.00584"}],"external_id":{"arxiv":["2010.00584"]},"oa":1,"publication":"arXiv","article_processing_charge":"No","month":"10","day":"01","oa_version":"Preprint","date_created":"2022-01-20T10:55:36Z","date_updated":"2022-01-24T08:05:51Z","author":[{"last_name":"Alexandradinata","first_name":"A","full_name":"Alexandradinata, A"},{"first_name":"N.P.","last_name":"Armitage","full_name":"Armitage, N.P."},{"last_name":"Baydin","first_name":"Andrey","full_name":"Baydin, Andrey"},{"first_name":"Wenli","last_name":"Bi","full_name":"Bi, Wenli"},{"full_name":"Cao, Yue","last_name":"Cao","first_name":"Yue"},{"full_name":"Changlani, Hitesh J.","last_name":"Changlani","first_name":"Hitesh J."},{"full_name":"Chertkov, Eli","last_name":"Chertkov","first_name":"Eli"},{"last_name":"da Silva Neto","first_name":"Eduardo H.","full_name":"da Silva Neto, Eduardo H."},{"last_name":"Delacretaz","first_name":"Luca","full_name":"Delacretaz, Luca"},{"first_name":"Ismail","last_name":"El Baggari","full_name":"El Baggari, Ismail"},{"full_name":"Ferguson, G.M.","first_name":"G.M.","last_name":"Ferguson"},{"last_name":"Gannon","first_name":"William J.","full_name":"Gannon, William J."},{"full_name":"Ghorashi, Sayed Ali Akbar","first_name":"Sayed Ali Akbar","last_name":"Ghorashi"},{"last_name":"Goodge","first_name":"Berit H.","full_name":"Goodge, Berit H."},{"full_name":"Goulko, Olga","last_name":"Goulko","first_name":"Olga"},{"full_name":"Grissonnache, G.","first_name":"G.","last_name":"Grissonnache"},{"full_name":"Hallas, Alannah","first_name":"Alannah","last_name":"Hallas"},{"first_name":"Ian M.","last_name":"Hayes","full_name":"Hayes, Ian M."},{"full_name":"He, Yu","last_name":"He","first_name":"Yu"},{"full_name":"Huang, Edwin W.","last_name":"Huang","first_name":"Edwin W."},{"full_name":"Kogar, Anshu","first_name":"Anshu","last_name":"Kogar"},{"full_name":"Kumah, Divine","first_name":"Divine","last_name":"Kumah"},{"last_name":"Lee","first_name":"Jong Yeon","full_name":"Lee, Jong Yeon"},{"first_name":"A.","last_name":"Legros","full_name":"Legros, A."},{"first_name":"Fahad","last_name":"Mahmood","full_name":"Mahmood, Fahad"},{"full_name":"Maximenko, Yulia","first_name":"Yulia","last_name":"Maximenko"},{"last_name":"Pellatz","first_name":"Nick","full_name":"Pellatz, Nick"},{"last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy"},{"first_name":"Tarapada","last_name":"Sarkar","full_name":"Sarkar, Tarapada"},{"first_name":"Allen","last_name":"Scheie","full_name":"Scheie, Allen"},{"full_name":"Seyler, Kyle L.","first_name":"Kyle L.","last_name":"Seyler"},{"full_name":"Shi, Zhenzhong","last_name":"Shi","first_name":"Zhenzhong"},{"first_name":"Brian","last_name":"Skinner","full_name":"Skinner, Brian"},{"last_name":"Steinke","first_name":"Lucia","full_name":"Steinke, Lucia"},{"last_name":"Thirunavukkuarasu","first_name":"K.","full_name":"Thirunavukkuarasu, K."},{"full_name":"Trevisan, Thaís Victa","first_name":"Thaís Victa","last_name":"Trevisan"},{"last_name":"Vogl","first_name":"Michael","full_name":"Vogl, Michael"},{"first_name":"Pavel A.","last_name":"Volkov","full_name":"Volkov, Pavel A."},{"full_name":"Wang, Yao","last_name":"Wang","first_name":"Yao"},{"first_name":"Yishu","last_name":"Wang","full_name":"Wang, Yishu"},{"last_name":"Wei","first_name":"Di","full_name":"Wei, Di"},{"full_name":"Wei, Kaya","first_name":"Kaya","last_name":"Wei"},{"first_name":"Shuolong","last_name":"Yang","full_name":"Yang, Shuolong"},{"first_name":"Xian","last_name":"Zhang","full_name":"Zhang, Xian"},{"last_name":"Zhang","first_name":"Ya-Hui","full_name":"Zhang, Ya-Hui"},{"full_name":"Zhao, Liuyan","first_name":"Liuyan","last_name":"Zhao"},{"last_name":"Zong","first_name":"Alfred","full_name":"Zong, Alfred"}],"title":"The future of the correlated electron problem","publication_status":"submitted","status":"public","_id":"10650","acknowledgement":"We thank NSF CMP program for suggestions regarding the topic and general structure of the workshop. This project was supported by the NSF DMR-2002329 and The Gordon and Betty Moore Foundation (GBMF) EPiQS initiative. We would like to sincerely thank A. Kapitulnik, A. J. Leggett, M.B. Maple, T.M. McQueen, M. Norman, P. S. Riseborough, and G. A. Sawatzky for their lectures at the workshop and advice on the writing of this manuscript. We would also like to thank G. Blumberg, C. Broholm, S. Crooker, N. Drichko, and A. Patel for helpful consultation on topics discussed\r\nherein. A number of individuals also had independent support: (AA, EH; GBMF-4305), (IMH; GBMF-9071), (HJC; NHMFL is supported by the NSF DMR-1644779 and the state of Florida), (YH, AZ; Miller Institute for Basic Research in Science), (YC; US DOE-BES DEAC02-06CH11357), (AS; Spallation Neutron Source, a DOE Office of Science User Facility operated by ORNL), (SAAG; ARO-W911NF-18-1-0290, NSF DMR-1455233), (YW; DOE-BES DE-SC0019331, GBMF-4532).","year":"2020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","abstract":[{"text":"The understanding of material systems with strong electron-electron interactions is the central problem in modern condensed matter physics. Despite this, the essential physics of many of these materials is still not understood and we have no overall perspective on their properties. Moreover, we have very little ability to make predictions in this class of systems. In this manuscript we share our personal views of what the major open problems are in correlated electron systems and we discuss some possible routes to make progress in this rich and fascinating field. This manuscript is the result of the vigorous discussions and deliberations that took place at Johns Hopkins University during a three-day workshop January 27, 28, and 29, 2020 that brought together six senior scientists and 46 more junior scientists. Our hope, is that the topics we have presented will provide inspiration for others working in this field and motivation for the idea that significant progress can be made on very hard problems if we focus our collective energies.","lang":"eng"}],"type":"preprint"}]