[{"doi":"10.1016/j.xpro.2023.102795","language":[{"iso":"eng"}],"acknowledgement":"We thank Florian Pauler for discussion and his expert technical support. This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging and Optics Facility (IOF) and Preclinical Facility (PCF). A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences.","project":[{"grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"pmid":1,"related_material":{"link":[{"relation":"software","url":"http://github.com/hippenmeyerlab"}]},"author":[{"full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"type":"journal_article","day":"01","title":"Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers","citation":{"mla":"Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 5, no. 1, 102795, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>.","ista":"Hansen AH, Hippenmeyer S. 2024. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 5(1), 102795.","ieee":"A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>.","apa":"Hansen, A. H., &#38; Hippenmeyer, S. (2024). Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>","ama":"Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>","short":"A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024)."},"intvolume":"         5","status":"public","department":[{"_id":"SiHi"}],"quality_controlled":"1","publication":"STAR Protocols","publisher":"Elsevier","date_created":"2024-01-14T23:00:56Z","month":"01","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["2666-1667"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-08-11T11:49:30Z","external_id":{"oaworkID":["34426698 "],"pmid":["38165800"]},"scopus_import":"1","oaworkID":1,"year":"2024","oa_version":"Published Version","article_type":"review","volume":5,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.xpro.2023.102795"}],"oa":1,"publication_status":"epub_ahead","_id":"14794","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3","lang":"eng"}],"date_published":"2024-01-01T00:00:00Z","article_number":"102795","issue":"1","article_processing_charge":"Yes"},{"has_accepted_license":"1","year":"2024","oa_version":"Published Version","article_type":"original","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"scopus_import":"1","external_id":{"arxiv":["2410.03589"]},"date_updated":"2025-07-22T14:58:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","issue":"1","arxiv":1,"_id":"14795","date_published":"2024-01-08T00:00:00Z","abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells.","lang":"eng"}],"file":[{"file_name":"2024_CurrentBiology_Arslan.pdf","file_size":5183861,"creator":"dernst","checksum":"51220b76d72a614208f84bdbfbaf9b72","date_updated":"2024-01-16T10:53:31Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"14813","date_created":"2024-01-16T10:53:31Z","success":1}],"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","volume":34,"file_date_updated":"2024-01-16T10:53:31Z","title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","citation":{"chicago":"Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>.","ista":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8.","ieee":"F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” <i>Current Biology</i>, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.","mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>.","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","ama":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. 2024;34(1):171-182.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>","apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., &#38; Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>"},"ec_funded":1,"type":"journal_article","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","last_name":"Arslan","full_name":"Arslan, Feyza N","first_name":"Feyza N"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"day":"08","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H.","doi":"10.1016/j.cub.2023.11.067","ddc":["570"],"language":[{"iso":"eng"}],"page":"171-182.e8","date_created":"2024-01-14T23:00:56Z","month":"01","publisher":"Elsevier","intvolume":"        34","status":"public","publication":"Current Biology","quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}]},{"publication_status":"inpress","article_processing_charge":"No","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"}],"_id":"14843","date_published":"2024-01-11T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"date_updated":"2024-03-05T09:31:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","external_id":{"pmid":["38215739"]},"year":"2024","oa_version":"None","article_type":"original","publisher":"Elsevier","status":"public","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"quality_controlled":"1","publication":"Neuron","date_created":"2024-01-21T23:00:56Z","month":"01","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.","project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"pmid":1,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}]},"doi":"10.1016/j.neuron.2023.12.002","language":[{"iso":"eng"}],"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","ec_funded":1,"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, n.d. <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. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron.","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>. Elsevier.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron (n.d.).","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (n.d.). 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>"},"type":"journal_article","author":[{"id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"JingJing","full_name":"Chen, JingJing"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chong","full_name":"Chen, Chong"},{"full_name":"Arai, Itaru","first_name":"Itaru","last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kim","full_name":"Kim, Olena","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"day":"11"},{"date_created":"2023-04-27T09:41:48Z","month":"01","page":"230-246.e11","status":"public","intvolume":"       112","quality_controlled":"1","department":[{"_id":"SiHi"},{"_id":"RySh"}],"publication":"Neuron","publisher":"Elsevier","author":[{"first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"first_name":"Thomas","full_name":"Krausgruber, Thomas","last_name":"Krausgruber"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher"},{"id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","last_name":"Schrammel","full_name":"Schrammel, Martin","first_name":"Martin"},{"last_name":"Özgen","full_name":"Özgen, Natalie Y","first_name":"Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090"},{"id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","full_name":"Ivec, Alexis","first_name":"Alexis","last_name":"Ivec"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"17","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","ddc":["570"],"doi":"10.1016/j.neuron.2023.11.009","language":[{"iso":"eng"}],"acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","pmid":1,"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","description":"News on ISTA Website","relation":"press_release"}]},"_id":"12875","abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"date_published":"2024-01-17T00:00:00Z","file":[{"success":1,"date_created":"2024-02-06T13:56:15Z","relation":"main_file","file_id":"14944","content_type":"application/pdf","access_level":"open_access","date_updated":"2024-02-06T13:56:15Z","checksum":"32b3788f7085cf44a84108d8faaff3ce","creator":"dernst","file_size":5942467,"file_name":"2024_Neuron_Cheung.pdf"}],"issue":"2","article_processing_charge":"Yes (via OA deal)","volume":112,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2024-02-06T13:56:15Z","oa":1,"publication_status":"published","has_accepted_license":"1","year":"2024","oa_version":"Published Version","article_type":"comment","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"publication_identifier":{"eisbn":["1234995621"],"issn":["0896-6273"],"issnl":["1234-5678"]},"date_updated":"2025-05-14T09:39:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38096816"]},"scopus_import":"1"},{"related_material":{"record":[{"status":"public","id":"7883","relation":"part_of_dissertation"}]},"project":[{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14323","ddc":["570"],"citation":{"mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023."},"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","day":"13","alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"id":"4CED352A-F248-11E8-B48F-1D18A9856A87","last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna","first_name":"Katarzyna"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"status":"public","page":"151","month":"09","date_created":"2023-09-13T10:07:18Z","supervisor":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-03-07T15:02:59Z","publication_identifier":{"issn":["2663 - 337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","year":"2023","has_accepted_license":"1","publication_status":"published","file_date_updated":"2023-09-13T10:08:25Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","file":[{"file_id":"14324","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","date_created":"2023-09-13T09:52:52Z","embargo":"2025-03-13","creator":"kkuzmicz","file_size":10147911,"file_name":"PhDThesis_KK_final_pdfA.pdf","access_level":"closed","date_updated":"2023-09-13T10:08:25Z","checksum":"bd83596869c814b24aeff7077d031c0e"},{"file_id":"14325","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-09-13T09:53:29Z","creator":"kkuzmicz","file_size":103980668,"file_name":"thesis_KK_final_corrections_092023.docx","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","access_level":"closed","date_updated":"2023-09-13T09:53:29Z"}],"date_published":"2023-09-13T00:00:00Z","_id":"14323","abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1016/j.isci.2023.107780","ddc":["570"],"pmid":1,"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.","day":"20","author":[{"full_name":"Maes, Margaret E","first_name":"Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085"},{"last_name":"Colombo","full_name":"Colombo, Gloria","first_name":"Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florianne E","full_name":"Schoot Uiterkamp, Florianne E","last_name":"Schoot Uiterkamp","id":"3526230C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Felix","full_name":"Sternberg, Felix","last_name":"Sternberg"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","last_name":"Venturino","full_name":"Venturino, Alessandro","first_name":"Alessandro"},{"last_name":"Pohl","first_name":"Elena E.","full_name":"Pohl, Elena E."},{"last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","citation":{"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>","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>","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (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>.","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.","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.","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>."},"title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","publication":"iScience","quality_controlled":"1","department":[{"_id":"SaSi"}],"intvolume":"        26","status":"public","publisher":"Elsevier","isi":1,"month":"10","date_created":"2023-09-24T22:01:11Z","external_id":{"pmid":["37731609"],"isi":["001080403500001"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-13T12:27:30Z","publication_identifier":{"eissn":["2589-0042"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"article_type":"original","has_accepted_license":"1","year":"2023","oa_version":"Published Version","file_date_updated":"2023-11-07T08:53:21Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":26,"publication_status":"published","oa":1,"file":[{"success":1,"date_created":"2023-11-07T08:53:21Z","file_id":"14497","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-11-07T08:53:21Z","checksum":"be1a560efdd96d20712311f4fc54aac2","file_size":8197935,"creator":"dernst","file_name":"2023_iScience_Maes.pdf"}],"article_number":"107780","_id":"14363","date_published":"2023-10-20T00:00:00Z","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"Yes","issue":"10"},{"oa_version":"Submitted Version","year":"2023","has_accepted_license":"1","type":"preprint","author":[{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","last_name":"Tluckova","first_name":"Katarina","full_name":"Tluckova, Katarina"},{"first_name":"Anita P","full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bernecky","full_name":"Bernecky, Carrie A","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"day":"05","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","citation":{"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>","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.","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>.","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>."},"ddc":["572"],"doi":"10.15479/AT:ISTA:14644","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-05T10:37:28Z","language":[{"iso":"eng"}],"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).","project":[{"grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"date_created":"2023-12-04T14:51:00Z","_id":"14644","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."}],"date_published":"2023-12-05T00:00:00Z","file":[{"relation":"main_file","file_id":"14646","content_type":"application/pdf","date_created":"2023-12-05T10:37:02Z","success":1,"file_size":4892920,"creator":"dernst","file_name":"2023_Tluckova_etal_REx.pdf","checksum":"c45608cb97ee36d7b50ba518db8e07b0","access_level":"open_access","date_updated":"2023-12-05T10:37:02Z"}],"month":"12","article_processing_charge":"No","status":"public","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file_date_updated":"2023-12-05T10:37:02Z","department":[{"_id":"CaBe"}],"oa":1,"publication_status":"submitted","publisher":"Institute of Science and Technology Austria"},{"month":"12","date_created":"2023-12-13T11:48:05Z","publication":"STAR Protocols","quality_controlled":"1","department":[{"_id":"SiHi"}],"intvolume":"         5","status":"public","publisher":"Elsevier","day":"08","type":"journal_article","author":[{"first_name":"Nicole","full_name":"Amberg, Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"citation":{"short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023).","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2023). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2023.","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>."},"ec_funded":1,"title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1016/j.xpro.2023.102771","pmid":1,"project":[{"grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","article_number":"102771","_id":"14683","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1","lang":"eng"}],"date_published":"2023-12-08T00:00:00Z","article_processing_charge":"No","issue":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":5,"publication_status":"epub_ahead","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.xpro.2023.102771"}],"oa":1,"article_type":"review","year":"2023","oa_version":"Submitted Version","external_id":{"pmid":["38070137"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-18T08:06:14Z","publication_identifier":{"issn":["2666-1667"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}]},{"related_material":{"record":[{"id":"12802","relation":"part_of_dissertation","status":"public"}]},"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"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.15479/at:ista:13107","ddc":["570"],"language":[{"iso":"eng"}],"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","ec_funded":1,"citation":{"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>","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>","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.","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>.","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>.","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.","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."},"alternative_title":["ISTA Thesis"],"author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","full_name":"Knaus, Lisa","last_name":"Knaus"}],"type":"dissertation","day":"31","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"page":"147","date_created":"2023-06-01T09:05:24Z","supervisor":[{"last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"month":"05","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663 - 337X"]},"date_updated":"2024-02-07T08:03:33Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","year":"2023","oa_version":"Published Version","oa":1,"publication_status":"published","file_date_updated":"2023-06-07T08:41:49Z","article_processing_charge":"No","_id":"13107","abstract":[{"lang":"eng","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."}],"date_published":"2023-05-31T00:00:00Z","file":[{"date_updated":"2023-06-01T13:48:41Z","access_level":"closed","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","file_name":"Thesis_Lisa Knaus_approved_final.docx","creator":"lknaus","file_size":12991551,"date_created":"2023-06-01T13:48:41Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"13112","relation":"source_file"},{"date_created":"2023-06-02T09:47:29Z","content_type":"application/pdf","file_id":"13114","relation":"main_file","date_updated":"2023-06-07T08:41:49Z","access_level":"open_access","checksum":"6903d152aa01181d87a696085af31c83","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","file_size":9309015,"creator":"lknaus"}]},{"status":"public","department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","date_created":"2023-06-07T07:15:12Z","month":"08","ddc":["610"],"doi":"10.15479/AT:ISTA:13126","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)","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14257"}],"link":[{"relation":"research_data","description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. ","url":"https://pub.ista.ac.at/group_danzl/data/CATS/"}]},"project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"}],"type":"research_data","author":[{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"day":"04","title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","ec_funded":1,"citation":{"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. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>","short":"J.G. Danzl, (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>.","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.","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>.","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>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"file_date_updated":"2023-08-04T13:19:47Z","oa":1,"date_published":"2023-08-04T00:00:00Z","_id":"13126","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 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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. 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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.).","doi":"10.1038/s41592-023-01936-6","language":[{"iso":"eng"}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","citation":{"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>.","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>.","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.","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.","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>","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>","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."},"ec_funded":1,"type":"journal_article","author":[{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky"},{"orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba","first_name":"Eder","full_name":"Miguel Villalba, Eder"},{"last_name":"Michalska","first_name":"Julia M","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia"},{"last_name":"Wei","full_name":"Wei, Donglai","first_name":"Donglai"},{"full_name":"Lin, Zudi","first_name":"Zudi","last_name":"Lin"},{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","first_name":"Jake","last_name":"Watson"},{"first_name":"Jakob","full_name":"Troidl, Jakob","last_name":"Troidl"},{"full_name":"Beyer, Johanna","first_name":"Johanna","last_name":"Beyer"},{"last_name":"Ben Simon","first_name":"Yoav","full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jahr, Wiebke","first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","full_name":"Cenameri, Alban","first_name":"Alban"},{"first_name":"Johannes","full_name":"Broichhagen, Johannes","last_name":"Broichhagen"},{"last_name":"Grant","full_name":"Grant, Seth G.N.","first_name":"Seth G.N."},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"day":"01"},{"publication_status":"published","volume":136,"file_date_updated":"2023-08-21T07:37:54Z","article_processing_charge":"No","issue":"15","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."}],"_id":"14082","date_published":"2023-08-01T00:00:00Z","file":[{"checksum":"a399389b7e3d072f1788b63e612a10b3","access_level":"closed","date_updated":"2023-08-21T07:37:54Z","creator":"dernst","file_size":18665315,"file_name":"2023_JourCellScience_Higashi.pdf","embargo":"2024-08-10","embargo_to":"open_access","date_created":"2023-08-21T07:37:54Z","file_id":"14092","relation":"main_file","content_type":"application/pdf"}],"article_number":"jcs260668","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"external_id":{"isi":["001070149000001"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-13T12:11:18Z","has_accepted_license":"1","year":"2023","oa_version":"None","article_type":"original","isi":1,"publisher":"The Company of Biologists","intvolume":"       136","status":"public","publication":"Journal of Cell Science","department":[{"_id":"CaHe"},{"_id":"EvBe"}],"quality_controlled":"1","date_created":"2023-08-20T22:01:13Z","month":"08","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"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.]. ","doi":"10.1242/jcs.260668","ddc":["570"],"language":[{"iso":"eng"}],"title":"ZnUMBA - a live imaging method to detect local barrier breaches","citation":{"short":"T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (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>","ista":"Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668.","ieee":"T. 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.","chicago":"Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>.","mla":"Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>."},"ec_funded":1,"author":[{"first_name":"Tomohito","full_name":"Higashi, Tomohito","last_name":"Higashi"},{"last_name":"Stephenson","first_name":"Rachel E.","full_name":"Stephenson, Rachel E."},{"orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","full_name":"Schwayer, Cornelia","first_name":"Cornelia"},{"first_name":"Karla","full_name":"Huljev, Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Higashi, Atsuko Y.","first_name":"Atsuko Y.","last_name":"Higashi"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"},{"last_name":"Chiba","full_name":"Chiba, Hideki","first_name":"Hideki"},{"full_name":"Miller, Ann L.","first_name":"Ann L.","last_name":"Miller"}],"type":"journal_article","day":"01"},{"month":"08","date_created":"2023-09-03T22:01:15Z","publisher":"Springer Nature","isi":1,"publication":"Nature Biotechnology","quality_controlled":"1","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"status":"public","citation":{"ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>. Springer Nature, 2023.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2023. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>"},"ec_funded":1,"title":"Imaging brain tissue architecture across millimeter to nanometer scales","day":"31","author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","first_name":"Julia M","full_name":"Michalska, Julia M","last_name":"Michalska"},{"first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Korinkova","first_name":"Hana","full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake"},{"last_name":"Cenameri","full_name":"Cenameri, Alban","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"last_name":"Amberg","full_name":"Amberg, Nicole","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","first_name":"Alessandro","last_name":"Venturino"},{"last_name":"Roessler","full_name":"Roessler, Karl","first_name":"Karl"},{"first_name":"Thomas","full_name":"Czech, Thomas","last_name":"Czech"},{"full_name":"Höftberger, Romana","first_name":"Romana","last_name":"Höftberger"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","full_name":"Siegert, Sandra","last_name":"Siegert"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G"}],"type":"journal_article","project":[{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"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"},{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13126"}],"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}]},"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","language":[{"iso":"eng"}],"doi":"10.1038/s41587-023-01911-8","article_processing_charge":"Yes (in subscription journal)","_id":"14257","date_published":"2023-08-31T00:00:00Z","abstract":[{"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.","lang":"eng"}],"publication_status":"epub_ahead","main_file_link":[{"url":"https://doi.org/10.1038/s41587-023-01911-8","open_access":"1"}],"oa":1,"article_type":"original","year":"2023","oa_version":"Published Version","external_id":{"isi":["001065254200001"]},"scopus_import":"1","date_updated":"2024-02-21T12:18:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}]},{"day":"01","author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","last_name":"Gupta","full_name":"Gupta, Divyansh","first_name":"Divyansh"},{"full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sumser","full_name":"Sumser, Anton L","first_name":"Anton L","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga","first_name":"Olga"},{"last_name":"Svaton","full_name":"Svaton, Jan","first_name":"Jan","orcid":"0000-0002-6198-2939","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2"},{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330"}],"type":"journal_article","citation":{"ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. 2023;26:606-614. doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &#38; Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. 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We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","month":"04","date_created":"2023-01-23T14:14:19Z","page":"606-614","publication":"Nature Neuroscience","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"quality_controlled":"1","status":"public","intvolume":"        26","publisher":"Springer Nature","isi":1,"article_type":"original","year":"2023","has_accepted_license":"1","oa_version":"Published Version","external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-04T11:41:05Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"file":[{"file_size":6144866,"creator":"dernst","file_name":"2023_NatureNeuroscience_Gupta.pdf","access_level":"open_access","date_updated":"2023-10-04T11:40:51Z","checksum":"a33d91e398e548f34003170e10988368","file_id":"14395","relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2023-10-04T11:40:51Z"}],"date_published":"2023-04-01T00:00:00Z","_id":"12349","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. 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L., &#38; Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023).","mla":"Gupta, Divyansh, et al. <i>Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","ieee":"D. Gupta, A. L. Sumser, and M. A. 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To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"12471","date_created":"2023-01-31T15:11:42Z","file_name":"20230109_PhD_thesis_JM_final.pdf","file_size":41771714,"creator":"cchlebak","embargo":"2023-07-09","checksum":"1a2306e5f59f52df598e7ecfadf921ac","date_updated":"2023-07-27T22:30:54Z","access_level":"open_access"},{"date_updated":"2023-07-10T22:30:04Z","access_level":"closed","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_name":"20230109_PhD_thesis_JM_final.docx","file_size":66983464,"creator":"cchlebak","date_created":"2023-01-31T15:11:51Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12472","relation":"source_file"}],"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-07-27T22:30:54Z","oa":1,"publication_status":"published"},{"page":"178","month":"03","supervisor":[{"last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-03-08T15:19:45Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"status":"public","citation":{"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.","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>","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>","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>.","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.","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.","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>."},"ec_funded":1,"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","day":"10","author":[{"orcid":"0000-0002-8937-410X","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","last_name":"Burnett"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"project":[{"name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12716","ddc":["599","573"],"article_processing_charge":"No","file":[{"access_level":"closed","date_updated":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_size":23029260,"creator":"lburnett","file_name":"Burnett_Thesis_2023.docx","date_created":"2023-03-08T15:08:46Z","file_id":"12717","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"12718","relation":"main_file","content_type":"application/pdf","date_created":"2023-03-08T15:08:46Z","success":1,"creator":"lburnett","file_size":11959869,"file_name":"Burnett_Thesis_2023_pdfA.pdf","checksum":"cebc77705288bf4382db9b3541483cd0","access_level":"open_access","date_updated":"2023-03-08T15:08:46Z"}],"_id":"12716","date_published":"2023-03-10T00:00:00Z","abstract":[{"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.","lang":"eng"}],"publication_status":"published","oa":1,"file_date_updated":"2023-03-08T15:08:46Z","has_accepted_license":"1","oa_version":"Published Version","year":"2023","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-04-05T10:59:04Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"publication_identifier":{"issn":["2663-337X"]}},{"date_created":"2023-04-05T08:15:40Z","month":"04","page":"1950-1967.e25","status":"public","intvolume":"       186","publication":"Cell","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"quality_controlled":"1","isi":1,"publisher":"Elsevier","type":"journal_article","author":[{"full_name":"Knaus, Lisa","first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Basilico","first_name":"Bernadette","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"first_name":"Daniel","full_name":"Malzl, Daniel","last_name":"Malzl"},{"first_name":"Maria","full_name":"Gerykova Bujalkova, Maria","last_name":"Gerykova Bujalkova"},{"first_name":"Mateja","full_name":"Smogavec, Mateja","last_name":"Smogavec"},{"last_name":"Schwarz","full_name":"Schwarz, Lena A.","first_name":"Lena A."},{"first_name":"Sarah","full_name":"Gorkiewicz, Sarah","last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole"},{"orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler"},{"last_name":"Knittl-Frank","full_name":"Knittl-Frank, Christian","first_name":"Christian"},{"first_name":"Marianna","full_name":"Tassinari, Marianna","last_name":"Tassinari","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e"},{"first_name":"Nuno","full_name":"Maulide, Nuno","last_name":"Maulide"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"first_name":"Jörg","full_name":"Menche, Jörg","last_name":"Menche"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino"}],"day":"27","title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","citation":{"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.","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. Elsevier, p. 1950–1967.e25, 2023.","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>.","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>.","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.","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>","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>"},"ec_funded":1,"doi":"10.1016/j.cell.2023.02.037","ddc":["570"],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"project":[{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"_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","grant_number":"715508"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13107"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/"}]},"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.","_id":"12802","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."}],"date_published":"2023-04-27T00:00:00Z","file":[{"content_type":"application/pdf","file_id":"12889","relation":"main_file","success":1,"date_created":"2023-05-02T09:26:21Z","file_name":"2023_Cell_Knaus.pdf","file_size":15712841,"creator":"dernst","date_updated":"2023-05-02T09:26:21Z","access_level":"open_access","checksum":"47e94fbe19e86505b429cb7a5b503ce6"}],"article_processing_charge":"Yes (via OA deal)","issue":"9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":186,"file_date_updated":"2023-05-02T09:26:21Z","oa":1,"publication_status":"published","oa_version":"Published Version","year":"2023","has_accepted_license":"1","article_type":"original","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["0092-8674"]},"scopus_import":"1","external_id":{"isi":["000991468700001"]},"date_updated":"2024-02-07T08:03:32Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_processing_charge":"No","_id":"12809","date_published":"2023-04-06T00:00:00Z","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. "}],"file":[{"date_updated":"2023-04-07T06:16:06Z","access_level":"closed","checksum":"35b5997d2b0acb461f9d33d073da0df5","embargo":"2024-04-07","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","file_size":9881969,"creator":"cchlebak","date_created":"2023-04-07T06:16:06Z","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"12814"},{"date_created":"2023-04-07T06:17:11Z","file_id":"12815","relation":"source_file","content_type":"application/pdf","access_level":"closed","date_updated":"2023-04-07T06:17:11Z","checksum":"81198f63c294890f6d58e8b29782efdc","creator":"cchlebak","file_size":44201583,"file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf"},{"date_created":"2023-04-07T06:18:05Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12816","relation":"source_file","date_updated":"2023-04-07T06:18:05Z","access_level":"closed","checksum":"0317bf7f457bb585f99d453ffa69eb53","file_name":"Thesis_CatarinaAlcarva_final.docx","creator":"cchlebak","file_size":84731244}],"publication_status":"published","file_date_updated":"2023-04-07T06:18:05Z","year":"2023","oa_version":"Published Version","has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2663 - 337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-04-26T12:16:56Z","page":"115","date_created":"2023-04-06T07:54:09Z","supervisor":[{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"month":"04","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"GradSch"},{"_id":"RySh"}],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","citation":{"ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","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>.","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>.","short":"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>","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>"},"alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"id":"3A96634C-F248-11E8-B48F-1D18A9856A87","last_name":"Alcarva","first_name":"Catarina","full_name":"Alcarva, Catarina"}],"day":"06","project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"doi":"10.15479/at:ista:12809","language":[{"iso":"eng"}]},{"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","citation":{"ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>","short":"J.G. Danzl, (2023).","mla":"Danzl, Johann G. <i>Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>.","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>."},"oa_version":"Published Version","has_accepted_license":"1","year":"2023","type":"research_data","author":[{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"contributor":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky"},{"first_name":"Eder","last_name":"Miguel Villalba","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"},{"first_name":"Jake","last_name":"Watson","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Jakob","last_name":"Troidl"},{"first_name":"Johanna","last_name":"Beyer"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","first_name":"Wiebke"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban"},{"last_name":"Broichhagen","first_name":"Johannes"},{"first_name":"Seth G. N. ","last_name":"Grant"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"last_name":"Pfister","first_name":"Hanspeter"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"day":"19","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. 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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 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