[{"article_processing_charge":"No","file":[{"embargo":"2024-04-07","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","file_size":9881969,"creator":"cchlebak","date_updated":"2023-04-07T06:16:06Z","access_level":"closed","checksum":"35b5997d2b0acb461f9d33d073da0df5","content_type":"application/pdf","file_id":"12814","relation":"main_file","date_created":"2023-04-07T06:16:06Z","embargo_to":"open_access"},{"date_created":"2023-04-07T06:17:11Z","content_type":"application/pdf","relation":"source_file","file_id":"12815","date_updated":"2023-04-07T06:17:11Z","access_level":"closed","checksum":"81198f63c294890f6d58e8b29782efdc","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","creator":"cchlebak","file_size":44201583},{"access_level":"closed","date_updated":"2023-04-07T06:18:05Z","checksum":"0317bf7f457bb585f99d453ffa69eb53","creator":"cchlebak","file_size":84731244,"file_name":"Thesis_CatarinaAlcarva_final.docx","date_created":"2023-04-07T06:18:05Z","relation":"source_file","file_id":"12816","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"_id":"12809","date_published":"2023-04-06T00:00:00Z","abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"publication_status":"published","file_date_updated":"2023-04-07T06:18:05Z","year":"2023","has_accepted_license":"1","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-04-26T12:16:56Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2663 - 337X"]},"page":"115","month":"04","supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"date_created":"2023-04-06T07:54:09Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"RySh"}],"status":"public","citation":{"mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023."},"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","day":"06","type":"dissertation","author":[{"id":"3A96634C-F248-11E8-B48F-1D18A9856A87","last_name":"Alcarva","first_name":"Catarina","full_name":"Alcarva, Catarina"}],"alternative_title":["ISTA Thesis"],"project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.15479/at:ista:12809"},{"volume":58,"publication_status":"published","_id":"12832","date_published":"2023-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2."}],"issue":"4","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T14:08:02Z","scopus_import":"1","external_id":{"isi":["000967601700001"]},"publication_identifier":{"eissn":["2405-8297"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"article_type":"original","oa_version":"None","year":"2023","quality_controlled":"1","department":[{"_id":"MaIb"}],"publication":"Energy Storage Materials","intvolume":"        58","status":"public","publisher":"Elsevier","isi":1,"month":"04","date_created":"2023-04-16T22:01:07Z","page":"287-298","language":[{"iso":"eng"}],"doi":"10.1016/j.ensm.2023.03.022","acknowledgement":"The authors thank the support from the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación. The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581 and 2021 SGR 00457. ICN2 acknowledges the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. Part of the present work has been performed in the frameworks of Universitat de Barcelona Nanoscience PhD program. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF). S. Lee. and M. Ibáñez acknowledge funding by IST Austria and the Werner Siemens Foundation. J. Llorca is a Serra Húnter Fellow and is grateful to ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2017 SGR 128. L. L.Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). Z. F. Liang acknowledges funding from MINECO SO-FPT PhD grant (SEV-2013-0295-17-1). J. W. Chen and Y. Xu thank the support from The Key Research and Development Program of Hebei Province (No. 20314305D) and the cooperative scientific research project of the “Chunhui Program” of the Ministry of Education (2018-7). This work was supported by the Natural Science Foundation of Sichuan province (NSFSC) and funded by the Science and Technology Department of Sichuan Province (2022NSFSC1229).","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"day":"01","type":"journal_article","author":[{"last_name":"He","first_name":"Ren","full_name":"He, Ren"},{"last_name":"Yang","full_name":"Yang, Linlin","first_name":"Linlin"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"last_name":"Wang","full_name":"Wang, Xiang","first_name":"Xiang"},{"last_name":"Lee","first_name":"Seungho","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Ting","full_name":"Zhang, Ting","last_name":"Zhang"},{"last_name":"Li","first_name":"Lingxiao","full_name":"Li, Lingxiao"},{"first_name":"Zhifu","full_name":"Liang, Zhifu","last_name":"Liang"},{"last_name":"Chen","full_name":"Chen, Jingwei","first_name":"Jingwei"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"last_name":"Ostovari Moghaddam","first_name":"Ahmad","full_name":"Ostovari Moghaddam, Ahmad"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"last_name":"Xu","full_name":"Xu, Ying","first_name":"Ying"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"citation":{"short":"R. He, L. Yang, Y. Zhang, X. Wang, S. Lee, T. Zhang, L. Li, Z. Liang, J. Chen, J. Li, A. Ostovari Moghaddam, J. Llorca, M. Ibáñez, J. Arbiol, Y. Xu, A. Cabot, Energy Storage Materials 58 (2023) 287–298.","apa":"He, R., Yang, L., Zhang, Y., Wang, X., Lee, S., Zhang, T., … Cabot, A. (2023). A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. <i>Energy Storage Materials</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">https://doi.org/10.1016/j.ensm.2023.03.022</a>","ama":"He R, Yang L, Zhang Y, et al. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. <i>Energy Storage Materials</i>. 2023;58(4):287-298. doi:<a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">10.1016/j.ensm.2023.03.022</a>","ieee":"R. He <i>et al.</i>, “A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance,” <i>Energy Storage Materials</i>, vol. 58, no. 4. Elsevier, pp. 287–298, 2023.","ista":"He R, Yang L, Zhang Y, Wang X, Lee S, Zhang T, Li L, Liang Z, Chen J, Li J, Ostovari Moghaddam A, Llorca J, Ibáñez M, Arbiol J, Xu Y, Cabot A. 2023. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 58(4), 287–298.","chicago":"He, Ren, Linlin Yang, Yu Zhang, Xiang Wang, Seungho Lee, Ting Zhang, Lingxiao Li, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” <i>Energy Storage Materials</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">https://doi.org/10.1016/j.ensm.2023.03.022</a>.","mla":"He, Ren, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” <i>Energy Storage Materials</i>, vol. 58, no. 4, Elsevier, 2023, pp. 287–98, doi:<a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">10.1016/j.ensm.2023.03.022</a>."},"title":"A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance"},{"month":"04","date_created":"2023-05-02T07:58:57Z","supervisor":[{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"}],"page":"82","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","day":"28","alternative_title":["ISTA Thesis"],"author":[{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","first_name":"Mariano","last_name":"Calcabrini"}],"type":"dissertation","ec_funded":1,"citation":{"mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023."},"title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","language":[{"iso":"eng"}],"ddc":["546","541"],"doi":"10.15479/at:ista:12885","related_material":{"record":[{"id":"10806","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"10042","status":"public"},{"id":"12237","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9118","relation":"part_of_dissertation"},{"id":"10123","relation":"part_of_dissertation","status":"public"}]},"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file":[{"date_created":"2023-05-02T07:43:18Z","file_id":"12887","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2023-05-02T07:43:18Z","checksum":"9347b0e09425f56fdcede5d3528404dc","creator":"mcalcabr","file_size":99627036,"file_name":"Thesis_Calcabrini.docx"},{"file_name":"Thesis_Calcabrini_pdfa.pdf","file_size":8742220,"creator":"mcalcabr","date_updated":"2023-05-02T07:42:45Z","access_level":"open_access","checksum":"2d188b76621086cd384f0b9264b0a576","content_type":"application/pdf","file_id":"12888","relation":"main_file","success":1,"date_created":"2023-05-02T07:42:45Z"}],"abstract":[{"lang":"eng","text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"_id":"12885","date_published":"2023-04-28T00:00:00Z","article_processing_charge":"No","file_date_updated":"2023-05-02T07:43:18Z","publication_status":"published","oa":1,"oa_version":"Published Version","has_accepted_license":"1","year":"2023","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-08-14T07:25:26Z","publication_identifier":{"isbn":["978-3-99078-028-2"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}]},{"article_type":"original","oa_version":"Published Version","year":"2022","date_updated":"2024-03-25T23:30:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["34919802"],"isi":["000768933800005"]},"scopus_import":"1","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes."}],"_id":"10703","date_published":"2022-01-10T00:00:00Z","issue":"1","article_processing_charge":"No","volume":57,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497"}],"day":"10","author":[{"full_name":"Gaertner, Florian","first_name":"Florian","last_name":"Gaertner"},{"last_name":"Reis-Rodrigues","first_name":"Patricia","full_name":"Reis-Rodrigues, Patricia"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Juan","full_name":"Aguilera, Juan","last_name":"Aguilera"},{"orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Riedl, Michael","last_name":"Riedl"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X"},{"first_name":"Aglaja","full_name":"Kopf, Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack"},{"full_name":"Zheden, Vanessa","first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","ec_funded":1,"citation":{"mla":"Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>, vol. 57, no. 1, Cell Press ; Elsevier, 2022, p. 47–62.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>.","chicago":"Gaertner, Florian, Patricia Reis-Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>. Cell Press ; Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>.","ista":"Gaertner F, Reis-Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9.","ieee":"F. Gaertner <i>et al.</i>, “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” <i>Developmental Cell</i>, vol. 57, no. 1. Cell Press ; Elsevier, p. 47–62.e9, 2022.","ama":"Gaertner F, Reis-Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. 2022;57(1):47-62.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>","apa":"Gaertner, F., Reis-Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. Cell Press ; Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>","short":"F. Gaertner, P. Reis-Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9."},"title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2021.11.024","ddc":["570"],"acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12726"},{"relation":"dissertation_contains","id":"14530","status":"public"},{"status":"public","id":"12401","relation":"dissertation_contains"}]},"pmid":1,"project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"01","date_created":"2022-01-30T23:01:33Z","page":"47-62.e9","department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"quality_controlled":"1","publication":"Developmental Cell","intvolume":"        57","status":"public","publisher":"Cell Press ; Elsevier","isi":1},{"date_created":"2022-02-20T23:01:31Z","month":"02","status":"public","intvolume":"       119","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"isi":1,"publisher":"Proceedings of the National Academy of Sciences","type":"journal_article","author":[{"id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana","first_name":"Jana","last_name":"Slovakova"},{"first_name":"Mateusz K","full_name":"Sikora, Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","full_name":"Arslan, Feyza N","first_name":"Feyza N","last_name":"Arslan"},{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo"},{"orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","first_name":"Gabriel"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"day":"14","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","citation":{"ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(8). doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>.","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022."},"ec_funded":1,"doi":"10.1073/pnas.2122030119","ddc":["570"],"language":[{"iso":"eng"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"9750","relation":"earlier_version"}]},"acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda  for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","_id":"10766","date_published":"2022-02-14T00:00:00Z","abstract":[{"lang":"eng","text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact."}],"article_number":"e2122030119","file":[{"file_size":1609678,"creator":"dernst","file_name":"2022_PNAS_Slovakova.pdf","access_level":"open_access","date_updated":"2022-02-21T08:45:11Z","checksum":"d49f83c3580613966f71768ddb9a55a5","relation":"main_file","file_id":"10780","content_type":"application/pdf","success":1,"date_created":"2022-02-21T08:45:11Z"}],"article_processing_charge":"No","issue":"8","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":119,"file_date_updated":"2022-02-21T08:45:11Z","oa":1,"publication_status":"published","year":"2022","has_accepted_license":"1","oa_version":"Published Version","article_type":"original","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["10916490"]},"external_id":{"isi":["000766926900009"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-02T14:26:51Z"},{"article_type":"original","year":"2022","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-02T14:46:48Z","scopus_import":"1","external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"_id":"10841","date_published":"2022-06-01T00:00:00Z","abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"issue":"6","article_processing_charge":"No","volume":34,"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"oa":1,"day":"01","author":[{"last_name":"Dahhan","full_name":"Dahhan, DA","first_name":"DA"},{"last_name":"Reynolds","first_name":"GD","full_name":"Reynolds, GD"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"full_name":"Eeckhout, D","first_name":"D","last_name":"Eeckhout"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J","first_name":"Alexander J"},{"last_name":"Yperman","full_name":"Yperman, K","first_name":"K"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"N","full_name":"Vang, N","last_name":"Vang"},{"last_name":"Yan","first_name":"X","full_name":"Yan, X"},{"first_name":"I","full_name":"Hwang, I","last_name":"Hwang"},{"last_name":"Heese","full_name":"Heese, A","first_name":"A"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"last_name":"Pan","first_name":"J","full_name":"Pan, J"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"}],"type":"journal_article","citation":{"ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford Academic, pp. 2150–2173, 2022.","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>"},"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","language":[{"iso":"eng"}],"doi":"10.1093/plcell/koac071","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"pmid":1,"month":"06","date_created":"2022-03-08T13:47:51Z","page":"2150-2173","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"quality_controlled":"1","publication":"Plant Cell","intvolume":"        34","status":"public","publisher":"Oxford Academic","isi":1},{"title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","citation":{"mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>.","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022)."},"type":"journal_article","author":[{"last_name":"Obr","first_name":"Martin","full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hagen","first_name":"Wim J.H.","full_name":"Hagen, Wim J.H."},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"first_name":"Lingbo","full_name":"Yu, Lingbo","last_name":"Yu"},{"last_name":"Kotecha","full_name":"Kotecha, Abhay","first_name":"Abhay"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"day":"01","pmid":1,"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","ddc":["570"],"doi":"10.1016/j.jsb.2022.107852","keyword":["Structural Biology"],"language":[{"iso":"eng"}],"date_created":"2022-04-15T07:10:26Z","month":"06","isi":1,"publisher":"Elsevier","intvolume":"       214","status":"public","publication":"Journal of Structural Biology","quality_controlled":"1","department":[{"_id":"FlSc"}],"has_accepted_license":"1","oa_version":"Published Version","year":"2022","article_type":"original","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["1047-8477"]},"external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T06:25:23Z","article_processing_charge":"Yes (via OA deal)","issue":"2","_id":"11155","date_published":"2022-06-01T00:00:00Z","abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"file":[{"content_type":"application/pdf","file_id":"11722","relation":"main_file","date_created":"2022-08-02T11:07:58Z","success":1,"file_name":"2022_JourStructuralBiology_Obr.pdf","creator":"dernst","file_size":7080863,"checksum":"0b1eb53447aae8e95ae4c12d193b0b00","date_updated":"2022-08-02T11:07:58Z","access_level":"open_access"}],"article_number":"107852","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":214,"file_date_updated":"2022-08-02T11:07:58Z"},{"year":"2022","oa_version":"Published Version","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-08-18T06:31:52Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2663-337X"]},"file":[{"date_updated":"2023-04-20T22:30:03Z","access_level":"open_access","checksum":"1616a8bf6f13a57c892dac873dcd0936","embargo":"2023-04-19","file_name":"Olena_KIM_thesis_final.pdf","file_size":21273537,"creator":"okim","date_created":"2022-04-20T14:21:56Z","content_type":"application/pdf","relation":"main_file","file_id":"11220"},{"file_size":59248569,"creator":"okim","file_name":"KIM_thesis_final.zip","access_level":"closed","date_updated":"2023-04-20T22:30:03Z","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","relation":"source_file","file_id":"11221","content_type":"application/x-zip-compressed","embargo_to":"open_access","date_created":"2022-04-20T14:22:56Z"}],"_id":"11196","date_published":"2022-04-20T00:00:00Z","abstract":[{"lang":"eng","text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n"}],"article_processing_charge":"No","file_date_updated":"2023-04-20T22:30:03Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"publication_status":"published","oa":1,"day":"20","alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"full_name":"Kim, Olena","first_name":"Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"citation":{"short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>","apa":"Kim, O. (2022). <i>Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>","chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>.","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","mla":"Kim, Olena. <i>Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>."},"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11196","ddc":["570"],"project":[{"grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11222","status":"public"},{"status":"public","id":"7473","relation":"part_of_dissertation"}]},"month":"04","date_created":"2022-04-20T09:47:12Z","supervisor":[{"first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"page":"132","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD"},{"article_processing_charge":"No","date_published":"2022-05-16T00:00:00Z","_id":"11393","abstract":[{"lang":"eng","text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits."}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"11395","relation":"source_file","date_created":"2022-05-17T09:08:06Z","embargo_to":"open_access","file_name":"MJ thesis.docx","file_size":56427603,"creator":"cchlebak","date_updated":"2023-05-17T22:30:03Z","access_level":"closed","checksum":"8fc695d88020d70d231dad0e9f10b138"},{"access_level":"open_access","date_updated":"2023-05-17T22:30:03Z","checksum":"c1dd20a1aece521b3500607b00e463d6","embargo":"2023-05-16","file_size":4351981,"creator":"cchlebak","file_name":"MJ_thesis_PDFA.pdf","date_created":"2022-05-17T12:09:25Z","file_id":"11397","relation":"main_file","content_type":"application/pdf"}],"oa":1,"publication_status":"published","file_date_updated":"2023-05-17T22:30:03Z","oa_version":"Published Version","has_accepted_license":"1","year":"2022","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-09-07T14:53:44Z","page":"108","supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-05-17T08:57:41Z","month":"05","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"GradSch"},{"_id":"RySh"}],"title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","citation":{"chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>.","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","mla":"Jevtic, Marijo. <i>Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>.","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>","apa":"Jevtic, M. (2022). <i>Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>"},"author":[{"id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo","full_name":"Jevtic, Marijo","last_name":"Jevtic"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"day":"16","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7391"}]},"doi":"10.15479/at:ista:11393","ddc":["570"],"language":[{"iso":"eng"}]},{"intvolume":"        61","status":"public","publication":"Angewandte Chemie - International Edition","quality_controlled":"1","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"isi":1,"publisher":"Wiley","date_created":"2022-07-31T22:01:48Z","month":"08","ddc":["540"],"doi":"10.1002/anie.202207002","language":[{"iso":"eng"}],"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","type":"journal_article","author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","full_name":"Chang, Cheng","last_name":"Chang"},{"first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","full_name":"Lee, Seungho","last_name":"Lee"},{"first_name":"Maria","full_name":"Spadaro, Maria","last_name":"Spadaro"},{"last_name":"Koskela","first_name":"Kristopher M.","full_name":"Koskela, Kristopher M."},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns"},{"orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Richard L.","full_name":"Brutchey, Richard L.","last_name":"Brutchey"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"}],"day":"26","title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","citation":{"short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>","ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. 2022;61(35). doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>","ieee":"C. Chang <i>et al.</i>, “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35. Wiley, 2022.","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002.","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>.","mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35, e202207002, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>."},"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":61,"file_date_updated":"2023-02-02T08:01:00Z","oa":1,"publication_status":"published","_id":"11705","date_published":"2022-08-26T00:00:00Z","abstract":[{"text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe.","lang":"eng"}],"article_number":"e202207002","file":[{"success":1,"date_created":"2023-02-02T08:01:00Z","relation":"main_file","file_id":"12476","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-02-02T08:01:00Z","checksum":"ad601f2b9e26e46ab4785162be58b5ed","creator":"dernst","file_size":4072650,"file_name":"2022_AngewandteChemieInternat_Chang.pdf"}],"article_processing_charge":"Yes (via OA deal)","issue":"35","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"scopus_import":"1","external_id":{"isi":["000828274200001"]},"date_updated":"2023-08-03T12:23:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","has_accepted_license":"1","oa_version":"Published Version","article_type":"original"},{"article_type":"original","year":"2022","oa_version":"Published Version","date_updated":"2023-08-02T13:52:33Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000779305000033"],"pmid":["35019710"]},"scopus_import":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["0022-538X"],"eissn":["1098-5514"]},"issue":"5","article_processing_charge":"No","article_number":"e02146-21","_id":"10639","date_published":"2022-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"With more than 80 members worldwide, the Orthobunyavirus genus in the Peribunyaviridae family is a large genus of enveloped RNA viruses, many of which are emerging pathogens in humans and livestock. How orthobunyaviruses (OBVs) penetrate and infect mammalian host cells remains poorly characterized. Here, we investigated the entry mechanisms of the OBV Germiston (GERV). Viral particles were visualized by cryo-electron microscopy and appeared roughly spherical with an average diameter of 98 nm. Labeling of the virus with fluorescent dyes did not adversely affect its infectivity and allowed the monitoring of single particles in fixed and live cells. Using this approach, we found that endocytic internalization of bound viruses was asynchronous and occurred within 30-40 min. The virus entered Rab5a+ early endosomes and, subsequently, late endosomal vacuoles containing Rab7a but not LAMP-1. Infectious entry did not require proteolytic cleavage, and endosomal acidification was sufficient and necessary for viral fusion. Acid-activated penetration began 15-25 min after initiation of virus internalization and relied on maturation of early endosomes to late endosomes. The optimal pH for viral membrane fusion was slightly below 6.0, and penetration was hampered when the potassium influx was abolished. Overall, our study provides real-time visualization of GERV entry into host cells and demonstrates the importance of late endosomal maturation in facilitating OBV penetration."}],"publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410","open_access":"1"}],"oa":1,"volume":96,"citation":{"chicago":"Windhaber, Stefan, Qilin Xin, Zina M. Uckeley, Jana Koch, Martin Obr, Céline Garnier, Catherine Luengo-Guyonnot, Maëva Duboeuf, Florian KM Schur, and Pierre-Yves Lozach. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” <i>Journal of Virology</i>. American Society for Microbiology, 2022. <a href=\"https://doi.org/10.1128/jvi.02146-21\">https://doi.org/10.1128/jvi.02146-21</a>.","ieee":"S. Windhaber <i>et al.</i>, “The Orthobunyavirus Germiston enters host cells from late endosomes,” <i>Journal of Virology</i>, vol. 96, no. 5. American Society for Microbiology, 2022.","ista":"Windhaber S, Xin Q, Uckeley ZM, Koch J, Obr M, Garnier C, Luengo-Guyonnot C, Duboeuf M, Schur FK, Lozach P-Y. 2022. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 96(5), e02146-21.","mla":"Windhaber, Stefan, et al. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” <i>Journal of Virology</i>, vol. 96, no. 5, e02146-21, American Society for Microbiology, 2022, doi:<a href=\"https://doi.org/10.1128/jvi.02146-21\">10.1128/jvi.02146-21</a>.","short":"S. Windhaber, Q. Xin, Z.M. Uckeley, J. Koch, M. Obr, C. Garnier, C. Luengo-Guyonnot, M. Duboeuf, F.K. Schur, P.-Y. Lozach, Journal of Virology 96 (2022).","ama":"Windhaber S, Xin Q, Uckeley ZM, et al. The Orthobunyavirus Germiston enters host cells from late endosomes. <i>Journal of Virology</i>. 2022;96(5). doi:<a href=\"https://doi.org/10.1128/jvi.02146-21\">10.1128/jvi.02146-21</a>","apa":"Windhaber, S., Xin, Q., Uckeley, Z. M., Koch, J., Obr, M., Garnier, C., … Lozach, P.-Y. (2022). The Orthobunyavirus Germiston enters host cells from late endosomes. <i>Journal of Virology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/jvi.02146-21\">https://doi.org/10.1128/jvi.02146-21</a>"},"title":"The Orthobunyavirus Germiston enters host cells from late endosomes","day":"01","author":[{"last_name":"Windhaber","full_name":"Windhaber, Stefan","first_name":"Stefan"},{"first_name":"Qilin","full_name":"Xin, Qilin","last_name":"Xin"},{"full_name":"Uckeley, Zina M.","first_name":"Zina M.","last_name":"Uckeley"},{"last_name":"Koch","full_name":"Koch, Jana","first_name":"Jana"},{"last_name":"Obr","full_name":"Obr, Martin","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Garnier","first_name":"Céline","full_name":"Garnier, Céline"},{"first_name":"Catherine","full_name":"Luengo-Guyonnot, Catherine","last_name":"Luengo-Guyonnot"},{"full_name":"Duboeuf, Maëva","first_name":"Maëva","last_name":"Duboeuf"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lozach","first_name":"Pierre-Yves","full_name":"Lozach, Pierre-Yves"}],"type":"journal_article","acknowledgement":"This work  was  supported  by  INRAE  starter  funds, Project IDEXLYON  (University  of  Lyon) within  the  Programme  Investissements  d’Avenir  (ANR-16-IDEX-0005),  and  FINOVIAO14 (Fondation  pour  l’Université  de  Lyon),  all  to  P.Y.L.  This  work  was  also  supported  by CellNetworks  Research  Group  funds  and  Deutsche  Forschungsgemeinschaft  (DFG)  funding (grant  numbers  LO-2338/1-1  and  LO-2338/3-1)  awarded  to  P.Y.L., Austrian  Science  Fund (FWF)  grant  P31445  to  F.K.M.S., a  Chinese  Scholarship  Council (CSC;no.  201904910701) fellowship  to   Q.X.,  and  a  ministére  de  l’enseignement  supérieur,  de  la  recherche  et  de l’innovation (MESRI) doctoral thesis grant to M.D.","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"pmid":1,"language":[{"iso":"eng"}],"keyword":["virology","insect science","immunology","microbiology"],"doi":"10.1128/jvi.02146-21","month":"03","date_created":"2022-01-18T10:04:18Z","publisher":"American Society for Microbiology","isi":1,"quality_controlled":"1","department":[{"_id":"FlSc"}],"publication":"Journal of Virology","status":"public","intvolume":"        96"},{"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.7554/eLife.78995","related_material":{"record":[{"id":"10316","relation":"earlier_version","status":"public"}]},"project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin"}],"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strains CFT073, UTI89, and 536, Frank Assen, Vlad Gavra, 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 IG, the European Research Council (CoG 724373), and the Austrian Science Fund (FWF P29911) to MS.","day":"26","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","full_name":"Tomasek, Kathrin","first_name":"Kathrin"},{"first_name":"Alexander F","full_name":"Leithner, Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","last_name":"Glatzová","first_name":"Ivana","full_name":"Glatzová, Ivana"},{"last_name":"Lukesch","first_name":"Michael S.","full_name":"Lukesch, Michael S."},{"last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"type":"journal_article","citation":{"apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (2022). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.78995\">https://doi.org/10.7554/eLife.78995</a>","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.78995\">10.7554/eLife.78995</a>","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, ELife 11 (2022).","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>ELife</i>, vol. 11, e78995, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.78995\">10.7554/eLife.78995</a>.","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. 2022. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. eLife. 11, e78995.","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.78995\">https://doi.org/10.7554/eLife.78995</a>."},"ec_funded":1,"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","publication":"eLife","quality_controlled":"1","department":[{"_id":"MiSi"},{"_id":"CaGu"}],"intvolume":"        11","status":"public","publisher":"eLife Sciences Publications","isi":1,"month":"07","date_created":"2022-08-14T22:01:46Z","scopus_import":"1","external_id":{"isi":["000838410200001"]},"date_updated":"2023-08-03T12:54:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["2050-084X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"article_type":"original","year":"2022","has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2022-08-16T08:57:37Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":11,"publication_status":"published","oa":1,"file":[{"file_name":"2022_eLife_Tomasek.pdf","file_size":2057577,"creator":"cchlebak","date_updated":"2022-08-16T08:57:37Z","access_level":"open_access","checksum":"002a3c7c7ea5caa9af9cfbea308f6ea4","content_type":"application/pdf","relation":"main_file","file_id":"11861","success":1,"date_created":"2022-08-16T08:57:37Z"}],"article_number":"e78995","date_published":"2022-07-26T00:00:00Z","_id":"11843","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 mouse dendritic cells (DCs) as a 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 the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. 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"}],"article_processing_charge":"Yes"},{"article_type":"original","year":"2022","has_accepted_license":"1","oa_version":"Published Version","external_id":{"isi":["000860787000001"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T13:47:56Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"M-Shop"}],"publication_identifier":{"eissn":["2380-8195"]},"article_processing_charge":"Yes (via OA deal)","issue":"9","file":[{"file_id":"12319","relation":"main_file","content_type":"application/pdf","date_created":"2023-01-20T08:43:51Z","success":1,"creator":"dernst","file_size":3827583,"file_name":"2022_ACSEnergyLetters_Prehal.pdf","checksum":"cf0bed3a2535c11d27244cd029dbc1d0","access_level":"open_access","date_updated":"2023-01-20T08:43:51Z"}],"_id":"12065","date_published":"2022-08-29T00:00:00Z","abstract":[{"lang":"eng","text":"Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution-mediated LiO2 disproportionation, bringing into question the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Determining particle morphology and achievable capacities are species mobilities, true areal rate, and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface growth are high, high capacities are also achieved with weakly solvating electrolytes, which were previously considered prototypical for low capacity via surface growth."}],"publication_status":"published","oa":1,"file_date_updated":"2023-01-20T08:43:51Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":7,"citation":{"ista":"Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.","ieee":"C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution discharge in Li-O₂ batteries?,” <i>ACS Energy Letters</i>, vol. 7, no. 9. American Chemical Society, pp. 3112–3119, 2022.","chicago":"Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>.","mla":"Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>, vol. 7, no. 9, American Chemical Society, 2022, pp. 3112–19, doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>.","short":"C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7 (2022) 3112–3119.","apa":"Prehal, C., Mondal, S., Lovicar, L., &#38; Freunberger, S. A. (2022). Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>","ama":"Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. 2022;7(9):3112-3119. doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>"},"title":"Exclusive solution discharge in Li-O₂ batteries?","day":"29","author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","full_name":"Mondal, Soumyadip","first_name":"Soumyadip"},{"full_name":"Lovicar, Ludek","first_name":"Ludek","last_name":"Lovicar","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319"}],"type":"journal_article","acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 636069). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution, Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science and Technology Austria (ISTA) for support. This research was supported by the Scientific Service Units of ISTA through resources provided by the Electron Microscopy Facility and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing support.","language":[{"iso":"eng"}],"doi":"10.1021/acsenergylett.2c01711","ddc":["540"],"page":"3112-3119","month":"08","date_created":"2022-09-08T09:51:09Z","publisher":"American Chemical Society","isi":1,"publication":"ACS Energy Letters","quality_controlled":"1","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"intvolume":"         7","status":"public"},{"title":"A universal coupling mechanism of respiratory complex I","ec_funded":1,"citation":{"mla":"Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14, doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>.","ista":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928), 808–814.","ieee":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” <i>Nature</i>, vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.","chicago":"Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason, Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>.","apa":"Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z., &#38; Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex I. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>","ama":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. A universal coupling mechanism of respiratory complex I. <i>Nature</i>. 2022;609(7928):808-814. doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>","short":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A. Sazanov, Nature 609 (2022) 808–814."},"author":[{"full_name":"Kravchuk, Vladyslav","first_name":"Vladyslav","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","full_name":"Petrova, Olga","last_name":"Petrova","id":"5D8C9660-5D49-11EA-8188-567B3DDC885E"},{"id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen","full_name":"Kampjut, Domen"},{"full_name":"Wojciechowska-Bason, Anna","first_name":"Anna","last_name":"Wojciechowska-Bason"},{"first_name":"Zara","full_name":"Breese, Zara","last_name":"Breese"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"type":"journal_article","day":"22","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance with collecting cryo-EM data and A. Charnagalov for the assistance with protein purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also supported by the Medical Research Council (UK).","project":[{"grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"12781","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41586-022-05457-8","relation":"erratum"},{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/proton-dominos-kick-off-life/","relation":"press_release"}]},"pmid":1,"doi":"10.1038/s41586-022-05199-7","ddc":["572"],"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"page":"808-814","date_created":"2023-01-12T12:04:33Z","month":"09","isi":1,"publisher":"Springer Nature","status":"public","intvolume":"       609","department":[{"_id":"LeSa"}],"quality_controlled":"1","publication":"Nature","has_accepted_license":"1","year":"2022","oa_version":"Submitted Version","article_type":"original","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T08:54:52Z","scopus_import":"1","external_id":{"isi":["000854788200001"],"pmid":["36104567"]},"issue":"7928","article_processing_charge":"No","_id":"12138","date_published":"2022-09-22T00:00:00Z","abstract":[{"text":"Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.","lang":"eng"}],"file":[{"date_updated":"2023-05-30T17:05:31Z","access_level":"open_access","checksum":"d42a93e24f59e883ef0b5429832391d0","file_name":"EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf","file_size":1425655,"creator":"lsazanov","success":1,"date_created":"2023-05-30T17:05:31Z","content_type":"application/pdf","file_id":"13104","relation":"main_file"},{"content_type":"application/pdf","relation":"main_file","file_id":"13105","success":1,"date_created":"2023-05-30T17:07:05Z","file_name":"EcCxI_manuscript_rev3_SI_All_opt_upd.pdf","file_size":9842513,"creator":"lsazanov","date_updated":"2023-05-30T17:07:05Z","access_level":"open_access","checksum":"5422bc0a73b3daadafa262c7ea6deae3"}],"oa":1,"publication_status":"published","volume":609,"file_date_updated":"2023-05-30T17:07:05Z"},{"article_processing_charge":"No","issue":"21","file":[{"success":1,"date_created":"2023-01-24T09:29:02Z","content_type":"application/pdf","file_id":"12354","relation":"main_file","date_updated":"2023-01-24T09:29:02Z","access_level":"open_access","checksum":"999e443b54e4fdaa2542ca5a97619731","file_name":"2022_MolecularCell_Zapletal.pdf","file_size":7368534,"creator":"dernst"}],"date_published":"2022-11-03T00:00:00Z","_id":"12143","abstract":[{"text":"MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.","lang":"eng"}],"publication_status":"published","oa":1,"file_date_updated":"2023-01-24T09:29:02Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":82,"article_type":"original","oa_version":"Published Version","has_accepted_license":"1","year":"2022","external_id":{"isi":["000898565300011"],"pmid":["36332606"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T08:57:17Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["1097-2765"]},"page":"4064-4079.e13","month":"11","date_created":"2023-01-12T12:05:36Z","publisher":"Elsevier","isi":1,"publication":"Molecular Cell","department":[{"_id":"CaBe"}],"quality_controlled":"1","intvolume":"        82","status":"public","citation":{"short":"D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C. Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka, M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R. Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.","ama":"Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. 2022;82(21):4064-4079.e13. doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>","apa":"Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., … Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>","chicago":"Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>.","ieee":"D. Zapletal <i>et al.</i>, “Structural and functional basis of mammalian microRNA biogenesis by Dicer,” <i>Molecular Cell</i>, vol. 82, no. 21. Elsevier, p. 4064–4079.e13, 2022.","ista":"Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 82(21), 4064–4079.e13.","mla":"Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>, vol. 82, no. 21, Elsevier, 2022, p. 4064–4079.e13, doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>."},"title":"Structural and functional basis of mammalian microRNA biogenesis by Dicer","day":"03","author":[{"last_name":"Zapletal","first_name":"David","full_name":"Zapletal, David"},{"full_name":"Taborska, Eliska","first_name":"Eliska","last_name":"Taborska"},{"full_name":"Pasulka, Josef","first_name":"Josef","last_name":"Pasulka"},{"last_name":"Malik","first_name":"Radek","full_name":"Malik, Radek"},{"last_name":"Kubicek","first_name":"Karel","full_name":"Kubicek, Karel"},{"last_name":"Zanova","first_name":"Martina","full_name":"Zanova, Martina"},{"full_name":"Much, Christian","first_name":"Christian","last_name":"Much"},{"last_name":"Sebesta","full_name":"Sebesta, Marek","first_name":"Marek"},{"last_name":"Buccheri","full_name":"Buccheri, Valeria","first_name":"Valeria"},{"last_name":"Horvat","full_name":"Horvat, Filip","first_name":"Filip"},{"last_name":"Jenickova","full_name":"Jenickova, Irena","first_name":"Irena"},{"first_name":"Michaela","full_name":"Prochazkova, Michaela","last_name":"Prochazkova"},{"first_name":"Jan","full_name":"Prochazka, Jan","last_name":"Prochazka"},{"full_name":"Pinkas, Matyas","first_name":"Matyas","last_name":"Pinkas"},{"full_name":"Novacek, Jiri","first_name":"Jiri","last_name":"Novacek"},{"last_name":"Joseph","full_name":"Joseph, Diego F.","first_name":"Diego F."},{"first_name":"Radislav","full_name":"Sedlacek, Radislav","last_name":"Sedlacek"},{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky"},{"full_name":"O’Carroll, Dónal","first_name":"Dónal","last_name":"O’Carroll"},{"first_name":"Richard","full_name":"Stefl, Richard","last_name":"Stefl"},{"full_name":"Svoboda, Petr","first_name":"Petr","last_name":"Svoboda"}],"type":"journal_article","pmid":1,"acknowledgement":"We thank Kristian Vlahovicek (University of Zagreb) for support of bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics and Bioinformatics Core Facility at the Institute of Molecular Genetics for help with RNA sequencing. The main funding was provided by the Czech Science Foundation (EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work were supported by European Research Council grants under the European Union’s Horizon 2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl). V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the Charles University; this work will be in part fulfilling requirements for a PhD degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050 from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861 CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities (CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127 from MEYS CR), and support from the Scientific Service Units of ISTA through resources from the Electron Microscopy Facility. Computational resources included e-Infrastruktura CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded by the European Structural and Investment Funds grants.","keyword":["Cell Biology","Molecular Biology"],"language":[{"iso":"eng"}],"doi":"10.1016/j.molcel.2022.10.010","ddc":["570"]},{"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["0006-8950"],"eissn":["1460-2156"]},"date_updated":"2023-08-04T09:13:08Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000807770000001"]},"oa_version":"Published Version","year":"2022","article_type":"original","volume":145,"main_file_link":[{"url":"https://doi.org/10.1093/brain/awac145","open_access":"1"}],"oa":1,"publication_status":"published","date_published":"2022-08-01T00:00:00Z","_id":"12174","abstract":[{"text":"Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease.\r\nHere we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs.</jats:p>\r\n               <jats:p>Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes.\r\nATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.","lang":"eng"}],"issue":"8","article_processing_charge":"No","doi":"10.1093/brain/awac145","language":[{"iso":"eng"}],"keyword":["Neurology (clinical)"],"acknowledgement":"We thank all patients and family members for their participation in this study. We thank Melanie Pieraks and Eva Reinthaler (Neurolentech, Austria) for generating the human iPSC lines and\r\nfor performing quality checks. We thank Vanessa Zheden and Daniel Gütl for their excellent technical support in the specimen preparation for transmission electron microscopy and Flavia Leite for preparing the lentiviruses. The support from Electron Microscopy Facility and Molecular Biology Services at IST Austria is greatly acknowledged. We would like to thank Doctors Jane Hurst and Richard Scott for their help in retrieving the detailed clinical information of Patient 17. The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. See Supplementary Material for Undiagnosed Disease Network consortium details. Genetic information on Patient 23 was made available through access to the data and findings generated by the 100 000 Genomes\r\nProject; www.genomicsengland.co.uk (to K.L.). \r\nThis work was supported by the EU 7th Framework Programme (FP7) under the project DESIRE grant N602531 (to R.G.); the Regione Toscana under the Call for Health 2018 (grant\r\nDECODE-EE) (to R.G.); the ‘Brain Project’ by Fondazione Cassa di Risparmio di Firenze (to R.G.); IRCCS Ospedale Policlinico San Martino 5×1000 and Ricerca Corrente (to A.F. and F.B.). The European Reference Network (ERN) for rare and complex epilepsies (EpiCARE) provided financial support for meetings organization. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute (grant number WT098051). The views expressed in this publication\r\nare those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). This study makes use of DECIPHER (https://www.deciphergenomics.org), which is funded by Wellcome. K.K.-S. was supported by the ISTplus fellowship. ","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"author":[{"full_name":"Guerrini, Renzo","first_name":"Renzo","last_name":"Guerrini"},{"full_name":"Mei, Davide","first_name":"Davide","last_name":"Mei"},{"first_name":"Margit Katalin","full_name":"Szigeti, Margit Katalin","last_name":"Szigeti","orcid":"0000-0001-9500-8758","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pepe, Sara","first_name":"Sara","last_name":"Pepe"},{"last_name":"Koenig","first_name":"Mary Kay","full_name":"Koenig, Mary Kay"},{"first_name":"Gretchen","full_name":"Von Allmen, Gretchen","last_name":"Von Allmen"},{"last_name":"Cho","first_name":"Megan T","full_name":"Cho, Megan T"},{"full_name":"McDonald, Kimberly","first_name":"Kimberly","last_name":"McDonald"},{"last_name":"Baker","first_name":"Janice","full_name":"Baker, Janice"},{"first_name":"Vikas","full_name":"Bhambhani, Vikas","last_name":"Bhambhani"},{"full_name":"Powis, Zöe","first_name":"Zöe","last_name":"Powis"},{"last_name":"Rodan","full_name":"Rodan, Lance","first_name":"Lance"},{"last_name":"Nabbout","first_name":"Rima","full_name":"Nabbout, Rima"},{"first_name":"Giulia","full_name":"Barcia, Giulia","last_name":"Barcia"},{"first_name":"Jill A","full_name":"Rosenfeld, Jill A","last_name":"Rosenfeld"},{"last_name":"Bacino","full_name":"Bacino, Carlos A","first_name":"Carlos A"},{"last_name":"Mignot","first_name":"Cyril","full_name":"Mignot, Cyril"},{"first_name":"Lillian H","full_name":"Power, Lillian H","last_name":"Power"},{"last_name":"Harris","first_name":"Catharine J","full_name":"Harris, Catharine J"},{"last_name":"Marjanovic","first_name":"Dragan","full_name":"Marjanovic, Dragan"},{"first_name":"Rikke S","full_name":"Møller, Rikke S","last_name":"Møller"},{"last_name":"Hammer","first_name":"Trine B","full_name":"Hammer, Trine B"},{"first_name":"Riikka","full_name":"Keski Filppula, Riikka","last_name":"Keski Filppula"},{"last_name":"Vieira","first_name":"Päivi","full_name":"Vieira, Päivi"},{"last_name":"Hildebrandt","full_name":"Hildebrandt, Clara","first_name":"Clara"},{"first_name":"Stephanie","full_name":"Sacharow, Stephanie","last_name":"Sacharow"},{"last_name":"Maragliano","full_name":"Maragliano, Luca","first_name":"Luca"},{"first_name":"Fabio","full_name":"Benfenati, Fabio","last_name":"Benfenati"},{"full_name":"Lachlan, Katherine","first_name":"Katherine","last_name":"Lachlan"},{"last_name":"Benneche","full_name":"Benneche, Andreas","first_name":"Andreas"},{"full_name":"Petit, Florence","first_name":"Florence","last_name":"Petit"},{"last_name":"de Sainte Agathe","full_name":"de Sainte Agathe, Jean Madeleine","first_name":"Jean Madeleine"},{"last_name":"Hallinan","first_name":"Barbara","full_name":"Hallinan, Barbara"},{"first_name":"Yue","full_name":"Si, Yue","last_name":"Si"},{"first_name":"Ingrid M","full_name":"Wentzensen, Ingrid M","last_name":"Wentzensen"},{"first_name":"Fanggeng","full_name":"Zou, Fanggeng","last_name":"Zou"},{"last_name":"Narayanan","first_name":"Vinodh","full_name":"Narayanan, Vinodh"},{"last_name":"Matsumoto","first_name":"Naomichi","full_name":"Matsumoto, Naomichi"},{"last_name":"Boncristiano","full_name":"Boncristiano, Alessandra","first_name":"Alessandra"},{"first_name":"Giancarlo","full_name":"la Marca, Giancarlo","last_name":"la Marca"},{"first_name":"Mitsuhiro","full_name":"Kato, Mitsuhiro","last_name":"Kato"},{"last_name":"Anderson","first_name":"Kristin","full_name":"Anderson, Kristin"},{"full_name":"Barba, Carmen","first_name":"Carmen","last_name":"Barba"},{"last_name":"Sturiale","full_name":"Sturiale, Luisa","first_name":"Luisa"},{"full_name":"Garozzo, Domenico","first_name":"Domenico","last_name":"Garozzo"},{"last_name":"Bei","full_name":"Bei, Roberto","first_name":"Roberto"},{"full_name":"Masuelli, Laura","first_name":"Laura","last_name":"Masuelli"},{"last_name":"Conti","first_name":"Valerio","full_name":"Conti, Valerio"},{"first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"first_name":"Anna","full_name":"Fassio, Anna","last_name":"Fassio"}],"type":"journal_article","day":"01","title":"Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis","ec_funded":1,"citation":{"short":"R. Guerrini, D. Mei, M.K. Szigeti, S. Pepe, M.K. Koenig, G. Von Allmen, M.T. Cho, K. McDonald, J. Baker, V. Bhambhani, Z. Powis, L. Rodan, R. Nabbout, G. Barcia, J.A. Rosenfeld, C.A. Bacino, C. Mignot, L.H. Power, C.J. Harris, D. Marjanovic, R.S. Møller, T.B. Hammer, R. Keski Filppula, P. Vieira, C. Hildebrandt, S. Sacharow, L. Maragliano, F. Benfenati, K. Lachlan, A. Benneche, F. Petit, J.M. de Sainte Agathe, B. Hallinan, Y. Si, I.M. Wentzensen, F. Zou, V. Narayanan, N. Matsumoto, A. Boncristiano, G. la Marca, M. Kato, K. Anderson, C. Barba, L. Sturiale, D. Garozzo, R. Bei, L. Masuelli, V. Conti, G. Novarino, A. Fassio, Brain 145 (2022) 2687–2703.","ama":"Guerrini R, Mei D, Szigeti MK, et al. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. <i>Brain</i>. 2022;145(8):2687-2703. doi:<a href=\"https://doi.org/10.1093/brain/awac145\">10.1093/brain/awac145</a>","apa":"Guerrini, R., Mei, D., Szigeti, M. K., Pepe, S., Koenig, M. K., Von Allmen, G., … Fassio, A. (2022). Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. <i>Brain</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awac145\">https://doi.org/10.1093/brain/awac145</a>","chicago":"Guerrini, Renzo, Davide Mei, Margit Katalin Szigeti, Sara Pepe, Mary Kay Koenig, Gretchen Von Allmen, Megan T Cho, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” <i>Brain</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/brain/awac145\">https://doi.org/10.1093/brain/awac145</a>.","ieee":"R. Guerrini <i>et al.</i>, “Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis,” <i>Brain</i>, vol. 145, no. 8. Oxford University Press, pp. 2687–2703, 2022.","ista":"Guerrini R, Mei D, Szigeti MK, Pepe S, Koenig MK, Von Allmen G, Cho MT, McDonald K, Baker J, Bhambhani V, Powis Z, Rodan L, Nabbout R, Barcia G, Rosenfeld JA, Bacino CA, Mignot C, Power LH, Harris CJ, Marjanovic D, Møller RS, Hammer TB, Keski Filppula R, Vieira P, Hildebrandt C, Sacharow S, Maragliano L, Benfenati F, Lachlan K, Benneche A, Petit F, de Sainte Agathe JM, Hallinan B, Si Y, Wentzensen IM, Zou F, Narayanan V, Matsumoto N, Boncristiano A, la Marca G, Kato M, Anderson K, Barba C, Sturiale L, Garozzo D, Bei R, Masuelli L, Conti V, Novarino G, Fassio A. 2022. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 145(8), 2687–2703.","mla":"Guerrini, Renzo, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” <i>Brain</i>, vol. 145, no. 8, Oxford University Press, 2022, pp. 2687–703, doi:<a href=\"https://doi.org/10.1093/brain/awac145\">10.1093/brain/awac145</a>."},"status":"public","intvolume":"       145","department":[{"_id":"GaNo"}],"quality_controlled":"1","publication":"Brain","isi":1,"publisher":"Oxford University Press","date_created":"2023-01-12T12:11:45Z","month":"08","page":"2687-2703"},{"publication_status":"published","oa":1,"file_date_updated":"2023-01-30T07:46:51Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":15,"article_processing_charge":"Yes (via OA deal)","issue":"10","file":[{"access_level":"open_access","date_updated":"2023-01-30T07:46:51Z","checksum":"04d5c12490052d03e4dc4412338a43dd","creator":"dernst","file_size":2307251,"file_name":"2022_MolecularPlant_Johnson.pdf","success":1,"date_created":"2023-01-30T07:46:51Z","file_id":"12435","relation":"main_file","content_type":"application/pdf"}],"abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"_id":"12239","date_published":"2022-10-03T00:00:00Z","scopus_import":"1","external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"date_updated":"2023-08-04T09:39:24Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"issn":["1674-2052"]},"article_type":"original","year":"2022","oa_version":"Published Version","has_accepted_license":"1","publisher":"Elsevier","isi":1,"publication":"Molecular Plant","quality_controlled":"1","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"status":"public","intvolume":"        15","page":"1533-1542","month":"10","date_created":"2023-01-16T09:51:49Z","pmid":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","keyword":["Plant Science","Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["580"],"doi":"10.1016/j.molp.2022.09.003","citation":{"mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542."},"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","day":"03","type":"journal_article","author":[{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J","first_name":"Alexander J"},{"last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo"},{"full_name":"Dahhan, Dana A.","first_name":"Dana A.","last_name":"Dahhan"},{"last_name":"Bednarek","full_name":"Bednarek, Sebastian Y.","first_name":"Sebastian Y."},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}]},{"isi":1,"publisher":"Springer Nature","status":"public","intvolume":"        29","publication":"Nature Structural & Molecular Biology","department":[{"_id":"EM-Fac"}],"quality_controlled":"1","page":"942-953","date_created":"2023-01-16T09:59:06Z","month":"09","pmid":1,"acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","doi":"10.1038/s41594-022-00832-5","ddc":["570"],"keyword":["Molecular Biology","Structural Biology"],"language":[{"iso":"eng"}],"title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","citation":{"mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>.","ieee":"M. Prattes <i>et al.</i>, “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural &#38; Molecular Biology. 29(9), 942–953.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. 2022;29(9):942-953. doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural &#38; Molecular Biology 29 (2022) 942–953."},"author":[{"last_name":"Prattes","first_name":"Michael","full_name":"Prattes, Michael"},{"last_name":"Grishkovskaya","first_name":"Irina","full_name":"Grishkovskaya, Irina"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina","first_name":"Christina"},{"last_name":"Zisser","full_name":"Zisser, Gertrude","first_name":"Gertrude"},{"last_name":"Sailer","first_name":"Carolin","full_name":"Sailer, Carolin"},{"full_name":"Kargas, Vasileios","first_name":"Vasileios","last_name":"Kargas"},{"last_name":"Loibl","full_name":"Loibl, Mathias","first_name":"Mathias"},{"first_name":"Magdalena","full_name":"Gerhalter, Magdalena","last_name":"Gerhalter"},{"last_name":"Kofler","full_name":"Kofler, Lisa","first_name":"Lisa"},{"last_name":"Warren","full_name":"Warren, Alan J.","first_name":"Alan J."},{"first_name":"Florian","full_name":"Stengel, Florian","last_name":"Stengel"},{"last_name":"Haselbach","full_name":"Haselbach, David","first_name":"David"},{"last_name":"Bergler","first_name":"Helmut","full_name":"Bergler, Helmut"}],"type":"journal_article","day":"12","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":29,"file_date_updated":"2023-01-30T10:00:04Z","article_processing_charge":"No","issue":"9","_id":"12262","abstract":[{"text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","lang":"eng"}],"date_published":"2022-09-12T00:00:00Z","file":[{"date_created":"2023-01-30T10:00:04Z","success":1,"relation":"main_file","file_id":"12447","content_type":"application/pdf","checksum":"2d5c3ec01718fefd7553052b0b8a0793","access_level":"open_access","date_updated":"2023-01-30T10:00:04Z","creator":"dernst","file_size":9935057,"file_name":"2022_NatureStrucMolecBio_Prattes.pdf"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:52:20Z","year":"2022","has_accepted_license":"1","oa_version":"Published Version","article_type":"original"},{"oa_version":"Submitted Version","year":"2022","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-07T08:16:09Z","article_processing_charge":"No","issue":"7927","date_published":"2022-09-15T00:00:00Z","_id":"12291","abstract":[{"lang":"eng","text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization."}],"file":[{"date_updated":"2023-11-02T17:12:37Z","access_level":"open_access","checksum":"a6055c606aefb900bf62ae3e7d15f921","file_name":"Friml Nature 2022_merged.pdf","creator":"amally","file_size":79774945,"success":1,"date_created":"2023-11-02T17:12:37Z","content_type":"application/pdf","relation":"main_file","file_id":"14483"}],"oa":1,"publication_status":"published","volume":609,"file_date_updated":"2023-11-02T17:12:37Z","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","citation":{"chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>"},"ec_funded":1,"type":"journal_article","author":[{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Michelle C","full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","full_name":"Gelová, Zuzana","last_name":"Gelová"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","first_name":"Aline","last_name":"Monzer"},{"last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten"},{"last_name":"Živanović","full_name":"Živanović, Branka D.","first_name":"Branka D."},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou","full_name":"Zou, Minxia","first_name":"Minxia"},{"first_name":"Lukas","full_name":"Fiedler, Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"full_name":"Giannini, Caterina","first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones"},{"last_name":"Hrtyan","first_name":"Mónika","full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter","first_name":"Walter"},{"last_name":"Kuhn","full_name":"Kuhn, Andre","first_name":"Andre"},{"orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","last_name":"Narasimhan"},{"first_name":"Marek","full_name":"Randuch, Marek","last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"first_name":"Nikola","full_name":"Rýdza, Nikola","last_name":"Rýdza"},{"first_name":"Koji","full_name":"Takahashi, Koji","last_name":"Takahashi"},{"last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova","first_name":"Anastasiia","full_name":"Teplova, Anastasiia"},{"last_name":"Kinoshita","full_name":"Kinoshita, Toshinori","first_name":"Toshinori"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Rakusová","full_name":"Rakusová, Hana","first_name":"Hana"}],"day":"15","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}],"pmid":1,"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","doi":"10.1038/s41586-022-05187-x","ddc":["580"],"language":[{"iso":"eng"}],"page":"575-581","date_created":"2023-01-16T10:04:48Z","month":"09","isi":1,"publisher":"Springer Nature","status":"public","intvolume":"       609","publication":"Nature","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"quality_controlled":"1"},{"oa_version":"Published Version","year":"2022","has_accepted_license":"1","date_updated":"2024-08-07T07:11:56Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-024-4"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"article_processing_charge":"No","file":[{"content_type":"application/pdf","file_id":"12367","relation":"main_file","date_created":"2023-01-25T09:41:49Z","embargo":"2022-12-28","file_name":"Final_Thesis_ES_Redchenko.pdf","creator":"cchlebak","file_size":56076868,"date_updated":"2023-01-26T23:30:44Z","access_level":"open_access","checksum":"39eabb1e006b41335f17f3b29af09648"}],"abstract":[{"text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n","lang":"eng"}],"_id":"12366","date_published":"2022-09-26T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2023-01-26T23:30:44Z","ec_funded":1,"citation":{"mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>","apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022."},"title":"Controllable states of superconducting Qubit ensembles","day":"26","alternative_title":["ISTA Thesis"],"author":[{"last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Quantum readout techniques and technologies","grant_number":"862644","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"}],"language":[{"iso":"eng"}],"ddc":["530"],"doi":"10.15479/at:ista:12132","page":"168","month":"09","date_created":"2023-01-25T09:17:02Z","supervisor":[{"last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"status":"public"}]