[{"intvolume":"        22","year":"2021","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","doi":"10.15252/embr.202051813","article_processing_charge":"Yes","publication":"EMBO Reports","date_published":"2021-09-06T00:00:00Z","abstract":[{"lang":"eng","text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate."}],"date_created":"2021-08-15T22:01:30Z","article_number":"e51813","volume":22,"oa_version":"Published Version","ddc":["580"],"publication_status":"published","has_accepted_license":"1","author":[{"first_name":"Andrea","full_name":"Vega, Andrea","last_name":"Vega"},{"first_name":"Isabel","full_name":"Fredes, Isabel","last_name":"Fredes"},{"last_name":"O’Brien","first_name":"José","full_name":"O’Brien, José"},{"first_name":"Zhouxin","full_name":"Shen, Zhouxin","last_name":"Shen"},{"full_name":"Ötvös, Krisztina","first_name":"Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Steven P.","full_name":"Briggs, Steven P.","last_name":"Briggs"},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."}],"scopus_import":"1","external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":3144854,"relation":"main_file","date_created":"2021-10-05T13:36:42Z","success":1,"file_id":"10090","creator":"cchlebak","date_updated":"2021-10-05T13:36:42Z","content_type":"application/pdf","access_level":"open_access","file_name":"2021_EmboR_Vega.pdf","checksum":"750de03dc3b715c37090126c1548ba13"}],"language":[{"iso":"eng"}],"day":"06","pmid":1,"oa":1,"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"related_material":{"record":[{"status":"public","id":"10303","relation":"dissertation_contains"}]},"department":[{"_id":"EvBe"},{"_id":"GradSch"}],"quality_controlled":"1","publisher":"Wiley","month":"09","type":"journal_article","title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"_id":"9913","isi":1,"citation":{"mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>, vol. 22, no. 9, e51813, Wiley, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>.","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. 2021;22(9). doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>.","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","ieee":"A. Vega <i>et al.</i>, “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” <i>EMBO Reports</i>, vol. 22, no. 9. Wiley, 2021.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. Wiley. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>"},"file_date_updated":"2021-10-05T13:36:42Z","date_updated":"2026-07-09T22:30:54Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_type":"original","issue":"9"},{"author":[{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","first_name":"Rashed","last_name":"Abualia"}],"publication_status":"published","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_created":"2021-11-22T14:48:21Z","file_size":28005730,"relation":"main_file","file_id":"10331","date_updated":"2022-12-20T23:30:06Z","file_name":"AbualiaPhDthesisfinalv3.pdf","access_level":"open_access","content_type":"application/pdf","creator":"rabualia","embargo":"2022-11-23","checksum":"dea38b98aa4da1cea03dcd0f10862818"},{"relation":"source_file","embargo_to":"open_access","file_size":62841883,"date_created":"2021-11-22T14:48:34Z","file_id":"10332","creator":"rabualia","file_name":"AbualiaPhDthesisfinalv3.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-12-20T23:30:06Z","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920"}],"language":[{"iso":"eng"}],"day":"22","oa":1,"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"year":"2021","abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.15479/at:ista:10303","article_processing_charge":"No","date_published":"2021-11-22T00:00:00Z","date_created":"2021-11-18T11:20:59Z","corr_author":"1","ddc":["580","581"],"supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"oa_version":"Published Version","date_updated":"2026-04-08T07:20:07Z","citation":{"apa":"Abualia, R. (2021). <i>Role of hormones in nitrate regulated growth</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>.","mla":"Abualia, Rashed. <i>Role of Hormones in Nitrate Regulated Growth</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>"},"file_date_updated":"2022-12-20T23:30:06Z","page":"139","degree_awarded":"PhD","license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"related_material":{"record":[{"status":"public","id":"47","relation":"part_of_dissertation"},{"status":"public","id":"9913","relation":"part_of_dissertation"},{"id":"9010","relation":"part_of_dissertation","status":"public"}]},"month":"11","type":"dissertation","alternative_title":["ISTA Thesis"],"title":"Role of hormones in nitrate regulated growth","status":"public","publisher":"Institute of Science and Technology Austria","_id":"10303","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"year":"2021","date_published":"2021-12-16T00:00:00Z","doi":"10.15479/AT:ISTA:10110","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"related_material":{"record":[{"id":"10816","relation":"used_for_analysis_in","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/","description":"News on IST Webpage"}]},"publisher":"IST Austria","date_created":"2021-10-08T06:44:22Z","status":"public","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","type":"software","month":"12","tmp":{"name":"GNU General Public License 3.0","short":"GPL 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html"},"ddc":["005"],"_id":"10110","file_date_updated":"2021-10-08T08:46:04Z","has_accepted_license":"1","citation":{"chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021)."},"date_updated":"2026-07-09T22:30:53Z","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","last_name":"Guzmán","first_name":"José","full_name":"Guzmán, José"},{"first_name":"Alois","full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Espinoza Martinez","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082"},{"last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0256-6529"},{"orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","full_name":"Suter, Benjamin","last_name":"Suter"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"license":"https://opensource.org/licenses/GPL-3.0","file":[{"file_id":"10114","success":1,"date_created":"2021-10-08T08:46:04Z","relation":"main_file","file_size":332990101,"checksum":"f92f8931cad0aa7e411c1715337bf408","access_level":"open_access","file_name":"patternseparation-main (1).zip","content_type":"application/x-zip-compressed","date_updated":"2021-10-08T08:46:04Z","creator":"cchlebak"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"day":"16"},{"_id":"9887","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","month":"12","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","status":"public","publisher":"National Academy of Sciences","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}],"record":[{"status":"public","id":"14988","relation":"research_data"},{"relation":"dissertation_contains","id":"14510","status":"public"}]},"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"quality_controlled":"1","issue":"51","article_type":"original","date_updated":"2026-07-09T22:31:00Z","citation":{"ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences of the United States of America. 118(51), e2113046118.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>"},"file_date_updated":"2021-12-15T08:59:40Z","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"}],"ddc":["580"],"article_number":"e2113046118","oa_version":"Published Version","volume":118,"date_created":"2021-08-11T14:11:43Z","corr_author":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1073/pnas.2113046118","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"No","date_published":"2021-12-14T00:00:00Z","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","year":"2021","intvolume":"       118","language":[{"iso":"eng"}],"day":"14","oa":1,"pmid":1,"publication_identifier":{"eissn":["1091-6490"]},"file":[{"creator":"cchlebak","file_name":"2021_PNAS_Johnson.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-12-15T08:59:40Z","checksum":"8d01e72e22c4fb1584e72d8601947069","relation":"main_file","file_size":2757340,"date_created":"2021-12-15T08:59:40Z","file_id":"10546","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"first_name":"Dana A","full_name":"Dahhan, Dana A","last_name":"Dahhan"},{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","last_name":"Zheden","full_name":"Zheden, Vanessa","first_name":"Vanessa"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","last_name":"Costanzo","full_name":"Costanzo, Tommaso","first_name":"Tommaso"},{"last_name":"Mahou","first_name":"Pierre","full_name":"Mahou, Pierre"},{"last_name":"Hrtyan","full_name":"Hrtyan, Mónika","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wang, Jie","first_name":"Jie","last_name":"Wang"},{"first_name":"Juan L","full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"last_name":"Beaurepaire","full_name":"Beaurepaire, Emmanuel","first_name":"Emmanuel"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"},{"last_name":"Bednarek","full_name":"Bednarek, Sebastian Y","first_name":"Sebastian Y"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"scopus_import":"1","external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"publication_status":"published","has_accepted_license":"1"},{"date_updated":"2024-10-09T21:00:28Z","citation":{"ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>.","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>."},"file_date_updated":"2021-09-16T22:30:03Z","page":"465-471","issue":"5","article_type":"original","department":[{"_id":"StFr"}],"quality_controlled":"1","type":"journal_article","month":"03","title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","status":"public","publisher":"Springer Nature","keyword":["General Chemistry","General Chemical Engineering"],"_id":"9250","isi":1,"author":[{"last_name":"Petit","full_name":"Petit, Yann K.","first_name":"Yann K."},{"last_name":"Mourad","first_name":"Eléonore","full_name":"Mourad, Eléonore"},{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"last_name":"Leypold","first_name":"Christian","full_name":"Leypold, Christian"},{"last_name":"Windischbacher","first_name":"Andreas","full_name":"Windischbacher, Andreas"},{"last_name":"Mijailovic","full_name":"Mijailovic, Daniel","first_name":"Daniel"},{"first_name":"Christian","full_name":"Slugovc, Christian","last_name":"Slugovc"},{"first_name":"Sergey M.","full_name":"Borisov, Sergey M.","last_name":"Borisov"},{"full_name":"Zojer, Egbert","first_name":"Egbert","last_name":"Zojer"},{"last_name":"Brutti","full_name":"Brutti, Sergio","first_name":"Sergio"},{"full_name":"Fontaine, Olivier","first_name":"Olivier","last_name":"Fontaine"},{"last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319"}],"external_id":{"isi":["000629296400001"],"pmid":["33723377"]},"scopus_import":"1","publication_status":"published","has_accepted_license":"1","file":[{"date_created":"2021-03-22T11:46:00Z","relation":"main_file","file_size":1811448,"file_id":"9276","content_type":"application/pdf","access_level":"open_access","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","date_updated":"2021-09-16T22:30:03Z","creator":"dernst","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","embargo":"2021-09-15"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"15","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"pmid":1,"oa":1,"acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","year":"2021","intvolume":"        13","abstract":[{"text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.","lang":"eng"}],"doi":"10.1038/s41557-021-00643-z","acknowledged_ssus":[{"_id":"M-Shop"}],"publication":"Nature Chemistry","article_processing_charge":"No","date_published":"2021-03-15T00:00:00Z","date_created":"2021-03-16T11:12:20Z","corr_author":"1","ddc":["540"],"oa_version":"Submitted Version","volume":13},{"ec_funded":1,"page":"2947–2967","file_date_updated":"2021-12-02T23:30:05Z","citation":{"ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. 2021;16(6):2947–2967. doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” <i>Nature Protocols</i>, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021."},"date_updated":"2025-04-22T22:30:43Z","article_type":"original","issue":"6","quality_controlled":"1","department":[{"_id":"PeJo"}],"isi":1,"_id":"9438","publisher":"Springer Nature","status":"public","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","month":"06","type":"journal_article","has_accepted_license":"1","publication_status":"published","external_id":{"isi":["000650528700003"],"pmid":["33990799"]},"scopus_import":"1","author":[{"orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","first_name":"David H","last_name":"Vandael"},{"last_name":"Okamoto","full_name":"Okamoto, Yuji","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094"},{"first_name":"Carolina","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M","first_name":"Victor M","last_name":"Vargas Barroso"},{"orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","full_name":"Suter, Benjamin","last_name":"Suter"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"oa":1,"pmid":1,"publication_identifier":{"issn":["1754-2189"],"eissn":["1750-2799"]},"day":"01","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"9639","file_size":38574802,"relation":"main_file","date_created":"2021-07-08T12:27:55Z","embargo":"2021-12-01","checksum":"7eb580abd8893cdb0b410cf41bc8c263","creator":"cziletti","date_updated":"2021-12-02T23:30:05Z","content_type":"application/pdf","file_name":"VandaeletalAuthorVersion2021.pdf","access_level":"open_access"}],"article_processing_charge":"No","date_published":"2021-06-01T00:00:00Z","publication":"Nature Protocols","acknowledged_ssus":[{"_id":"M-Shop"}],"doi":"10.1038/s41596-021-00526-0","abstract":[{"text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.","lang":"eng"}],"intvolume":"        16","year":"2021","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","oa_version":"Submitted Version","volume":16,"project":[{"grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF"},{"name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739","call_identifier":"FWF"}],"ddc":["570"],"corr_author":"1","date_created":"2021-05-30T22:01:24Z"},{"article_type":"review","issue":"6","page":"675–685","ec_funded":1,"citation":{"ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” <i>Nature Physics</i>, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","apa":"Serbyn, M., Abanin, D. A., &#38; Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. 2021;17(6):675–685. doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>."},"file_date_updated":"2021-12-02T23:30:03Z","date_updated":"2025-04-14T07:52:09Z","_id":"9428","isi":1,"publisher":"Nature Research","type":"journal_article","month":"06","title":"Quantum many-body scars and weak breaking of ergodicity","status":"public","department":[{"_id":"MaSe"}],"quality_controlled":"1","language":[{"iso":"eng"}],"day":"01","oa":1,"publication_identifier":{"eissn":["1745-2481"]},"file":[{"embargo":"2021-12-01","checksum":"316ed42ea1b42b0f1a3025bb476266fc","date_updated":"2021-12-02T23:30:03Z","file_name":"RevisedQMBSreview.pdf","content_type":"application/pdf","access_level":"open_access","creator":"patrickd","file_id":"10026","date_created":"2021-09-20T09:27:43Z","file_size":10028836,"relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","has_accepted_license":"1","author":[{"last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A.","first_name":"Dmitry A."},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"scopus_import":"1","oa_version":"Preprint","volume":17,"ddc":["539"],"project":[{"call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"date_created":"2021-05-28T09:03:50Z","doi":"10.1038/s41567-021-01230-2","article_processing_charge":"No","publication":"Nature Physics","date_published":"2021-06-01T00:00:00Z","abstract":[{"text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology.","lang":"eng"}],"year":"2021","intvolume":"        17","arxiv":1,"acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015."},{"publication_status":"published","has_accepted_license":"1","author":[{"first_name":"Karla","full_name":"Huljev, Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"file":[{"relation":"source_file","embargo_to":"open_access","file_size":47799741,"date_created":"2021-05-17T12:29:12Z","file_id":"9398","creator":"khuljev","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"KHuljev_Thesis_corrections.docx","date_updated":"2022-05-21T22:30:04Z","checksum":"7f98532f5324a0b2f3fa8de2967baa19"},{"date_created":"2021-05-18T14:50:28Z","relation":"main_file","file_size":16542131,"file_id":"9401","content_type":"application/pdf","access_level":"open_access","file_name":"new_KHuljev_Thesis_corrections.pdf","date_updated":"2022-05-21T22:30:04Z","creator":"khuljev","checksum":"bf512f8a1e572a543778fc4b227c01ba","embargo":"2022-05-20"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"18","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"oa":1,"OA_place":"publisher","year":"2021","doi":"10.15479/at:ista:9397","article_processing_charge":"No","date_published":"2021-05-18T00:00:00Z","abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"corr_author":"1","date_created":"2021-05-17T12:31:30Z","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"oa_version":"Published Version","ddc":["571"],"citation":{"ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>."},"file_date_updated":"2022-05-21T22:30:04Z","date_updated":"2026-04-08T07:12:51Z","page":"101","degree_awarded":"PhD","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"type":"dissertation","month":"05","status":"public","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","_id":"9397"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"month":"01","status":"public","title":"Parameterized and algebro-geometric advances in static program analysis","publisher":"Institute of Science and Technology Austria","_id":"8934","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"related_material":{"record":[{"status":"public","id":"6490","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6780"},{"status":"public","relation":"part_of_dissertation","id":"7158"},{"status":"public","relation":"part_of_dissertation","id":"66"},{"id":"6378","relation":"part_of_dissertation","status":"public"},{"id":"311","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"6175","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6340","status":"public"},{"id":"7014","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6009"},{"id":"1437","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8728","status":"public"},{"status":"public","id":"8089","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6380"},{"id":"5977","relation":"part_of_dissertation","status":"public"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"639","status":"public"},{"relation":"part_of_dissertation","id":"1386","status":"public"},{"status":"public","id":"6918","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7810"},{"id":"949","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2026-04-16T10:07:18Z","citation":{"ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>"},"file_date_updated":"2021-12-23T23:30:04Z","page":"278","degree_awarded":"PhD","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2020-12-10T12:17:07Z","corr_author":"1","project":[{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"ddc":["005"],"oa_version":"Published Version","supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","year":"2021","abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"doi":"10.15479/AT:ISTA:8934","article_processing_charge":"No","date_published":"2021-01-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"embargo":"2021-12-22","checksum":"d1b9db3725aed34dadd81274aeb9426c","date_updated":"2021-12-23T23:30:04Z","content_type":"application/pdf","access_level":"open_access","file_name":"Thesis-pdfa.pdf","creator":"akafshda","file_id":"8969","date_created":"2020-12-22T20:08:44Z","file_size":5251507,"relation":"main_file"},{"embargo_to":"open_access","relation":"source_file","file_size":10636756,"date_created":"2020-12-22T20:08:50Z","file_id":"8970","creator":"akafshda","file_name":"source.zip","access_level":"closed","content_type":"application/zip","date_updated":"2021-03-04T23:30:04Z","checksum":"1661df7b393e6866d2460eba3c905130"}],"day":"01","language":[{"iso":"eng"}],"OA_place":"publisher","oa":1,"publication_identifier":{"issn":["2663-337X"]},"author":[{"last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"publication_status":"published","has_accepted_license":"1"},{"degree_awarded":"PhD","page":"118","date_updated":"2026-04-16T08:43:20Z","file_date_updated":"2022-07-29T22:30:05Z","citation":{"ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>."},"_id":"9728","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Transition to turbulence and drag reduction in particle-laden pipe flows","status":"public","month":"07","type":"dissertation","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6189"}]},"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","oa":1,"language":[{"iso":"eng"}],"day":"29","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"relation":"source_file","embargo_to":"open_access","file_size":22859658,"date_created":"2021-07-28T13:32:02Z","file_id":"9744","creator":"nagrawal","content_type":"application/x-zip-compressed","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","access_level":"closed","date_updated":"2022-07-29T22:30:05Z","checksum":"77436be3563a90435024307b1b5ee7e8"},{"file_size":18658048,"relation":"main_file","date_created":"2021-07-28T13:32:05Z","file_id":"9745","creator":"nagrawal","date_updated":"2022-07-29T22:30:05Z","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","access_level":"open_access","content_type":"application/pdf","embargo":"2022-07-28","checksum":"72a891d7daba85445c29b868c22575ed"}],"author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","first_name":"Nishchal","full_name":"Agrawal, Nishchal","last_name":"Agrawal"}],"has_accepted_license":"1","publication_status":"published","ddc":["532"],"oa_version":"Published Version","supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof"}],"date_created":"2021-07-27T13:40:30Z","corr_author":"1","abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"date_published":"2021-07-29T00:00:00Z","article_processing_charge":"No","doi":"10.15479/at:ista:9728","acknowledged_ssus":[{"_id":"M-Shop"}],"year":"2021"},{"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"_id":"9992","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"month":"09","type":"dissertation","status":"public","title":"Wound healing in the Arabidopsis root meristem","related_material":{"record":[{"status":"public","id":"6943","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8002","status":"public"},{"id":"6351","relation":"part_of_dissertation","status":"public"}]},"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"page":"168","ec_funded":1,"degree_awarded":"PhD","citation":{"ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>."},"file_date_updated":"2021-09-15T22:30:26Z","date_updated":"2026-04-08T07:11:47Z","oa_version":"Published Version","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"}],"ddc":["575"],"project":[{"call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"corr_author":"1","date_created":"2021-09-09T07:37:20Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/at:ista:9992","date_published":"2021-09-13T00:00:00Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"year":"2021","language":[{"iso":"eng"}],"day":"13","oa":1,"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","file":[{"date_created":"2021-09-09T07:29:48Z","relation":"source_file","embargo_to":"open_access","file_size":25179004,"file_id":"9993","file_name":"Thesis_vupload.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2021-09-15T22:30:26Z","creator":"lhoermaye","checksum":"c763064adaa720e16066c1a4f9682bbb"},{"embargo":"2021-09-09","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","date_updated":"2021-09-15T22:30:26Z","content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_vfinal_pdfa.pdf","creator":"lhoermaye","file_id":"9996","date_created":"2021-09-09T14:25:08Z","file_size":6246900,"relation":"main_file"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","has_accepted_license":"1","author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","first_name":"Lukas"}]},{"author":[{"first_name":"Andi H","full_name":"Hansen, Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","publication_status":"published","oa":1,"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","language":[{"iso":"eng"}],"day":"02","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_updated":"2022-09-03T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Hansen.docx","access_level":"closed","creator":"ahansen","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","date_created":"2021-08-30T09:17:39Z","file_size":10629190,"relation":"source_file","embargo_to":"open_access","file_id":"9971"},{"file_id":"9972","date_created":"2021-08-30T09:29:44Z","relation":"main_file","file_size":13457469,"checksum":"204fa40321a1c6289b68c473634c4bf3","embargo":"2022-09-02","content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Hansen_PDFA-1a.pdf","date_updated":"2022-09-03T22:30:04Z","creator":"ahansen"}],"abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"date_published":"2021-09-02T00:00:00Z","article_processing_charge":"No","doi":"10.15479/at:ista:9962","year":"2021","project":[{"name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"ddc":["570"],"oa_version":"Published Version","supervisor":[{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"}],"date_created":"2021-08-29T12:36:50Z","corr_author":"1","degree_awarded":"PhD","page":"182","date_updated":"2026-04-08T07:19:09Z","file_date_updated":"2022-09-03T22:30:04Z","citation":{"apa":"Hansen, A. H. (2021). <i>Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>","mla":"Hansen, Andi H. <i>Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>."},"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"related_material":{"record":[{"id":"8569","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"960","relation":"part_of_dissertation"}]},"_id":"9962","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","status":"public","month":"09","type":"dissertation","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"]},{"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"_id":"9623","publisher":"Institute of Science and Technology Austria","type":"dissertation","month":"07","alternative_title":["ISTA Thesis"],"status":"public","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9006"},{"relation":"part_of_dissertation","id":"9750","status":"public"}]},"page":"111","degree_awarded":"PhD","citation":{"apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>.","mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>"},"file_date_updated":"2022-07-02T22:30:06Z","date_updated":"2026-07-06T12:45:39Z","supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"oa_version":"Published Version","ddc":["570"],"corr_author":"1","date_created":"2021-07-01T14:50:17Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"doi":"10.15479/at:ista:9623","date_published":"2021-07-01T00:00:00Z","article_processing_charge":"No","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"year":"2021","language":[{"iso":"eng"}],"OA_place":"publisher","oa":1,"publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"creator":"scaballe","access_level":"closed","file_name":"PhDThesis_SCM.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-07-02T22:30:06Z","checksum":"e039225a47ef32666d59bf35ddd30ecf","embargo_to":"open_access","relation":"source_file","file_size":131946790,"date_created":"2021-07-01T14:48:54Z","file_id":"9624"},{"embargo":"2022-07-01","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","date_updated":"2022-07-02T22:30:06Z","content_type":"application/pdf","access_level":"open_access","file_name":"PhDThesis_SCM.pdf","creator":"scaballe","file_id":"9625","date_created":"2021-07-01T14:46:25Z","file_size":17094958,"relation":"main_file"}],"publication_status":"published","has_accepted_license":"1","author":[{"orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo"}]},{"date_updated":"2026-07-06T12:48:19Z","citation":{"chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>.","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."},"file_date_updated":"2022-12-20T23:30:05Z","page":"73","degree_awarded":"PhD","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"related_material":{"record":[{"status":"public","id":"10316","relation":"part_of_dissertation"}]},"type":"dissertation","month":"11","alternative_title":["ISTA Thesis"],"status":"public","title":"Pathogenic Escherichia coli hijack the host immune response","publisher":"Institute of Science and Technology Austria","_id":"10307","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin"}],"publication_status":"published","has_accepted_license":"1","file":[{"date_created":"2021-11-18T15:07:31Z","relation":"main_file","file_size":13266088,"file_id":"10308","file_name":"ThesisTomasekKathrin.pdf","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek","checksum":"b39c9e0ef18d0484d537a67551effd02","embargo":"2022-11-18"},{"checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"ThesisTomasekKathrin.docx","file_id":"10309","file_size":7539509,"relation":"source_file","embargo_to":"open_access","date_created":"2021-11-18T15:07:46Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"day":"18","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","oa":1,"year":"2021","abstract":[{"text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response.","lang":"eng"}],"doi":"10.15479/at:ista:10307","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"date_published":"2021-11-18T00:00:00Z","article_processing_charge":"No","date_created":"2021-11-18T15:05:06Z","corr_author":"1","ddc":["570"],"supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet"}],"oa_version":"Published Version"},{"_id":"9006","isi":1,"month":"01","type":"journal_article","title":"Cytoplasm's got moves","status":"public","publisher":"Elsevier","related_material":{"record":[{"status":"public","id":"9623","relation":"dissertation_contains"}]},"department":[{"_id":"CaHe"}],"quality_controlled":"1","issue":"2","article_type":"original","page":"P213-226","date_updated":"2026-07-09T22:31:23Z","citation":{"ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” <i>Developmental Cell</i>, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","apa":"Shamipour, S., Caballero Mancebo, S., &#38; Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. <i>Developmental Cell</i>. 2021;56(2):P213-226. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>."},"ddc":["570"],"oa_version":"Published Version","volume":56,"date_created":"2021-01-17T23:01:10Z","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2020.12.002","open_access":"1"}],"corr_author":"1","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.","lang":"eng"}],"doi":"10.1016/j.devcel.2020.12.002","publication":"Developmental Cell","article_processing_charge":"No","date_published":"2021-01-25T00:00:00Z","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","intvolume":"        56","year":"2021","language":[{"iso":"eng"}],"day":"25","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"oa":1,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Shayan","full_name":"Shamipour, Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","last_name":"Caballero Mancebo"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"scopus_import":"1","publication_status":"published"},{"date_updated":"2026-07-09T22:31:23Z","author":[{"last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X"},{"first_name":"Alexander F","full_name":"Leithner, Alexander F","last_name":"Leithner","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","full_name":"Glatzová, Ivana","first_name":"Ivana","last_name":"Glatzová"},{"last_name":"Lukesch","first_name":"Michael S.","full_name":"Lukesch, Michael S."},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"},{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"das_tickbox":"1","citation":{"mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>bioRxiv</i>. ."},"publication_status":"draft","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"day":"18","language":[{"iso":"eng"}],"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","year":"2021","abstract":[{"text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.","lang":"eng"}],"department":[{"_id":"CaGu"},{"_id":"MiSi"}],"related_material":{"record":[{"status":"public","id":"11843","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"10307"}]},"publication":"bioRxiv","article_processing_charge":"No","date_published":"2021-10-18T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"doi":"10.1101/2021.10.18.464770","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","status":"public","date_created":"2021-11-19T12:24:16Z","type":"preprint","month":"10","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1","open_access":"1"}],"corr_author":"1","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","grant_number":"724373"},{"name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","call_identifier":"FWF"}],"_id":"10316","oa_version":"Preprint"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","language":[{"iso":"eng"}],"oa":1,"citation":{"chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. .","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.)."},"publication_status":"draft","das_tickbox":"1","author":[{"orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","full_name":"Savin, Cristina","last_name":"Savin"}],"date_updated":"2026-07-09T22:31:22Z","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"month":"09","type":"preprint","status":"public","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","date_created":"2021-10-04T06:23:34Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"oa_version":"Preprint","_id":"10077","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281511"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"year":"2021","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","doi":"10.1101/2021.09.28.460602","article_processing_charge":"No","publication":"bioRxiv","date_published":"2021-09-29T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"11932","status":"public"},{"id":"14656","relation":"later_version","status":"public"}]},"department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"6ebcb79999f889766f7cd79ee134ad28","creator":"cziletti","file_name":"2021_eLife_Bhandari.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-05-31T09:43:09Z","file_id":"9440","success":1,"relation":"main_file","file_size":8174719,"date_created":"2021-05-31T09:43:09Z"}],"pmid":1,"publication_identifier":{"eissn":["2050-084X"]},"oa":1,"day":"29","language":[{"iso":"eng"}],"external_id":{"pmid":["33913808"],"isi":["000651761700001"]},"scopus_import":"1","author":[{"first_name":"Pradeep","full_name":"Bhandari, Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","last_name":"Vandael","full_name":"Vandael, David H","first_name":"David H"},{"first_name":"Diego","full_name":"Fernández-Fernández, Diego","last_name":"Fernández-Fernández"},{"last_name":"Fritzius","full_name":"Fritzius, Thorsten","first_name":"Thorsten"},{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David","full_name":"Kleindienst, David"},{"last_name":"Önal","full_name":"Önal, Hüseyin C","first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2771-2011"},{"first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gassmann, Martin","first_name":"Martin","last_name":"Gassmann"},{"last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"full_name":"Kulik, Akos","first_name":"Akos","last_name":"Kulik"},{"last_name":"Bettler","full_name":"Bettler, Bernhard","first_name":"Bernhard"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"},{"first_name":"Peter","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","publication_status":"published","date_created":"2021-05-30T22:01:23Z","project":[{"call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","grant_number":"692692"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"ddc":["570"],"oa_version":"Published Version","volume":10,"article_number":"e68274","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","intvolume":"        10","year":"2021","abstract":[{"text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation.","lang":"eng"}],"date_published":"2021-04-29T00:00:00Z","article_processing_charge":"No","publication":"eLife","doi":"10.7554/ELIFE.68274","article_type":"original","date_updated":"2026-07-09T22:31:25Z","file_date_updated":"2021-05-31T09:43:09Z","citation":{"ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal C, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","ieee":"P. Bhandari <i>et al.</i>, “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>, vol. 10, e68274, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>.","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Cihan Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>."},"ec_funded":1,"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","status":"public","type":"journal_article","month":"04","publisher":"eLife Sciences Publications","isi":1,"_id":"9437","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"quality_controlled":"1","department":[{"_id":"RySh"},{"_id":"PeJo"}],"related_material":{"record":[{"id":"19271","relation":"dissertation_contains","status":"public"},{"id":"9562","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://doi.org/10.1101/2020.04.16.045112","relation":"earlier_version"}]}},{"supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"oa_version":"Published Version","ddc":["570"],"corr_author":"1","date_created":"2021-06-17T14:10:47Z","article_processing_charge":"No","date_published":"2021-06-01T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.15479/at:ista:9562","abstract":[{"lang":"eng","text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry."}],"year":"2021","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","oa":1,"day":"01","language":[{"iso":"eng"}],"file":[{"file_id":"9563","file_size":77299142,"relation":"main_file","date_created":"2021-06-17T14:03:14Z","embargo":"2022-07-01","checksum":"659df5518db495f679cb1df9e9bd1d94","creator":"dkleindienst","date_updated":"2022-07-02T22:30:04Z","file_name":"Thesis.pdf","access_level":"open_access","content_type":"application/pdf"},{"creator":"dkleindienst","date_updated":"2022-07-02T22:30:04Z","file_name":"Thesis_source.zip","access_level":"closed","content_type":"application/zip","checksum":"3bcf63a2b19e5b6663be051bea332748","file_size":369804895,"embargo_to":"open_access","relation":"source_file","date_created":"2021-06-17T14:04:30Z","file_id":"9564"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","publication_status":"published","author":[{"last_name":"Kleindienst","full_name":"Kleindienst, David","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"_id":"9562","publisher":"Institute of Science and Technology Austria","status":"public","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","alternative_title":["ISTA Thesis"],"type":"dissertation","month":"06","related_material":{"record":[{"id":"9437","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"612","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8532","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9756"}]},"department":[{"_id":"GradSch"},{"_id":"RySh"}],"degree_awarded":"PhD","page":"124","file_date_updated":"2022-07-02T22:30:04Z","citation":{"ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). <i>2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>","mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>."},"date_updated":"2026-07-06T13:11:44Z"},{"quality_controlled":"1","related_material":{"record":[{"id":"9562","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"series_title":"Neuromethods","_id":"9756","publisher":"Humana Press","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"status":"public","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","type":"book_chapter","alternative_title":["Neuromethods"],"month":"07","place":"New York","ec_funded":1,"page":"267-283","citation":{"chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i>Receptor and Ion Channel Detection in the Brain</i>, 169:267–83. Neuromethods. New York: Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, vol. 169, Humana Press, 2021, pp. 267–83, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Vol 169. Neuromethods. New York: Humana Press; 2021:267-283. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>","apa":"Kaufmann, W., Kleindienst, D., Harada, H., &#38; Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (Vol. 169, pp. 267–283). New York: Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, vol. 169, New York: Humana Press, 2021, pp. 267–283.","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana Press, New York, 2021, pp. 267–283.","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283."},"date_updated":"2026-07-09T22:31:25Z","date_published":"2021-07-27T00:00:00Z","article_processing_charge":"No","publication":"Receptor and Ion Channel Detection in the Brain","doi":"10.1007/978-1-0716-1522-5_19","abstract":[{"lang":"eng","text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms."}],"year":"2021","intvolume":"       169","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","oa_version":"None","volume":169,"project":[{"grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1","grant_number":"720270","call_identifier":"H2020"}],"ddc":["573"],"corr_author":"1","date_created":"2021-07-30T09:34:56Z","has_accepted_license":"1","das_tickbox":"1","publication_status":"published","scopus_import":"1","author":[{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter","first_name":"Walter"},{"first_name":"David","full_name":"Kleindienst, David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Harada","first_name":"Harumi","full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"}],"publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"language":[{"iso":"eng"}],"day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]