[{"volume":5,"publication":"STAR Protocols","abstract":[{"text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1","lang":"eng"}],"acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","status":"public","language":[{"iso":"eng"}],"intvolume":"         5","quality_controlled":"1","issue":"3","article_number":"103168","external_id":{"pmid":["38968076"]},"publisher":"Elsevier","article_processing_charge":"Yes","_id":"17232","author":[{"orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"first_name":"Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","date_published":"2024-09-20T00:00:00Z","has_accepted_license":"1","year":"2024","publication_status":"published","day":"20","APC_amount":"804 EUR","article_type":"original","OA_type":"gold","file_date_updated":"2025-01-09T12:16:53Z","file":[{"relation":"main_file","date_created":"2025-01-09T12:16:53Z","date_updated":"2025-01-09T12:16:53Z","file_name":"2024_STARProtoc_Cheung2.pdf","file_size":6445556,"file_id":"18810","checksum":"464f52ecc6ec92f509552823bb82bf79","content_type":"application/pdf","creator":"dernst","success":1,"access_level":"open_access"}],"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","citation":{"apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168."},"publication_identifier":{"eissn":["2666-1667"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"OA_place":"publisher","scopus_import":"1","oa":1,"type":"journal_article","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"pmid":1,"ddc":["570"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","month":"09","date_updated":"2025-12-30T10:54:12Z","date_created":"2024-07-14T22:01:10Z","doi":"10.1016/j.xpro.2024.103168"},{"article_processing_charge":"No","_id":"18688","publication":"bioRxiv","abstract":[{"lang":"eng","text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits."}],"acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","language":[{"iso":"eng"}],"status":"public","year":"2024","publication_status":"draft","title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","author":[{"full_name":"Watson, Jake F.","first_name":"Jake F.","last_name":"Watson"},{"first_name":"Victor","last_name":"Vargas-Barroso","full_name":"Vargas-Barroso, Victor"},{"full_name":"Morse-Mora, Rebecca J.","first_name":"Rebecca J.","last_name":"Morse-Mora"},{"full_name":"Navas-Olive, Andrea","first_name":"Andrea","last_name":"Navas-Olive"},{"first_name":"Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Tomschik, Matthias","first_name":"Matthias","last_name":"Tomschik"},{"first_name":"Karl","last_name":"Rössler","full_name":"Rössler, Karl"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"date_published":"2024-05-02T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"citation":{"ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>.","short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).","ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>"},"fulldoi":"https://doi.org/10.1101/2024.05.02.592169","OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.1101/2024.05.02.592169","open_access":"1"}],"oa":1,"day":"02","oa_version":"Preprint","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","date_updated":"2026-07-28T08:33:51Z","doi":"10.1101/2024.05.02.592169","date_created":"2024-12-19T11:35:08Z","type":"preprint","ec_funded":1,"department":[{"_id":"JoDa"},{"_id":"PeJo"}],"project":[{"grant_number":"101026635","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"}],"related_material":{"record":[{"id":"18879","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"18681"}]}},{"related_material":{"record":[{"id":"11160","status":"public","relation":"part_of_dissertation"},{"id":"18688","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18677"},{"status":"public","relation":"part_of_dissertation","id":"18689"}]},"project":[{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"page":"230","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"type":"dissertation","date_created":"2024-12-19T02:30:39Z","date_updated":"2026-07-28T08:33:52Z","doi":"10.15479/at:ista:18681","month":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","corr_author":"1","ddc":["600","570"],"oa_version":"Published Version","file":[{"creator":"mtavakol","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"b61651d417cafddd740a8528f46068c5","file_id":"18699","file_name":"Thesis_Mojtaba Tavakoli_.docx","file_size":118593521,"date_created":"2024-12-20T10:23:17Z","date_updated":"2024-12-20T10:31:37Z","relation":"source_file","access_level":"closed"},{"date_updated":"2026-07-28T08:33:51Z","date_created":"2024-12-20T10:25:12Z","relation":"main_file","file_id":"18700","file_name":"Thesis_Mojtaba Tavakoli_.pdf","file_size":63885521,"embargo":"2027-08-01","checksum":"c80bcfd1a34c23afc3538052325283e5","creator":"mtavakol","content_type":"application/pdf","access_level":"closed","embargo_to":"open_access"}],"doi_confirm":"1","file_date_updated":"2026-07-28T08:33:51Z","day":"20","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"fulldoi":"https://doi.org/10.15479/at:ista:18681","citation":{"short":"M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024.","chicago":"Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>.","ista":"Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.","ieee":"M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.","mla":"Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>.","apa":"Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>","ama":"Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>"},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-048-0"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G"}],"date_published":"2024-12-20T00:00:00Z","title":"Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy","author":[{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","first_name":"Mojtaba","orcid":"0000-0002-7667-6854"}],"OA_embargo":"20","publication_status":"published","year":"2024","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","_id":"18681","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","das_tickbox":"1","alternative_title":["ISTA Thesis"]},{"file":[{"access_level":"open_access","file_id":"15354","file_name":"Murmann_Thesis_final_2024_2.pdf","embargo":"2025-05-02","file_size":5936142,"date_updated":"2025-05-02T22:30:04Z","date_created":"2024-05-02T12:26:13Z","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","checksum":"095817a6c944954ac3f277e547031a33"},{"content_type":"application/x-zip-compressed","creator":"cchlebak","checksum":"43b632255372973a437ac87739cfd4db","file_size":20645510,"file_name":"Murmann_Thesis_final_2024.zip","file_id":"15355","date_created":"2024-05-02T12:37:56Z","date_updated":"2025-05-02T22:30:04Z","relation":"source_file","embargo_to":"open_access","access_level":"closed"}],"file_date_updated":"2025-05-02T22:30:04Z","day":"02","oa":1,"OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"supervisor":[{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert"}],"fulldoi":"https://doi.org/10.15479/at:ista:15352","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"citation":{"ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>."},"publication_identifier":{"issn":["2791-4585"]},"page":"54","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"type":"dissertation","doi":"10.15479/at:ista:15352","date_updated":"2026-04-07T13:05:00Z","date_created":"2024-05-02T08:31:38Z","month":"05","ddc":["570"],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","abstract":[{"text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. ","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","_id":"15352","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","degree_awarded":"MS","alternative_title":["ISTA Master's Thesis"],"date_published":"2024-05-02T00:00:00Z","author":[{"id":"1d390868-f128-11eb-9611-a0ca5f7833b5","full_name":"Murmann, Julie Stefanie","last_name":"Murmann","first_name":"Julie Stefanie"}],"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","publication_status":"published","has_accepted_license":"1","year":"2024"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"fulldoi":"https://doi.org/10.1016/j.neuron.2023.12.002","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"citation":{"chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>"},"oa":1,"scopus_import":"1","OA_place":"publisher","PlanS_conform":"1","OA_type":"hybrid","article_type":"original","day":"06","file":[{"success":1,"access_level":"open_access","date_created":"2025-04-23T14:02:08Z","date_updated":"2025-04-23T14:02:08Z","relation":"main_file","file_size":8192355,"file_name":"2024_Neuron_Chen.pdf","file_id":"19614","checksum":"30098b4f0209556ddfb3540a23d07ca5","content_type":"application/pdf","creator":"dernst"}],"file_date_updated":"2025-04-23T14:02:08Z","month":"03","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa_version":"Published Version","date_created":"2024-01-21T23:00:56Z","date_updated":"2026-09-12T22:30:35Z","doi":"10.1016/j.neuron.2023.12.002","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"ec_funded":1,"type":"journal_article","related_material":{"record":[{"id":"15101","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}]},"pmid":1,"page":"755-771.e9","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383"}],"external_id":{"isi":["001202925700001"],"pmid":["38215739"]},"issue":"5","quality_controlled":"1","_id":"14843","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","publication":"Neuron","volume":112,"status":"public","language":[{"iso":"eng"}],"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","intvolume":"       112","abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"publication_status":"published","year":"2024","has_accepted_license":"1","isi":1,"author":[{"first_name":"JingJing","last_name":"Chen","full_name":"Chen, JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chong","first_name":"Chong","last_name":"Chen"},{"full_name":"Arai, Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru","last_name":"Arai"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena","last_name":"Kim","orcid":"0000-0003-2344-1039","first_name":"Olena"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","date_published":"2024-03-06T00:00:00Z"},{"status":"public","language":[{"iso":"eng"}],"abstract":[{"text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","_id":"18471","author":[{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","first_name":"Nathalie"}],"title":"Visualizing the neuronal transcriptional landscape with tissue context","date_published":"2024-10-28T00:00:00Z","year":"2024","has_accepted_license":"1","publication_status":"published","day":"28","file_date_updated":"2025-05-05T22:30:04Z","file":[{"checksum":"6d7c7725d040d8debc070dcb35ac965d","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"nagudelo","relation":"source_file","date_updated":"2025-05-05T22:30:04Z","date_created":"2024-10-26T22:29:06Z","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","file_size":183077763,"file_id":"18475","access_level":"closed","embargo_to":"open_access"},{"access_level":"open_access","file_id":"18476","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","embargo":"2025-05-05","file_size":47027710,"relation":"main_file","date_created":"2024-10-26T23:13:33Z","date_updated":"2025-05-05T22:30:04Z","creator":"nagudelo","content_type":"application/pdf","checksum":"52f9c0bf2bdafa3baf827b73814a53ff"}],"fulldoi":"https://doi.org/10.15479/at:ista:18471","supervisor":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-044-2"],"issn":["2663-337X"]},"citation":{"ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","oa":1,"type":"dissertation","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"ec_funded":1,"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","name":"Molecular Drug Targets"}],"page":"97","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","ddc":["570"],"month":"10","doi":"10.15479/at:ista:18471","date_updated":"2026-04-14T08:34:37Z","date_created":"2024-10-26T20:02:42Z"},{"related_material":{"record":[{"id":"12349","relation":"part_of_dissertation","status":"public"},{"relation":"research_data","status":"public","id":"12370"}]},"page":"86","project":[{"grant_number":"101086580","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"}],"ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"type":"dissertation","date_updated":"2026-04-07T13:24:48Z","doi":"10.15479/at:ista:18574","date_created":"2024-11-20T21:30:44Z","month":"11","oa_version":"Published Version","ddc":["573"],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"access_level":"closed","embargo_to":"open_access","date_created":"2024-11-25T14:44:03Z","date_updated":"2025-11-11T23:30:02Z","relation":"source_file","file_name":"PhD Thesis - Divyansh Gupta.zip","file_size":75512262,"file_id":"18589","checksum":"ebb000d361c36b22ed6e639a931c6b7c","content_type":"application/zip","creator":"dgupta"},{"access_level":"open_access","checksum":"1282401eb71598bc311058b0fcefc6a1","content_type":"application/pdf","creator":"dgupta","relation":"main_file","date_updated":"2025-11-11T23:30:02Z","date_created":"2024-11-26T11:43:19Z","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","file_size":6412619,"embargo":"2025-11-11","file_id":"18591"}],"file_date_updated":"2025-11-11T23:30:02Z","day":"22","oa":1,"OA_place":"publisher","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"fulldoi":"https://doi.org/10.15479/at:ista:18574","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"supervisor":[{"last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"}],"publication_identifier":{"isbn":["978-3-99078-050-3"],"issn":["2663-337X"]},"citation":{"mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>.","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria."},"date_published":"2024-11-22T00:00:00Z","OA_embargo":"12","title":"Visual adaptations to natural statistics","author":[{"first_name":"Divyansh","orcid":"0000-0001-7400-6665","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Divyansh"}],"publication_status":"published","has_accepted_license":"1","year":"2024","abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","language":[{"iso":"eng"}],"acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","status":"public","_id":"18574","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","alternative_title":["ISTA Thesis"]},{"day":"01","article_type":"original","file_date_updated":"2025-01-01T23:30:03Z","file":[{"relation":"main_file","date_updated":"2025-01-01T23:30:03Z","date_created":"2024-05-14T11:57:56Z","file_name":"megacomplex_submit_NSMB_withFigures.pdf","file_size":24424729,"embargo":"2025-01-01","file_id":"15392","checksum":"21f05d188762acd7f49a97f3d09c8d9f","content_type":"application/pdf","creator":"lsazanov","access_level":"open_access"}],"fulldoi":"https://doi.org/10.1038/s41594-024-01255-0","citation":{"short":"I. Vercellino, L.A. Sazanov, Nature Structural and Molecular Biology 31 (2024) 1061–1071.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>.","ista":"Vercellino I, Sazanov LA. 2024. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 31, 1061–1071.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2024). SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>","mla":"Vercellino, Irene, and Leonid A. Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1061–71, doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>.","ieee":"I. Vercellino and L. A. Sazanov, “SCAF1 drives the compositional diversity of mammalian respirasomes,” <i>Nature Structural and Molecular Biology</i>, vol. 31. Springer Nature, pp. 1061–1071, 2024.","ama":"Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. 2024;31:1061-1071. doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>"},"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"ScienComp"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"type":"journal_article","ec_funded":1,"department":[{"_id":"LeSa"}],"project":[{"call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines"}],"page":"1061-1071","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41594-025-01721-3"}]},"pmid":1,"oa_version":"Submitted Version","ddc":["572"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","month":"07","date_updated":"2025-11-24T08:35:04Z","date_created":"2024-04-14T22:01:03Z","doi":"10.1038/s41594-024-01255-0","volume":31,"publication":"Nature Structural and Molecular Biology","abstract":[{"text":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.","lang":"eng"}],"language":[{"iso":"eng"}],"acknowledgement":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.","status":"public","intvolume":"        31","quality_controlled":"1","external_id":{"pmid":["38575788"],"isi":["001196897300001"]},"publisher":"Springer Nature","article_processing_charge":"No","_id":"15323","author":[{"full_name":"Vercellino, Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene","orcid":"0000-0001-5618-3449","last_name":"Vercellino"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"title":"SCAF1 drives the compositional diversity of mammalian respirasomes","date_published":"2024-07-01T00:00:00Z","has_accepted_license":"1","year":"2024","publication_status":"published","isi":1},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":121,"status":"public","intvolume":"       121","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n            <jats:sup>2+</jats:sup>\r\n            -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"external_id":{"isi":["001208567300006"],"pmid":["38346189"]},"issue":"8","article_number":"e2301449121","quality_controlled":"1","_id":"15084","article_processing_charge":"Yes (in subscription journal)","publisher":"National Academy of Sciences","author":[{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","first_name":"Peter"},{"full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari"},{"last_name":"Önal","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","full_name":"Önal, Hüseyin C"},{"last_name":"Borges Merjane","first_name":"Carolina","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","last_name":"Le Monnier","first_name":"Elodie"},{"id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2","full_name":"Roy, Utsa","last_name":"Roy","first_name":"Utsa"},{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"first_name":"Tetsushi","last_name":"Sadakata","full_name":"Sadakata, Tetsushi"},{"first_name":"Makoto","last_name":"Sanbo","full_name":"Sanbo, Makoto"},{"last_name":"Hirabayashi","first_name":"Masumi","full_name":"Hirabayashi, Masumi"},{"first_name":"JeongSeop","last_name":"Rhee","full_name":"Rhee, JeongSeop"},{"full_name":"Brose, Nils","last_name":"Brose","first_name":"Nils"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"}],"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","date_published":"2024-02-20T00:00:00Z","publication_status":"published","year":"2024","has_accepted_license":"1","isi":1,"APC_amount":"5887,8 EUR","OA_type":"hybrid","article_type":"original","day":"20","file":[{"access_level":"open_access","success":1,"checksum":"b25b2a057c266ff317a48b0d54d6fc8a","content_type":"application/pdf","creator":"dernst","date_updated":"2024-03-12T13:42:42Z","date_created":"2024-03-12T13:42:42Z","relation":"main_file","file_name":"2024_PNAS_Koppensteiner.pdf","file_size":13648221,"file_id":"15110"}],"file_date_updated":"2024-03-12T13:42:42Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"fulldoi":"https://doi.org/10.1073/pnas.2301449121","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <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.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>","ieee":"P. Koppensteiner <i>et al.</i>, “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8. National Academy of Sciences, 2024.","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(8). doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"scopus_import":"1","oa":1,"OA_place":"publisher","department":[{"_id":"RySh"},{"_id":"PeJo"}],"ec_funded":1,"type":"journal_article","pmid":1,"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/"}],"record":[{"status":"public","relation":"research_data","id":"13173"},{"id":"19271","status":"public","relation":"dissertation_contains"}]},"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"month":"02","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","oa_version":"Published Version","ddc":["570"],"doi":"10.1073/pnas.2301449121","date_updated":"2026-09-12T22:30:39Z","date_created":"2024-03-05T09:23:55Z"},{"language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","_id":"12716","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","date_published":"2023-03-10T00:00:00Z","author":[{"full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","first_name":"Laura","last_name":"Burnett"}],"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","year":"2023","has_accepted_license":"1","publication_status":"published","file_date_updated":"2023-03-08T15:08:46Z","file":[{"access_level":"closed","file_id":"12717","file_name":"Burnett_Thesis_2023.docx","file_size":23029260,"date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","relation":"source_file","creator":"lburnett","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332"},{"content_type":"application/pdf","creator":"lburnett","checksum":"cebc77705288bf4382db9b3541483cd0","file_name":"Burnett_Thesis_2023_pdfA.pdf","file_size":11959869,"file_id":"12718","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","relation":"main_file","access_level":"open_access","success":1}],"day":"10","OA_place":"publisher","oa":1,"fulldoi":"https://doi.org/10.15479/at:ista:12716","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"citation":{"mla":"Burnett, Laura. <i>To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>.","apa":"Burnett, L. (2023). <i>To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023."},"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"}],"project":[{"grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Circuits of Visual Attention"}],"page":"178","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"ec_funded":1,"date_created":"2023-03-08T15:19:45Z","doi":"10.15479/at:ista:12716","date_updated":"2026-04-07T13:25:15Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","oa_version":"Published Version","ddc":["599","573"],"month":"03"},{"author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa"},{"full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico"},{"first_name":"Daniel","last_name":"Malzl","full_name":"Malzl, Daniel"},{"full_name":"Gerykova Bujalkova, Maria","first_name":"Maria","last_name":"Gerykova Bujalkova"},{"first_name":"Mateja","last_name":"Smogavec","full_name":"Smogavec, Mateja"},{"last_name":"Schwarz","first_name":"Lena A.","full_name":"Schwarz, Lena A."},{"last_name":"Gorkiewicz","first_name":"Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","full_name":"Gorkiewicz, Sarah"},{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Knittl-Frank","full_name":"Knittl-Frank, Christian"},{"full_name":"Tassinari, Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","first_name":"Marianna","last_name":"Tassinari"},{"full_name":"Maulide, Nuno","last_name":"Maulide","first_name":"Nuno"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","date_published":"2023-04-27T00:00:00Z","publication_status":"published","year":"2023","has_accepted_license":"1","isi":1,"publication":"Cell","volume":186,"language":[{"iso":"eng"}],"intvolume":"       186","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","status":"public","abstract":[{"lang":"eng","text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction."}],"external_id":{"isi":["000991468700001"],"pmid":["36996814"]},"issue":"9","quality_controlled":"1","keyword":["General Biochemistry","Genetics and Molecular Biology"],"_id":"12802","article_processing_charge":"Yes (via OA deal)","publisher":"Elsevier","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"ec_funded":1,"type":"journal_article","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"19557"},{"id":"13107","relation":"dissertation_contains","status":"public"}]},"pmid":1,"project":[{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"}],"page":"1950-1967.e25","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","oa_version":"Published Version","ddc":["570"],"doi":"10.1016/j.cell.2023.02.037","date_updated":"2026-04-14T08:34:36Z","date_created":"2023-04-05T08:15:40Z","article_type":"original","day":"27","file":[{"date_updated":"2023-05-02T09:26:21Z","relation":"main_file","date_created":"2023-05-02T09:26:21Z","file_name":"2023_Cell_Knaus.pdf","file_size":15712841,"file_id":"12889","checksum":"47e94fbe19e86505b429cb7a5b503ce6","content_type":"application/pdf","creator":"dernst","success":1,"access_level":"open_access"}],"file_date_updated":"2023-05-02T09:26:21Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. 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Danzl, (2023)."},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13267"}]},"department":[{"_id":"JoDa"}],"type":"research_data","date_created":"2023-04-07T11:37:40Z","date_updated":"2026-04-14T08:34:34Z","doi":"10.15479/AT:ISTA:12817","month":"05","oa_version":"Published Version","ddc":["570"],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. ","license":"https://creativecommons.org/licenses/by-sa/4.0/","status":"public","_id":"12817","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","contributor":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky"},{"last_name":"Miguel Villalba","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Donglai","last_name":"Wei"},{"first_name":"Zudi","last_name":"Lin"},{"last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"Troidl","first_name":"Jakob"},{"first_name":"Johanna","last_name":"Beyer"},{"first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"last_name":"Broichhagen","first_name":"Johannes"},{"first_name":"Seth G. N. ","last_name":"Grant"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"first_name":"Hanspeter","last_name":"Pfister"},{"first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-05-19T00:00:00Z","author":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","has_accepted_license":"1","year":"2023"},{"abstract":[{"lang":"eng","text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization."}],"language":[{"iso":"eng"}],"acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","status":"public","intvolume":"        58","volume":58,"publication":"Developmental Cell","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","_id":"12830","quality_controlled":"1","issue":"7","external_id":{"pmid":["36931269"],"isi":["000982111800001"]},"date_published":"2023-04-10T00:00:00Z","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","first_name":"Karla","last_name":"Huljev"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","orcid":"0000-0003-4333-7503","last_name":"Nunes Pinheiro"},{"full_name":"Preusser, Friedrich","first_name":"Friedrich","last_name":"Preusser"},{"full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene","last_name":"Steccari"},{"last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Naik","orcid":"0000-0001-8421-5508","first_name":"Suyash","full_name":"Naik, Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"has_accepted_license":"1","year":"2023","publication_status":"published","file_date_updated":"2023-04-17T07:41:25Z","file":[{"access_level":"open_access","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","file_id":"12842","file_size":7925886,"file_name":"2023_DevelopmentalCell_Huljev.pdf","date_created":"2023-04-17T07:41:25Z","date_updated":"2023-04-17T07:41:25Z","relation":"main_file"}],"day":"10","article_type":"original","scopus_import":"1","oa":1,"fulldoi":"https://doi.org/10.1016/j.devcel.2023.02.016","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"citation":{"short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. 2023;58(7):582-596.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>","ieee":"K. Huljev <i>et al.</i>, “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” <i>Developmental Cell</i>, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","grant_number":"LT000429"}],"page":"582-596.e7","pmid":1,"type":"journal_article","ec_funded":1,"department":[{"_id":"CaHe"},{"_id":"Bio"}],"doi":"10.1016/j.devcel.2023.02.016","date_updated":"2025-04-23T08:51:34Z","date_created":"2023-04-16T22:01:07Z","ddc":["570"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","month":"04"},{"publication_status":"published","year":"2023","has_accepted_license":"1","title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","author":[{"last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-05-31T00:00:00Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"_id":"13107","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans.","lang":"eng"}],"month":"05","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"oa_version":"Published Version","date_updated":"2026-04-14T08:34:36Z","date_created":"2023-06-01T09:05:24Z","doi":"10.15479/at:ista:13107","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"ec_funded":1,"type":"dissertation","related_material":{"record":[{"id":"12802","status":"public","relation":"part_of_dissertation"}]},"project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular Drug Targets","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"147","fulldoi":"https://doi.org/10.15479/at:ista:13107","supervisor":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>.","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","mla":"Knaus, Lisa. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>.","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>"},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa":1,"OA_place":"publisher","day":"31","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lknaus","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","file_size":12991551,"file_name":"Thesis_Lisa Knaus_approved_final.docx","file_id":"13112","date_updated":"2023-06-01T13:48:41Z","date_created":"2023-06-01T13:48:41Z","relation":"source_file","access_level":"closed"},{"access_level":"open_access","content_type":"application/pdf","creator":"lknaus","checksum":"6903d152aa01181d87a696085af31c83","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","file_size":9309015,"file_id":"13114","relation":"main_file","date_updated":"2023-06-07T08:41:49Z","date_created":"2023-06-02T09:47:29Z"}],"file_date_updated":"2023-06-07T08:41:49Z"},{"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","_id":"13126","contributor":[{"last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia"},{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana","last_name":"Stefanickova"},{"last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban"},{"orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Amberg","orcid":"0000-0002-3183-8207","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Venturino","orcid":"0000-0003-2356-9403","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roessler","first_name":"Karl"},{"last_name":"Czech","first_name":"Thomas"},{"last_name":"Höftberger","first_name":"Romana"},{"orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","status":"public","has_accepted_license":"1","year":"2023","date_published":"2023-08-04T00:00:00Z","title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"oa":1,"fulldoi":"https://doi.org/10.15479/AT:ISTA:13126","citation":{"short":"J.G. Danzl, (2023).","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>.","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","mla":"Danzl, Johann G. <i>Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>","ama":"Danzl JG. 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Higashi <i>et al.</i>, “ZnUMBA - a live imaging method to detect local barrier breaches,” <i>Journal of Cell Science</i>, vol. 136, no. 15. The Company of Biologists, 2023.","apa":"Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>","ama":"Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. 2023;136(15). doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>"},"fulldoi":"https://doi.org/10.1242/jcs.260668","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"date_published":"2023-08-01T00:00:00Z","title":"ZnUMBA - a live imaging method to detect local barrier breaches","author":[{"last_name":"Higashi","first_name":"Tomohito","full_name":"Higashi, Tomohito"},{"full_name":"Stephenson, Rachel E.","last_name":"Stephenson","first_name":"Rachel E."},{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia","last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226"},{"last_name":"Huljev","first_name":"Karla","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Higashi","first_name":"Atsuko Y.","full_name":"Higashi, Atsuko Y."},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Hideki","last_name":"Chiba","full_name":"Chiba, Hideki"},{"last_name":"Miller","first_name":"Ann L.","full_name":"Miller, Ann L."}],"isi":1,"has_accepted_license":"1","year":"2023","publication_status":"published","abstract":[{"lang":"eng","text":"Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision."}],"status":"public","language":[{"iso":"eng"}],"intvolume":"       136","acknowledgement":"The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. ","volume":136,"publication":"Journal of Cell Science","article_processing_charge":"No","publisher":"The Company of Biologists","_id":"14082","quality_controlled":"1","article_number":"jcs260668","issue":"15","external_id":{"pmid":["37461809"],"isi":["001070149000001"]}},{"date_updated":"2024-10-09T21:07:01Z","date_created":"2023-09-24T22:01:11Z","doi":"10.1016/j.isci.2023.107780","month":"10","oa_version":"Published Version","ddc":["570"],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"SaSi"}],"type":"journal_article","oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>.","ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780.","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023).","apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., &#38; Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>","ieee":"M. E. Maes <i>et al.</i>, “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” <i>iScience</i>, vol. 26, no. 10. Elsevier, 2023.","mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>, vol. 26, no. 10, 107780, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>.","ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>iScience</i>. 2023;26(10). doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>"},"fulldoi":"https://doi.org/10.1016/j.isci.2023.107780","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["2589-0042"]},"file":[{"access_level":"open_access","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"be1a560efdd96d20712311f4fc54aac2","file_id":"14497","file_name":"2023_iScience_Maes.pdf","file_size":8197935,"date_updated":"2023-11-07T08:53:21Z","date_created":"2023-11-07T08:53:21Z","relation":"main_file"}],"file_date_updated":"2023-11-07T08:53:21Z","article_type":"original","day":"20","isi":1,"publication_status":"published","has_accepted_license":"1","year":"2023","date_published":"2023-10-20T00:00:00Z","title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","author":[{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes"},{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","first_name":"Gloria","last_name":"Colombo"},{"full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","last_name":"Schoot Uiterkamp","first_name":"Florianne E"},{"last_name":"Sternberg","first_name":"Felix","full_name":"Sternberg, Felix"},{"full_name":"Venturino, Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","first_name":"Alessandro","last_name":"Venturino"},{"full_name":"Pohl, Elena E.","first_name":"Elena E.","last_name":"Pohl"},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"_id":"14363","publisher":"Elsevier","article_processing_charge":"Yes","issue":"10","article_number":"107780","external_id":{"isi":["001080403500001"],"pmid":["37731609"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies."}],"acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","status":"public","language":[{"iso":"eng"}],"intvolume":"        26","volume":26,"publication":"iScience"},{"title":"Mechanism of mammalian transcriptional repression by noncoding RNA","author":[{"last_name":"Tluckova","first_name":"Katarina","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P"},{"last_name":"Bernecky","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"}],"date_published":"2023-12-05T00:00:00Z","publication_status":"draft","has_accepted_license":"1","year":"2023","abstract":[{"lang":"eng","text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression."}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","language":[{"iso":"eng"}],"status":"public","_id":"14644","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","type":"preprint","related_material":{"record":[{"id":"18778","relation":"later_version","status":"public"}]},"project":[{"name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"month":"12","oa_version":"Submitted Version","ddc":["572"],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-11-20T10:28:37Z","date_created":"2023-12-04T14:51:00Z","doi":"10.15479/AT:ISTA:14644","day":"05","file":[{"checksum":"c45608cb97ee36d7b50ba518db8e07b0","content_type":"application/pdf","creator":"dernst","date_created":"2023-12-05T10:37:02Z","relation":"main_file","date_updated":"2023-12-05T10:37:02Z","file_size":4892920,"file_name":"2023_Tluckova_etal_REx.pdf","file_id":"14646","access_level":"open_access","success":1}],"file_date_updated":"2023-12-05T10:37:02Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"fulldoi":"https://doi.org/10.15479/AT:ISTA:14644","citation":{"chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>.","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","mla":"Tluckova, Katarina, et al. <i>Mechanism of Mammalian Transcriptional Repression by Noncoding RNA</i>. Institute of Science and Technology Austria, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","apa":"Tluckova, K., Testa Salmazo, A. P., &#38; Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"oa":1},{"date_created":"2023-07-23T22:01:13Z","doi":"10.1038/s41592-023-01936-6","date_updated":"2026-07-06T12:49:46Z","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa_version":"Published Version","month":"08","project":[{"name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"page":"1256-1265","pmid":1,"related_material":{"record":[{"id":"12817","status":"public","relation":"research_data"},{"status":"public","relation":"shorter_version","id":"14770"},{"relation":"dissertation_contains","status":"public","id":"18674"},{"id":"11943","relation":"earlier_version","status":"public"}],"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}]},"type":"journal_article","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"ec_funded":1,"OA_place":"publisher","oa":1,"scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"fulldoi":"https://doi.org/10.1038/s41592-023-01936-6","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"citation":{"apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023.","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2025-02-26T08:01:57Z","file":[{"creator":"dernst","content_type":"application/pdf","checksum":"a68e845780a82ea36d0d4d3212a87c10","file_id":"19088","file_size":14103039,"file_name":"2023_NatureMethods_Velicky.pdf","relation":"main_file","date_updated":"2025-02-26T08:01:57Z","date_created":"2025-02-26T08:01:57Z","access_level":"open_access","success":1}],"day":"01","article_type":"original","OA_type":"hybrid","isi":1,"year":"2023","has_accepted_license":"1","publication_status":"published","date_published":"2023-08-01T00:00:00Z","title":"Dense 4D nanoscale reconstruction of living brain tissue","author":[{"full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"orcid":"0000-0001-5665-0430","first_name":"Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","full_name":"Miguel Villalba, Eder"},{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","orcid":"0000-0003-3862-1235","first_name":"Julia M"},{"last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia"},{"last_name":"Wei","first_name":"Donglai","full_name":"Wei, Donglai"},{"last_name":"Lin","first_name":"Zudi","full_name":"Lin, Zudi"},{"orcid":"0000-0002-8698-3823","first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake"},{"last_name":"Troidl","first_name":"Jakob","full_name":"Troidl, Jakob"},{"first_name":"Johanna","last_name":"Beyer","full_name":"Beyer, Johanna"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"last_name":"Jahr","first_name":"Wiebke","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cenameri","first_name":"Alban","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"full_name":"Broichhagen, Johannes","first_name":"Johannes","last_name":"Broichhagen"},{"last_name":"Grant","first_name":"Seth G.N.","full_name":"Grant, Seth G.N."},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G"}],"publisher":"Springer Nature","article_processing_charge":"Yes (in subscription journal)","_id":"13267","quality_controlled":"1","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"status":"public","intvolume":"        20","language":[{"iso":"eng"}],"acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","abstract":[{"text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"publication":"Nature Methods","volume":20},{"status":"public","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","_id":"12809","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","author":[{"first_name":"Catarina","last_name":"Alcarva","full_name":"Alcarva, Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-04-06T00:00:00Z","year":"2023","has_accepted_license":"1","publication_status":"published","day":"06","file_date_updated":"2024-04-08T22:30:03Z","file":[{"embargo":"2024-04-07","file_size":9881969,"file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","file_id":"12814","date_created":"2023-04-07T06:16:06Z","relation":"main_file","date_updated":"2024-04-08T22:30:03Z","content_type":"application/pdf","creator":"cchlebak","checksum":"35b5997d2b0acb461f9d33d073da0df5","access_level":"open_access"},{"file_size":44201583,"file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","file_id":"12815","relation":"source_file","date_created":"2023-04-07T06:17:11Z","date_updated":"2024-04-08T22:30:03Z","content_type":"application/pdf","creator":"cchlebak","checksum":"81198f63c294890f6d58e8b29782efdc","embargo_to":"open_access","access_level":"closed"},{"date_updated":"2024-04-08T22:30:03Z","date_created":"2023-04-07T06:18:05Z","relation":"source_file","file_id":"12816","file_name":"Thesis_CatarinaAlcarva_final.docx","file_size":84731244,"checksum":"0317bf7f457bb585f99d453ffa69eb53","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access"}],"fulldoi":"https://doi.org/10.15479/at:ista:12809","citation":{"ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023."},"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"OA_place":"publisher","oa":1,"type":"dissertation","department":[{"_id":"GradSch"},{"_id":"RySh"}],"project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"page":"115","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","oa_version":"Published Version","ddc":["570"],"month":"04","date_updated":"2026-04-07T13:53:28Z","doi":"10.15479/at:ista:12809","date_created":"2023-04-06T07:54:09Z"}]