[{"ec_funded":1,"scopus_import":"1","day":"04","citation":{"ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>."},"volume":187,"date_created":"2024-01-17T12:45:40Z","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","file_date_updated":"2024-01-22T13:41:41Z","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"issue":"1","publication_status":"published","publisher":"Elsevier","page":"130-148.e17","year":"2024","department":[{"_id":"JiFr"}],"date_published":"2024-01-04T00:00:00Z","doi":"10.1016/j.cell.2023.11.021","language":[{"iso":"eng"}],"acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","article_processing_charge":"Yes (in subscription journal)","file":[{"file_name":"2024_Cell_Kuhn.pdf","success":1,"file_size":13194060,"relation":"main_file","date_updated":"2024-01-22T13:41:41Z","file_id":"14874","content_type":"application/pdf","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","date_created":"2024-01-22T13:41:41Z","access_level":"open_access","creator":"dernst"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","call_identifier":"FWF"}],"author":[{"full_name":"Kuhn, Andre","last_name":"Kuhn","first_name":"Andre"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"full_name":"Mutte, Sumanth","first_name":"Sumanth","last_name":"Mutte"},{"full_name":"Dubey, Shiv Mani","last_name":"Dubey","first_name":"Shiv Mani"},{"first_name":"Vanessa Polet","last_name":"Carrillo Carrasco","full_name":"Carrillo Carrasco, Vanessa Polet"},{"full_name":"Boeren, Sjef","first_name":"Sjef","last_name":"Boeren"},{"full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"last_name":"Koehorst","first_name":"Jasper","full_name":"Koehorst, Jasper"},{"last_name":"Kohchi","first_name":"Takayuki","full_name":"Kohchi, Takayuki"},{"first_name":"Ryuichi","last_name":"Nishihama","full_name":"Nishihama, Ryuichi"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sprakel, Joris","first_name":"Joris","last_name":"Sprakel"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"has_accepted_license":"1","isi":1,"_id":"14826","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"publication":"Cell","ddc":["580"],"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"status":"public","article_type":"original","intvolume":"       187","pmid":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","related_material":{"record":[{"id":"19395","status":"public","relation":"dissertation_contains"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"oa_version":"Published Version","quality_controlled":"1","date_updated":"2026-08-14T09:33:45Z","abstract":[{"text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.","lang":"eng"}],"month":"01","external_id":{"isi":["001152705700001"],"pmid":["38128538"]}},{"date_created":"2024-12-22T23:01:47Z","volume":15364,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2024/1097"}],"citation":{"ieee":"M. Anastos <i>et al.</i>, “The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging,” in <i>22nd International Conference on Theory of Cryptography</i>, Milan, Italy, 2024, vol. 15364, pp. 413–443.","chicago":"Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” In <i>22nd International Conference on Theory of Cryptography</i>, 15364:413–43. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>.","mla":"Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” <i>22nd International Conference on Theory of Cryptography</i>, vol. 15364, Springer Nature, 2024, pp. 413–43, doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>.","short":"M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography, Springer Nature, 2024, pp. 413–443.","ama":"Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In: <i>22nd International Conference on Theory of Cryptography</i>. Vol 15364. Springer Nature; 2024:413-443. doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>","ista":"Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G, Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. 22nd International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.","apa":"Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual Perez, G., &#38; Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In <i>22nd International Conference on Theory of Cryptography</i> (Vol. 15364, pp. 413–443). Milan, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>"},"OA_type":"green","day":"02","conference":{"end_date":"2024-12-06","name":"TCC: Theory of Cryptography","location":"Milan, Italy","start_date":"2024-12-02"},"scopus_import":"1","corr_author":"1","year":"2024","page":"413-443","publisher":"Springer Nature","publication_status":"published","type":"conference","title":"The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging","publication":"22nd International Conference on Theory of Cryptography","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031780103"],"eissn":["1611-3349"]},"_id":"18702","alternative_title":["LNCS"],"isi":1,"author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","full_name":"Anastos, Michael","last_name":"Anastos","first_name":"Michael"},{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt","first_name":"Benedikt","last_name":"Auerbach"},{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","first_name":"Mirza Ahad","full_name":"Baig, Mirza Ahad"},{"full_name":"Cueto Noval, Miguel","orcid":"0000-0002-2505-4246","first_name":"Miguel","last_name":"Cueto Noval","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan"},{"first_name":"Guillermo","last_name":"Pascual Perez","orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"repository","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-78011-0_14","department":[{"_id":"MaKw"},{"_id":"KrPi"}],"date_published":"2024-12-02T00:00:00Z","external_id":{"isi":["001545628900014"]},"month":"12","abstract":[{"lang":"eng","text":"In this work we prove lower bounds on the (communication) cost of maintaining a shared key among a dynamic group of users. Being “dynamic” means one can add and remove users from the group. This captures important protocols like multicast encryption (ME) and continuous group-key agreement (CGKA), which is the primitive underlying many group messaging applications. We prove our bounds in a combinatorial setting where the state of the protocol progresses in rounds. The state of the protocol in each round is captured by a set system, with each of its elements specifying a set of users who share a secret key. We show this combinatorial model implies bounds in symbolic models for ME and CGKA that capture, as building blocks, PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable public-key encryption in the setting of CGKA. The models are related to the ones used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality – that the cost (number of uploaded ciphertexts) for replacing a set of d users in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of Ω(log(n)) for d=1. "}],"date_updated":"2026-08-21T10:53:16Z","quality_controlled":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"status":"public","id":"22664","relation":"dissertation_contains"}]},"intvolume":"     15364","status":"public"},{"month":"07","abstract":[{"lang":"eng","text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results."}],"date_updated":"2026-08-27T11:42:44Z","external_id":{"isi":["001281681100003"]},"oa":1,"related_material":{"record":[{"status":"public","id":"22684","relation":"dissertation_contains"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       136","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"status":"public","quality_controlled":"1","oa_version":"Published Version","_id":"17373","isi":1,"has_accepted_license":"1","author":[{"first_name":"Isaac C","last_name":"Lenton","orcid":"0000-0002-5010-6984","full_name":"Lenton, Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb"},{"full_name":"Pertl, Felix","orcid":"0000-0003-0463-5794","first_name":"Felix","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af"},{"first_name":"Lubuna B","last_name":"Shafeek","full_name":"Shafeek, Lubuna B","orcid":"0000-0001-7180-6050","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"ddc":["530"],"publication_identifier":{"issn":["0021-8979"],"eissn":["1089-7550"]},"publication":"Journal of Applied Physics","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank the contributions of the whole Waitukaitis Group for useful discussions and feedback.","language":[{"iso":"eng"}],"doi":"10.1063/5.0215151","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"date_published":"2024-07-28T00:00:00Z","file":[{"file_name":"2024_JourApplPhysics_Lenton.pdf","success":1,"file_size":2537502,"relation":"main_file","date_updated":"2024-08-05T08:19:58Z","date_created":"2024-08-05T08:19:58Z","creator":"dernst","access_level":"open_access","checksum":"6141d05cd68d540a7446dce9490975db","content_type":"application/pdf","file_id":"17386"}],"project":[{"grant_number":"949120","call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}],"article_processing_charge":"No","publisher":"AIP Publishing","publication_status":"published","corr_author":"1","year":"2024","type":"journal_article","title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging","file_date_updated":"2024-08-05T08:19:58Z","issue":"4","citation":{"ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” <i>Journal of Applied Physics</i>, vol. 136, no. 4. AIP Publishing, 2024.","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024).","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. 2024;136(4). doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.","apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>.","mla":"Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>."},"article_number":"045305","date_created":"2024-08-04T22:01:21Z","volume":136,"ec_funded":1,"scopus_import":"1","day":"28"},{"day":"13","scopus_import":"1","series_title":"MIMB","date_created":"2024-08-13T12:16:41Z","volume":2831,"citation":{"ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299."},"edition":"1","type":"book_chapter","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","corr_author":"1","year":"2024","page":"283-299","publication_status":"published","publisher":"Springer Nature","project":[{"grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"article_processing_charge":"No","doi":"10.1007/978-1-0716-3969-6_19","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"date_published":"2024-08-13T00:00:00Z","acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"publication":"Neuronal Morphogenesis","publication_identifier":{"isbn":["9781071639689"],"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071639696"]},"author":[{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889","last_name":"Miranda","first_name":"Osvaldo"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"_id":"17425","alternative_title":["Methods in Molecular Biology"],"editor":[{"first_name":"Kazuhito","last_name":"Toyooka","full_name":"Toyooka, Kazuhito"}],"quality_controlled":"1","oa_version":"None","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"20212","relation":"dissertation_contains"}]},"pmid":1,"intvolume":"      2831","external_id":{"pmid":["39134857"]},"date_updated":"2026-08-29T22:30:06Z","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology."}],"place":"New York, NY","month":"08"},{"oa_version":"Published Version","status":"public","related_material":{"record":[{"status":"public","id":"11420","relation":"part_of_dissertation"},{"status":"public","id":"14459","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9198","status":"public"},{"relation":"part_of_dissertation","id":"17469","status":"public"}]},"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n"}],"date_updated":"2026-06-18T17:55:53Z","degree_awarded":"PhD","month":"08","file":[{"file_id":"17482","checksum":"da6dd3166078934577f6af93d27000e2","content_type":"application/pdf","date_created":"2024-09-02T09:23:32Z","creator":"ashevche","access_level":"open_access","file_size":4468610,"relation":"main_file","date_updated":"2024-10-05T22:30:05Z","embargo":"2024-10-04","file_name":"thesis_a2b.pdf"},{"file_name":"Thesis Alex - ISTA.zip","date_created":"2024-09-02T09:23:46Z","creator":"ashevche","access_level":"closed","file_id":"17483","checksum":"76a39ef252239560923cdda4ce0a31a4","embargo_to":"open_access","content_type":"application/zip","file_size":15930999,"date_updated":"2024-10-05T22:30:05Z","relation":"source_file"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":"W1260-N35"}],"article_processing_charge":"No","OA_place":"repository","doi":"10.15479/at:ista:17465","date_published":"2024-08-29T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["519"],"publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko","first_name":"Aleksandr"}],"_id":"17465","alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"type":"dissertation","file_date_updated":"2024-10-05T22:30:05Z","title":"High-dimensional limits in artificial neural networks","corr_author":"1","year":"2024","page":"232","publication_status":"published","publisher":"Institute of Science and Technology Austria","day":"29","date_created":"2024-08-28T15:14:25Z","citation":{"mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024."}},{"author":[{"full_name":"Kögler, Kevin","first_name":"Kevin","last_name":"Kögler","id":"94ec913c-dc85-11ea-9058-e5051ab2428b"},{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"_id":"17469","alternative_title":["PMLR"],"ddc":["000"],"publication":"Proceedings of the 41st International Conference on Machine Learning","department":[{"_id":"DaAl"},{"_id":"MaMo"}],"date_published":"2024-07-01T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"article_processing_charge":"No","date_updated":"2026-08-29T22:30:17Z","abstract":[{"lang":"eng","text":"Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST."}],"month":"07","external_id":{"arxiv":["2402.05013"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"17465","status":"public"}]},"intvolume":"       235","quality_controlled":"1","oa_version":"Published Version","arxiv":1,"citation":{"mla":"Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 24964–5015.","chicago":"Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:24964–15. ML Research Press, 2024.","ista":"Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.","apa":"Kögler, K., Shevchenko, A., Hassani, H., &#38; Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.","short":"K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015.","ama":"Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:24964-25015.","ieee":"K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 24964–25015."},"main_file_link":[{"url":"https://proceedings.mlr.press/v235/kogler24a.html","open_access":"1"}],"date_created":"2024-08-29T11:47:57Z","volume":235,"scopus_import":"1","conference":{"end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21","location":"Vienna, Austria"},"day":"01","publication_status":"published","publisher":"ML Research Press","corr_author":"1","year":"2024","page":"24964-25015","type":"conference","title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth"},{"day":"10","date_created":"2024-09-08T10:23:25Z","citation":{"apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024."},"supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P"}],"file_date_updated":"2025-03-13T23:30:04Z","title":"Thermal effects in one dimensional Josephson chains","type":"dissertation","page":"82","year":"2024","corr_author":"1","publisher":"Institute of Science and Technology Austria","publication_status":"published","article_processing_charge":"No","OA_place":"publisher","file":[{"file_size":10297052,"date_updated":"2025-03-13T23:30:04Z","relation":"main_file","access_level":"open_access","date_created":"2024-09-12T10:46:04Z","creator":"smukhopa","file_id":"18059","content_type":"application/pdf","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","embargo":"2025-03-13"},{"file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","date_created":"2024-09-12T10:50:58Z","creator":"smukhopa","access_level":"closed","embargo_to":"open_access","checksum":"e352667482701dd18a9a0e7418aef465","content_type":"application/zip","file_id":"18060","relation":"source_file","date_updated":"2025-03-13T23:30:04Z","file_size":29178634}],"project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"date_published":"2024-09-10T00:00:00Z","doi":"10.15479/at:ista:17881","ddc":["539"],"publication_identifier":{"isbn":["978-3-99078-043-5"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"alternative_title":["ISTA Thesis"],"_id":"17881","author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","first_name":"Soham","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559"}],"has_accepted_license":"1","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14032"},{"id":"18057","status":"public","relation":"part_of_dissertation"}]},"status":"public","degree_awarded":"PhD","month":"09","abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"date_updated":"2026-06-03T07:16:04Z"},{"day":"14","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2408.07829","open_access":"1"}],"date_created":"2024-09-11T09:25:22Z","article_number":"2408.07829","citation":{"apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.).","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, 2408.07829, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>.","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>.","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” <i>arXiv</i>. ."},"title":"Dual relaxation oscillations in a Josephson junction array","type":"preprint","year":"2024","corr_author":"1","publication_status":"draft","article_processing_charge":"No","OA_place":"repository","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"date_published":"2024-08-14T00:00:00Z","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"doi":"10.48550/arXiv.2408.07829","acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","language":[{"iso":"eng"}],"publication":"arXiv","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"author":[{"first_name":"Soham","last_name":"Mukhopadhyay","orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"},{"full_name":"Lancheros Naranjo, Diego A","first_name":"Diego A","last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L","first_name":"Jorden L","last_name":"Senior"},{"first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"_id":"18057","oa_version":"Preprint","arxiv":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","id":"20324","status":"public"},{"relation":"dissertation_contains","status":"public","id":"17881"}]},"oa":1,"external_id":{"arxiv":["2408.07829"]},"date_updated":"2026-08-29T22:30:18Z","abstract":[{"text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations.","lang":"eng"}],"month":"08"},{"citation":{"ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>"},"article_number":"e1011376","OA_type":"gold","APC_amount":"3145,39 EUR","date_created":"2024-09-08T22:01:11Z","volume":20,"scopus_import":"1","day":"30","publisher":"Public Library of Science","publication_status":"published","corr_author":"1","year":"2024","type":"journal_article","title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","file_date_updated":"2024-09-11T07:54:12Z","issue":"8","_id":"17890","isi":1,"has_accepted_license":"1","author":[{"last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"PLoS Genetics","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"ddc":["570"],"DOAJ_listed":"1","language":[{"iso":"eng"}],"acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","doi":"10.1371/journal.pgen.1011376","department":[{"_id":"BeVi"}],"date_published":"2024-08-30T00:00:00Z","file":[{"file_size":8962687,"relation":"main_file","date_updated":"2024-09-11T07:54:12Z","content_type":"application/pdf","checksum":"f5d96b9af57126fc1063e951440477d6","file_id":"18056","access_level":"open_access","creator":"dernst","date_created":"2024-09-11T07:54:12Z","file_name":"2024_PloSGenetics_Elkrewi.pdf","success":1}],"project":[{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"OA_place":"publisher","article_processing_charge":"Yes","month":"08","abstract":[{"text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group.","lang":"eng"}],"date_updated":"2026-08-29T22:30:30Z","external_id":{"pmid":["39213449"],"isi":["001304090200001"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project"}],"record":[{"relation":"research_data","status":"public","id":"17362"},{"status":"public","id":"19386","relation":"dissertation_contains"}]},"pmid":1,"intvolume":"        20","article_type":"original","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)"},"status":"public","quality_controlled":"1","oa_version":"Published Version"},{"year":"2024","page":"105","corr_author":"1","publication_status":"published","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"file_date_updated":"2025-01-10T23:30:10Z","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"type":"dissertation","date_created":"2024-06-07T16:14:13Z","citation":{"ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024."},"day":"20","ec_funded":1,"date_updated":"2026-04-07T13:21:37Z","abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"month":"06","degree_awarded":"PhD","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"related_material":{"record":[{"id":"542","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10767","relation":"part_of_dissertation"}]},"ddc":["576"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","first_name":"Réka K"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"_id":"17119","article_processing_charge":"No","OA_place":"publisher","file":[{"file_name":"thesis.zip","file_size":180557931,"date_updated":"2025-01-10T23:30:10Z","relation":"source_file","access_level":"closed","creator":"rkelemen","date_created":"2024-06-07T16:09:17Z","file_id":"17121","content_type":"application/zip","checksum":"fab59146e3b3dc2e5d214576984a2a63","embargo_to":"open_access"},{"file_name":"thesis_to_archive.pdf","embargo":"2025-01-10","date_updated":"2025-01-10T23:30:10Z","relation":"main_file","file_size":19405484,"content_type":"application/pdf","file_id":"17213","checksum":"91cc4c25a792239e8a7688e8aec7c62a","creator":"rkelemen","access_level":"open_access","date_created":"2024-07-10T08:00:20Z"}],"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"date_published":"2024-06-20T00:00:00Z","doi":"10.15479/at:ista:17119","language":[{"iso":"eng"}]},{"degree_awarded":"PhD","month":"10","abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"date_updated":"2026-04-07T13:23:59Z","oa_version":"Published Version","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","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)"},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"ddc":["572"],"publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"_id":"18477","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","author":[{"id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M","last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M"}],"file":[{"file_name":"20241029_PhD_thesis_BKaczmarek.docx","creator":"bkaczmar","access_level":"closed","date_created":"2024-10-29T11:56:36Z","checksum":"2053294ea4d770c495e4cc501e2a218b","embargo_to":"open_access","file_id":"18485","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_updated":"2025-10-29T23:30:02Z","file_size":23136626},{"date_updated":"2025-10-29T23:30:02Z","relation":"main_file","file_size":11707360,"date_created":"2024-10-29T11:56:44Z","access_level":"open_access","creator":"bkaczmar","content_type":"application/pdf","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","file_id":"18486","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","embargo":"2025-10-29"}],"article_processing_charge":"No","OA_place":"publisher","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:18477","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"date_published":"2024-10-29T00:00:00Z","corr_author":"1","year":"2024","page":"124","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","title":"Biochemical and structural insights into ADAR1 RNA editing","file_date_updated":"2025-10-29T23:30:02Z","date_created":"2024-10-27T07:35:13Z","citation":{"ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>"},"day":"29"},{"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":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)"},"status":"public","degree_awarded":"MS","month":"05","abstract":[{"text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. ","lang":"eng"}],"date_updated":"2026-04-07T13:05:00Z","OA_place":"publisher","article_processing_charge":"No","file":[{"checksum":"095817a6c944954ac3f277e547031a33","file_id":"15354","content_type":"application/pdf","date_created":"2024-05-02T12:26:13Z","creator":"cchlebak","access_level":"open_access","file_size":5936142,"date_updated":"2025-05-02T22:30:04Z","relation":"main_file","embargo":"2025-05-02","file_name":"Murmann_Thesis_final_2024_2.pdf"},{"relation":"source_file","date_updated":"2025-05-02T22:30:04Z","file_size":20645510,"date_created":"2024-05-02T12:37:56Z","creator":"cchlebak","access_level":"closed","content_type":"application/x-zip-compressed","embargo_to":"open_access","checksum":"43b632255372973a437ac87739cfd4db","file_id":"15355","file_name":"Murmann_Thesis_final_2024.zip"}],"language":[{"iso":"eng"}],"department":[{"_id":"SaSi"},{"_id":"GradSch"}],"date_published":"2024-05-02T00:00:00Z","doi":"10.15479/at:ista:15352","publication_identifier":{"issn":["2791-4585"]},"ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"alternative_title":["ISTA Master's Thesis"],"_id":"15352","author":[{"id":"1d390868-f128-11eb-9611-a0ca5f7833b5","full_name":"Murmann, Julie Stefanie","first_name":"Julie Stefanie","last_name":"Murmann"}],"has_accepted_license":"1","supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"file_date_updated":"2025-05-02T22:30:04Z","title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","type":"dissertation","page":"54","year":"2024","corr_author":"1","publisher":"Institute of Science and Technology Austria","publication_status":"published","day":"02","date_created":"2024-05-02T08:31:38Z","citation":{"ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>."}},{"publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"_id":"14821","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","author":[{"last_name":"Chiossi","first_name":"Heloisa","full_name":"Chiossi, Heloisa","orcid":"0009-0004-2973-278X","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"file":[{"file_name":"PhD_Thesis_190124.docx","file_size":8656268,"relation":"source_file","date_updated":"2025-01-19T23:30:04Z","date_created":"2024-01-19T11:04:05Z","creator":"hchiossi","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"d3fa3de1abd5af5204c13e9d55375615","file_id":"14838"},{"file_name":"PhD_Thesis_190124.pdf","embargo":"2025-01-19","relation":"main_file","date_updated":"2025-01-19T23:30:04Z","file_size":6567275,"creator":"hchiossi","date_created":"2024-01-19T11:03:59Z","access_level":"open_access","file_id":"14839","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","content_type":"application/pdf"}],"article_processing_charge":"No","OA_place":"publisher","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14821","date_published":"2024-01-19T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"month":"01","degree_awarded":"PhD","date_updated":"2026-04-07T13:21:56Z","abstract":[{"lang":"eng","text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour."}],"oa_version":"Published Version","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_created":"2024-01-16T14:25:21Z","citation":{"ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>"},"day":"19","ec_funded":1,"corr_author":"1","year":"2024","page":"89","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"type":"dissertation","title":"Adaptive hierarchical representations in the hippocampus","file_date_updated":"2025-01-19T23:30:04Z"},{"publisher":"Elsevier","publication_status":"published","corr_author":"1","page":"755-771.e9","year":"2024","type":"journal_article","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","file_date_updated":"2025-04-23T14:02:08Z","issue":"5","citation":{"ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024."},"OA_type":"hybrid","date_created":"2024-01-21T23:00:56Z","volume":112,"scopus_import":"1","ec_funded":1,"day":"06","month":"03","abstract":[{"lang":"eng","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."}],"date_updated":"2026-08-29T22:30:33Z","external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"oa":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","description":"News on ISTA Website","relation":"press_release"}],"record":[{"id":"15101","status":"public","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       112","pmid":1,"article_type":"original","PlanS_conform":"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)"},"status":"public","quality_controlled":"1","oa_version":"Published Version","_id":"14843","isi":1,"has_accepted_license":"1","author":[{"last_name":"Chen","first_name":"JingJing","full_name":"Chen, JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chong","last_name":"Chen","first_name":"Chong"},{"full_name":"Arai, Itaru","first_name":"Itaru","last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2344-1039","full_name":"Kim, Olena","last_name":"Kim","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"publication":"Neuron","ddc":["570"],"language":[{"iso":"eng"}],"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","doi":"10.1016/j.neuron.2023.12.002","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"date_published":"2024-03-06T00:00:00Z","project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","grant_number":"Z00312"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"file":[{"file_size":8192355,"relation":"main_file","date_updated":"2025-04-23T14:02:08Z","date_created":"2025-04-23T14:02:08Z","creator":"dernst","access_level":"open_access","checksum":"30098b4f0209556ddfb3540a23d07ca5","file_id":"19614","content_type":"application/pdf","file_name":"2024_Neuron_Chen.pdf","success":1}],"article_processing_charge":"Yes (via OA deal)","OA_place":"publisher"},{"citation":{"ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>."},"date_created":"2024-03-11T10:09:54Z","ec_funded":1,"day":"11","publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2024","page":"84","corr_author":"1","file_date_updated":"2024-04-02T22:30:03Z","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","type":"dissertation","supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"alternative_title":["ISTA Thesis"],"_id":"15101","author":[{"id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","last_name":"Chen","full_name":"Chen, JingJing"}],"has_accepted_license":"1","ddc":["570"],"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"PeJo"}],"date_published":"2024-03-11T00:00:00Z","doi":"10.15479/at:ista:15101","OA_place":"publisher","article_processing_charge":"No","file":[{"relation":"source_file","date_updated":"2024-04-02T22:30:03Z","file_size":11271363,"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"15104","checksum":"db4947474ffa271e66c254b6fe876a55","access_level":"closed","date_created":"2024-03-11T14:10:58Z","creator":"jchen","file_name":"Thesis_Jingjing CHEN.docx"},{"date_created":"2024-03-11T14:11:06Z","access_level":"open_access","creator":"jchen","content_type":"application/pdf","file_id":"15105","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_size":16627311,"date_updated":"2024-04-02T22:30:03Z","relation":"main_file","embargo":"2024-04-01","file_name":"Thesis_Jingjing CHEN_merged.pdf"}],"project":[{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383"}],"month":"03","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission."}],"date_updated":"2026-04-07T13:24:22Z","oa":1,"related_material":{"record":[{"id":"14843","status":"public","relation":"part_of_dissertation"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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)"},"status":"public","oa_version":"Published Version"},{"date_created":"2024-10-26T20:02:42Z","citation":{"chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024."},"day":"28","ec_funded":1,"year":"2024","page":"97","corr_author":"1","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"}],"file_date_updated":"2025-05-05T22:30:04Z","title":"Visualizing the neuronal transcriptional landscape with tissue context","type":"dissertation","ddc":["570"],"publication_identifier":{"isbn":["978-3-99078-044-2"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"_id":"18471","author":[{"full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","article_processing_charge":"No","OA_place":"publisher","file":[{"relation":"source_file","date_updated":"2025-05-05T22:30:04Z","file_size":183077763,"creator":"nagudelo","date_created":"2024-10-26T22:29:06Z","access_level":"closed","embargo_to":"open_access","checksum":"6d7c7725d040d8debc070dcb35ac965d","file_id":"18475","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx"},{"embargo":"2025-05-05","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","date_created":"2024-10-26T23:13:33Z","access_level":"open_access","creator":"nagudelo","file_id":"18476","content_type":"application/pdf","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","relation":"main_file","date_updated":"2025-05-05T22:30:04Z","file_size":47027710}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232"}],"language":[{"iso":"eng"}],"date_published":"2024-10-28T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"doi":"10.15479/at:ista:18471","degree_awarded":"PhD","month":"10","date_updated":"2026-04-14T08:34:37Z","abstract":[{"lang":"eng","text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. "}],"oa_version":"Published Version","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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)"},"status":"public"},{"oa_version":"Published Version","related_material":{"record":[{"id":"12349","status":"public","relation":"part_of_dissertation"},{"relation":"research_data","status":"public","id":"12370"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"month":"11","degree_awarded":"PhD","OA_embargo":"12","date_updated":"2026-04-07T13:24:48Z","abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"file":[{"file_size":75512262,"relation":"source_file","date_updated":"2025-11-11T23:30:02Z","file_id":"18589","checksum":"ebb000d361c36b22ed6e639a931c6b7c","content_type":"application/zip","embargo_to":"open_access","creator":"dgupta","date_created":"2024-11-25T14:44:03Z","access_level":"closed","file_name":"PhD Thesis - Divyansh Gupta.zip"},{"embargo":"2025-11-11","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","checksum":"1282401eb71598bc311058b0fcefc6a1","file_id":"18591","content_type":"application/pdf","creator":"dgupta","access_level":"open_access","date_created":"2024-11-26T11:43:19Z","file_size":6412619,"relation":"main_file","date_updated":"2025-11-11T23:30:02Z"}],"project":[{"grant_number":"101086580","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"756502","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"OA_place":"publisher","article_processing_charge":"No","language":[{"iso":"eng"}],"acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","doi":"10.15479/at:ista:18574","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"date_published":"2024-11-22T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"ddc":["573"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-050-3"]},"_id":"18574","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","author":[{"full_name":"Gupta, Divyansh","orcid":"0000-0001-7400-6665","first_name":"Divyansh","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330"}],"type":"dissertation","file_date_updated":"2025-11-11T23:30:02Z","title":"Visual adaptations to natural statistics","corr_author":"1","page":"86","year":"2024","publisher":"Institute of Science and Technology Austria","publication_status":"published","day":"22","ec_funded":1,"date_created":"2024-11-20T21:30:44Z","citation":{"ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria."}},{"publication":"Nature Structural and Molecular Biology","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"ddc":["572"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"ScienComp"}],"isi":1,"_id":"15323","author":[{"orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","first_name":"Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"has_accepted_license":"1","article_processing_charge":"No","file":[{"embargo":"2025-01-01","file_name":"megacomplex_submit_NSMB_withFigures.pdf","checksum":"21f05d188762acd7f49a97f3d09c8d9f","content_type":"application/pdf","file_id":"15392","access_level":"open_access","date_created":"2024-05-14T11:57:56Z","creator":"lsazanov","relation":"main_file","date_updated":"2025-01-01T23:30:03Z","file_size":24424729}],"project":[{"grant_number":"101020697","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"acknowledgement":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.","language":[{"iso":"eng"}],"department":[{"_id":"LeSa"}],"date_published":"2024-07-01T00:00:00Z","doi":"10.1038/s41594-024-01255-0","external_id":{"pmid":["38575788"],"isi":["001196897300001"]},"month":"07","abstract":[{"lang":"eng","text":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions."}],"date_updated":"2025-11-24T08:35:04Z","oa_version":"Submitted Version","quality_controlled":"1","intvolume":"        31","pmid":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41594-025-01721-3","relation":"erratum"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":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)"},"status":"public","article_type":"original","volume":31,"date_created":"2024-04-14T22:01:03Z","citation":{"ieee":"I. Vercellino and L. A. Sazanov, “SCAF1 drives the compositional diversity of mammalian respirasomes,” <i>Nature Structural and Molecular Biology</i>, vol. 31. Springer Nature, pp. 1061–1071, 2024.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1061–71, doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>.","short":"I. Vercellino, L.A. Sazanov, Nature Structural and Molecular Biology 31 (2024) 1061–1071.","ama":"Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. 2024;31:1061-1071. doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>","apa":"Vercellino, I., &#38; Sazanov, L. A. (2024). SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>","ista":"Vercellino I, Sazanov LA. 2024. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 31, 1061–1071."},"day":"01","scopus_import":"1","ec_funded":1,"page":"1061-1071","year":"2024","corr_author":"1","publisher":"Springer Nature","publication_status":"published","title":"SCAF1 drives the compositional diversity of mammalian respirasomes","file_date_updated":"2025-01-01T23:30:03Z","type":"journal_article"},{"citation":{"mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(8). doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"P. Koppensteiner <i>et al.</i>, “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8. National Academy of Sciences, 2024."},"article_number":"e2301449121","OA_type":"hybrid","APC_amount":"5887,8 EUR","date_created":"2024-03-05T09:23:55Z","volume":121,"scopus_import":"1","ec_funded":1,"day":"20","publisher":"National Academy of Sciences","publication_status":"published","corr_author":"1","year":"2024","type":"journal_article","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","file_date_updated":"2024-03-12T13:42:42Z","issue":"8","_id":"15084","isi":1,"has_accepted_license":"1","author":[{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481"},{"last_name":"Önal","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","first_name":"Elodie","last_name":"Le Monnier"},{"last_name":"Roy","first_name":"Utsa","full_name":"Roy, Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"full_name":"Nakamura, Yukihiro","first_name":"Yukihiro","last_name":"Nakamura"},{"first_name":"Tetsushi","last_name":"Sadakata","full_name":"Sadakata, Tetsushi"},{"full_name":"Sanbo, Makoto","first_name":"Makoto","last_name":"Sanbo"},{"first_name":"Masumi","last_name":"Hirabayashi","full_name":"Hirabayashi, Masumi"},{"full_name":"Rhee, JeongSeop","first_name":"JeongSeop","last_name":"Rhee"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"ddc":["570"],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","language":[{"iso":"eng"}],"acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","doi":"10.1073/pnas.2301449121","department":[{"_id":"RySh"},{"_id":"PeJo"}],"date_published":"2024-02-20T00:00:00Z","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","grant_number":"694539"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file":[{"file_size":13648221,"relation":"main_file","date_updated":"2024-03-12T13:42:42Z","date_created":"2024-03-12T13:42:42Z","access_level":"open_access","creator":"dernst","file_id":"15110","content_type":"application/pdf","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","file_name":"2024_PNAS_Koppensteiner.pdf","success":1}],"article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","month":"02","date_updated":"2026-08-29T22:30:37Z","abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n            <jats:sup>2+</jats:sup>\r\n            -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"external_id":{"pmid":["38346189"],"isi":["001208567300006"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/"}],"record":[{"relation":"research_data","status":"public","id":"13173"},{"relation":"dissertation_contains","id":"19271","status":"public"}]},"intvolume":"       121","pmid":1,"article_type":"original","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","oa_version":"Published Version"},{"month":"08","date_updated":"2026-08-29T22:30:39Z","abstract":[{"text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.","lang":"eng"}],"external_id":{"isi":["001289684800001"],"pmid":["38776925"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"intvolume":"        59","pmid":1,"article_type":"original","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","oa_version":"Published Version","_id":"17148","isi":1,"has_accepted_license":"1","author":[{"full_name":"Krammer, Teresa","last_name":"Krammer","first_name":"Teresa"},{"full_name":"Stuart, Hannah T.","first_name":"Hannah T.","last_name":"Stuart"},{"first_name":"Elena","last_name":"Gromberg","full_name":"Gromberg, Elena"},{"full_name":"Ishihara, Keisuke","last_name":"Ishihara","first_name":"Keisuke"},{"full_name":"Cislo, Dillon","last_name":"Cislo","first_name":"Dillon"},{"full_name":"Melchionda, Manuela","last_name":"Melchionda","first_name":"Manuela"},{"last_name":"Becerril Perez","first_name":"Fernando","full_name":"Becerril Perez, Fernando"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"full_name":"Costantini, Elena","last_name":"Costantini","first_name":"Elena"},{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","last_name":"Rus","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093"},{"first_name":"Laura","last_name":"Arbanas","full_name":"Arbanas, Laura"},{"full_name":"Hörmann, Alexandra","first_name":"Alexandra","last_name":"Hörmann"},{"full_name":"Neumüller, Ralph A.","last_name":"Neumüller","first_name":"Ralph A."},{"full_name":"Elvassore, Nicola","first_name":"Nicola","last_name":"Elvassore"},{"first_name":"Eric","last_name":"Siggia","full_name":"Siggia, Eric"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"first_name":"Elly M.","last_name":"Tanaka","full_name":"Tanaka, Elly M."}],"publication":"Developmental Cell","ddc":["570"],"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2024.04.021","date_published":"2024-08-01T00:00:00Z","department":[{"_id":"AnKi"}],"project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"file":[{"access_level":"open_access","creator":"dernst","date_created":"2025-01-13T10:59:12Z","content_type":"application/pdf","checksum":"fefdea9c02862b4bb74de49b65ce638a","file_id":"18841","file_size":6249076,"date_updated":"2025-01-13T10:59:12Z","relation":"main_file","success":1,"file_name":"2024_DevelopmentalCell_Krammer.pdf"}],"article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","publisher":"Elsevier","publication_status":"published","page":"1940-1953.e10","year":"2024","type":"journal_article","title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","file_date_updated":"2025-01-13T10:59:12Z","issue":"15","OA_type":"hybrid","citation":{"ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>","ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. 2024;59(15):1940-1953.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10.","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>.","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>.","ieee":"T. Krammer <i>et al.</i>, “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” <i>Developmental Cell</i>, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024."},"date_created":"2024-06-16T22:01:07Z","volume":59,"scopus_import":"1","day":"01"}]