[{"page":"1177-1187","abstract":[{"lang":"eng","text":"By codesigning a metaoptical front end in conjunction with an image‐processing back end, we demonstrate noise sensitivity and compactness substantially superior to either an optics‐only or a computation‐only approach, illustrated by two examples: subwavelength imaging and reconstruction of the full polarization coherence matrices of multiple light sources. Our end‐to‐end inverse designs couple the solution of the full Maxwell equations—exploiting all aspects of wave physics arising in subwavelength scatterers—with inverse‐scattering algorithms in a single large‐scale optimization involving degrees of freedom. The resulting structures scatter light in a way that is radically different from either a conventional lens or a random microstructure, and suppress the noise sensitivity of the inverse‐scattering computation by several orders of magnitude. Incorporating the full wave physics is especially crucial for detecting spectral and polarization information that is discarded by geometric optics and scalar diffraction theory."}],"date_created":"2026-03-30T12:22:48Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","extern":"1","author":[{"last_name":"Lin","full_name":"Lin, Zin","first_name":"Zin"},{"first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes"},{"last_name":"Pestourie","full_name":"Pestourie, Raphaël","first_name":"Raphaël"},{"first_name":"Marin","last_name":"Soljačić","full_name":"Soljačić, Marin"},{"last_name":"Majumdar","full_name":"Majumdar, Arka","first_name":"Arka"},{"full_name":"Johnson, Steven G.","last_name":"Johnson","first_name":"Steven G."}],"citation":{"apa":"Lin, Z., Roques-Carmes, C., Pestourie, R., Soljačić, M., Majumdar, A., & Johnson, S. G. (2020). End‐to‐end nanophotonic inverse design for imaging and polarimetry. Nanophotonics. Wiley. https://doi.org/10.1515/nanoph-2020-0579","ieee":"Z. Lin, C. Roques-Carmes, R. Pestourie, M. Soljačić, A. Majumdar, and S. G. Johnson, “End‐to‐end nanophotonic inverse design for imaging and polarimetry,” Nanophotonics, vol. 10, no. 3. Wiley, pp. 1177–1187, 2020.","ista":"Lin Z, Roques-Carmes C, Pestourie R, Soljačić M, Majumdar A, Johnson SG. 2020. End‐to‐end nanophotonic inverse design for imaging and polarimetry. Nanophotonics. 10(3), 1177–1187.","short":"Z. Lin, C. Roques-Carmes, R. Pestourie, M. Soljačić, A. Majumdar, S.G. Johnson, Nanophotonics 10 (2020) 1177–1187.","ama":"Lin Z, Roques-Carmes C, Pestourie R, Soljačić M, Majumdar A, Johnson SG. End‐to‐end nanophotonic inverse design for imaging and polarimetry. Nanophotonics. 2020;10(3):1177-1187. doi:10.1515/nanoph-2020-0579","chicago":"Lin, Zin, Charles Roques-Carmes, Raphaël Pestourie, Marin Soljačić, Arka Majumdar, and Steven G. Johnson. “End‐to‐end Nanophotonic Inverse Design for Imaging and Polarimetry.” Nanophotonics. Wiley, 2020. https://doi.org/10.1515/nanoph-2020-0579.","mla":"Lin, Zin, et al. “End‐to‐end Nanophotonic Inverse Design for Imaging and Polarimetry.” Nanophotonics, vol. 10, no. 3, Wiley, 2020, pp. 1177–87, doi:10.1515/nanoph-2020-0579."},"title":"End‐to‐end nanophotonic inverse design for imaging and polarimetry","DOAJ_listed":"1","oa":1,"oa_version":"Published Version","scopus_import":"1","year":"2020","OA_place":"publisher","keyword":["computational imaging","end-to-end photonic inverse design","inverse scattering","meta-optics","polarimetry"],"publisher":"Wiley","intvolume":" 10","publication_identifier":{"eissn":["2192-8614"],"issn":["2192-8614"]},"volume":10,"language":[{"iso":"eng"}],"day":"23","publication":"Nanophotonics","external_id":{"arxiv":["2006.09145"]},"publication_status":"published","issue":"3","ddc":["530"],"arxiv":1,"doi":"10.1515/nanoph-2020-0579","month":"12","_id":"21642","quality_controlled":"1","date_updated":"2026-04-27T09:29:25Z","date_published":"2020-12-23T00:00:00Z","OA_type":"gold","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","main_file_link":[{"url":"https://doi.org/10.1515/nanoph-2020-0579","open_access":"1"}],"type":"journal_article","article_processing_charge":"No"},{"citation":{"mla":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84.","chicago":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press."},"author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko"},{"last_name":"Mondelli","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020"}],"title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","file":[{"creator":"dernst","file_id":"9217","success":1,"content_type":"application/pdf","file_name":"2020_PMLR_Shevchenko.pdf","file_size":5336380,"checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","date_created":"2021-03-02T15:38:14Z","access_level":"open_access","relation":"main_file","date_updated":"2021-03-02T15:38:14Z"}],"date_created":"2021-02-25T09:36:22Z","abstract":[{"text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks.","lang":"eng"}],"file_date_updated":"2021-03-02T15:38:14Z","acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"page":"8773-8784","has_accepted_license":"1","year":"2020","oa_version":"Published Version","oa":1,"publication":"Proceedings of the 37th International Conference on Machine Learning","external_id":{"arxiv":["1912.10095"]},"publication_status":"published","language":[{"iso":"eng"}],"day":"13","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"volume":119,"related_material":{"record":[{"relation":"dissertation_contains","id":"17465","status":"public"}]},"publisher":"ML Research Press","intvolume":" 119","article_processing_charge":"No","date_published":"2020-07-13T00:00:00Z","type":"conference","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","quality_controlled":"1","date_updated":"2026-05-19T22:30:05Z","_id":"9198","arxiv":1,"ddc":["000"],"month":"07"},{"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","date_published":"2020-09-09T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"dissertation","_id":"8350","date_updated":"2025-09-11T07:08:52Z","ddc":["570"],"month":"09","doi":"10.15479/AT:ISTA:8350","corr_author":"1","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_status":"published","language":[{"iso":"eng"}],"day":"09","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7001"},{"id":"6508","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"735","status":"public"},{"status":"public","id":"661","relation":"part_of_dissertation"}]},"supervisor":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2020","oa_version":"None","oa":1,"author":[{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"}],"citation":{"mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350"},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","file":[{"file_name":"Shayan-Thesis-Final.docx","relation":"source_file","date_updated":"2021-09-11T22:30:05Z","embargo_to":"open_access","checksum":"6e47871c74f85008b9876112eb3fcfa1","date_created":"2020-09-09T11:06:27Z","access_level":"closed","file_size":65194814,"creator":"sshamip","file_id":"8351","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","creator":"sshamip","file_id":"8352","file_size":23729605,"checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","access_level":"open_access","date_created":"2020-09-09T11:06:13Z","date_updated":"2021-09-11T22:30:05Z","relation":"main_file","embargo":"2021-09-10","file_name":"Shayan-Thesis-Final.pdf"}],"file_date_updated":"2021-09-11T22:30:05Z","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"date_created":"2020-09-09T11:12:10Z","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","page":"107"},{"page":"98","department":[{"_id":"CaGu"}],"date_created":"2020-04-24T16:00:51Z","abstract":[{"text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo.","lang":"eng"}],"file_date_updated":"2021-10-31T23:30:05Z","file":[{"file_size":3268017,"access_level":"open_access","checksum":"fb9a4468eb27be92690728e35c823796","date_created":"2020-04-28T11:19:21Z","date_updated":"2021-10-31T23:30:05Z","relation":"main_file","embargo":"2021-10-30","file_name":"Thesis_without-signatures_PDFA.pdf","content_type":"application/pdf","file_id":"7692","creator":"stgingl"},{"file_name":"Thesis_without signatures.docx","file_size":5167703,"date_created":"2020-04-28T11:19:24Z","checksum":"f6c80ca97104a631a328cb79a2c53493","access_level":"closed","embargo_to":"open_access","relation":"source_file","date_updated":"2021-10-31T23:30:05Z","creator":"stgingl","file_id":"7693","content_type":"application/octet-stream"}],"title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","citation":{"apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680."},"author":[{"first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6709-2195","last_name":"Kainrath","full_name":"Kainrath, Stephanie"}],"oa":1,"oa_version":"None","year":"2020","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"related_material":{"record":[{"id":"1028","status":"public","relation":"dissertation_contains"}]},"publication_identifier":{"eissn":["2663-337X"]},"day":"24","language":[{"iso":"eng"}],"publication_status":"published","corr_author":"1","degree_awarded":"PhD","month":"04","doi":"10.15479/AT:ISTA:7680","ddc":["570"],"date_updated":"2025-11-03T23:30:47Z","_id":"7680","type":"dissertation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2020-04-24T00:00:00Z","article_processing_charge":"No","alternative_title":["ISTA Thesis"]},{"date_published":"2020-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","article_processing_charge":"Yes (via OA deal)","issue":"3","ddc":["570"],"month":"12","doi":"10.1016/j.jsb.2020.107633","_id":"8586","quality_controlled":"1","date_updated":"2026-05-19T22:30:09Z","language":[{"iso":"eng"}],"day":"01","publication":"Journal of Structural Biology","external_id":{"isi":["000600997800008"],"pmid":["32987119"]},"corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_status":"published","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"isi":1,"intvolume":" 212","publisher":"Elsevier","volume":212,"publication_identifier":{"issn":["1047-8477"]},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14592"},{"status":"public","id":"12491","relation":"dissertation_contains"}]},"year":"2020","article_number":"107633","has_accepted_license":"1","oa":1,"oa_version":"Published Version","scopus_import":"1","pmid":1,"article_type":"original","file":[{"success":1,"creator":"dernst","file_id":"8937","content_type":"application/pdf","file_name":"2020_JourStrucBiology_Faessler.pdf","date_updated":"2020-12-10T14:01:10Z","relation":"main_file","checksum":"c48cbf594e84fc2f91966ffaafc0918c","access_level":"open_access","date_created":"2020-12-10T14:01:10Z","file_size":7076870}],"author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"full_name":"Zens, Bettina","last_name":"Zens","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur"}],"citation":{"ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.","apa":"Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier, 2020. https://doi.org/10.1016/j.jsb.2020.107633.","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633"},"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","department":[{"_id":"FlSc"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","file_date_updated":"2020-12-10T14:01:10Z","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"date_created":"2020-09-29T13:24:06Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"year":"2020","article_number":"jcs239020","has_accepted_license":"1","oa":1,"oa_version":"Published Version","scopus_import":"1","file":[{"creator":"dernst","file_id":"8435","content_type":"application/pdf","file_name":"2020_JournalCellScience_Dimchev.pdf","embargo":"2020-10-10","relation":"main_file","date_updated":"2020-10-11T22:30:02Z","checksum":"ba917e551acc4ece2884b751434df9ae","access_level":"open_access","date_created":"2020-09-17T14:07:51Z","file_size":13493302}],"article_type":"original","pmid":1,"author":[{"orcid":"0000-0001-8370-6161","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","last_name":"Dimchev"},{"first_name":"Behnam","last_name":"Amiri","full_name":"Amiri, Behnam"},{"first_name":"Ashley C.","full_name":"Humphries, Ashley C.","last_name":"Humphries"},{"full_name":"Schaks, Matthias","last_name":"Schaks","first_name":"Matthias"},{"last_name":"Dimchev","full_name":"Dimchev, Vanessa","first_name":"Vanessa"},{"full_name":"Stradal, Theresia E. B.","last_name":"Stradal","first_name":"Theresia E. B."},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"full_name":"Krause, Matthias","last_name":"Krause","first_name":"Matthias"},{"last_name":"Way","full_name":"Way, Michael","first_name":"Michael"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"}],"citation":{"mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020.","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 2020;133(7). doi:10.1242/jcs.239020","ieee":"G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” Journal of Cell Science, vol. 133, no. 7. The Company of Biologists, 2020.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.239020"},"title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","department":[{"_id":"FlSc"}],"date_created":"2020-09-17T14:00:33Z","file_date_updated":"2020-10-11T22:30:02Z","abstract":[{"lang":"eng","text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. "}],"date_published":"2020-04-09T00:00:00Z","type":"journal_article","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","ddc":["570"],"issue":"7","month":"04","doi":"10.1242/jcs.239020","quality_controlled":"1","date_updated":"2025-04-15T07:52:13Z","_id":"8434","language":[{"iso":"eng"}],"day":"09","external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"publication":"Journal of Cell Science","publication_status":"published","isi":1,"keyword":["Cell Biology"],"publisher":"The Company of Biologists","intvolume":" 133","project":[{"grant_number":"M02495","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"volume":133,"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]}},{"has_accepted_license":"1","year":"2020","oa_version":"Submitted Version","scopus_import":"1","oa":1,"author":[{"full_name":"Mitiouchkina, Tatiana","last_name":"Mitiouchkina","first_name":"Tatiana"},{"first_name":"Alexander S.","full_name":"Mishin, Alexander S.","last_name":"Mishin"},{"first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa"},{"last_name":"Markina","full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M."},{"last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V."},{"last_name":"Guglya","full_name":"Guglya, Elena B.","first_name":"Elena B."},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"last_name":"Palkina","full_name":"Palkina, Kseniia A.","first_name":"Kseniia A."},{"last_name":"Shakhova","full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S."},{"first_name":"Liliia I.","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia I."},{"full_name":"Chekova, Sofia V.","last_name":"Chekova","first_name":"Sofia V."},{"full_name":"Tsarkova, Aleksandra S.","last_name":"Tsarkova","first_name":"Aleksandra S."},{"first_name":"Yaroslav V.","last_name":"Golubev","full_name":"Golubev, Yaroslav V."},{"full_name":"Negrebetsky, Vadim V.","last_name":"Negrebetsky","first_name":"Vadim V."},{"last_name":"Dolgushin","full_name":"Dolgushin, Sergey A.","first_name":"Sergey A."},{"first_name":"Pavel V.","full_name":"Shalaev, Pavel V.","last_name":"Shalaev"},{"first_name":"Dmitry","last_name":"Shlykov","full_name":"Shlykov, Dmitry"},{"full_name":"Melnik, Olesya A.","last_name":"Melnik","first_name":"Olesya A."},{"full_name":"Shipunova, Victoria O.","last_name":"Shipunova","first_name":"Victoria O."},{"first_name":"Sergey M.","last_name":"Deyev","full_name":"Deyev, Sergey M."},{"last_name":"Bubyrev","full_name":"Bubyrev, Andrey I.","first_name":"Andrey I."},{"first_name":"Alexander S.","full_name":"Pushin, Alexander S.","last_name":"Pushin"},{"first_name":"Vladimir V.","last_name":"Choob","full_name":"Choob, Vladimir V."},{"first_name":"Sergey V.","full_name":"Dolgov, Sergey V.","last_name":"Dolgov"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."},{"first_name":"Karen S.","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S."}],"citation":{"ieee":"T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9","chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946."},"title":"Plants with genetically encoded autoluminescence","file":[{"file_id":"8316","creator":"dernst","content_type":"application/pdf","embargo":"2021-03-01","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","relation":"main_file","date_updated":"2021-03-02T23:30:03Z","file_size":1180086,"access_level":"open_access","checksum":"1b30467500ec6277229a875b06e196d0","date_created":"2020-08-28T08:57:07Z"}],"article_type":"original","pmid":1,"date_created":"2020-05-25T15:02:00Z","file_date_updated":"2021-03-02T23:30:03Z","abstract":[{"lang":"eng","text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants."}],"acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","department":[{"_id":"FyKo"}],"page":"944-946","article_processing_charge":"No","date_published":"2020-04-27T00:00:00Z","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","quality_controlled":"1","date_updated":"2025-04-14T07:49:47Z","_id":"7889","ddc":["570"],"doi":"10.1038/s41587-020-0500-9","month":"04","publication":"Nature Biotechnology","external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"publication_status":"published","language":[{"iso":"eng"}],"day":"27","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"volume":38,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41587-020-0578-0","relation":"erratum"}]},"isi":1,"intvolume":" 38","publisher":"Springer Nature","ec_funded":1},{"scopus_import":"1","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_number":"e55190","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2020-05-25T15:01:40Z","file_date_updated":"2020-07-14T12:48:04Z","abstract":[{"lang":"eng","text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order."}],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","citation":{"ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190."},"author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","orcid":"0000-0001-7659-9142","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"file":[{"creator":"dernst","file_id":"7890","content_type":"application/pdf","file_name":"2020_eLife_Schauer.pdf","file_size":7744848,"date_created":"2020-05-25T15:15:43Z","access_level":"open_access","checksum":"f6aad884cf706846ae9357fcd728f8b5","relation":"main_file","date_updated":"2020-07-14T12:48:04Z"}],"pmid":1,"article_type":"original","quality_controlled":"1","date_updated":"2026-05-19T22:30:13Z","_id":"7888","month":"04","doi":"10.7554/elife.55190","ddc":["570"],"article_processing_charge":"No","type":"journal_article","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-04-06T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"project":[{"grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"},{"grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429"}],"publication_identifier":{"issn":["2050-084X"]},"volume":9,"ec_funded":1,"intvolume":" 9","publisher":"eLife Sciences Publications","isi":1,"publication_status":"published","corr_author":"1","external_id":{"isi":["000531544400001"],"pmid":["32250246"]},"publication":"eLife","day":"06","language":[{"iso":"eng"}]},{"oa":1,"scopus_import":"1","oa_version":"Published Version","conference":{"end_date":"2020-12-12","name":"NeurIPS: Conference on Neural Information Processing Systems","location":"Vancouver, Canada","start_date":"2020-12-06"},"year":"2020","page":"16398-16408","acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","department":[{"_id":"TiVo"}],"date_created":"2021-07-04T22:01:27Z","abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","citation":{"mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020.","ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada."},"author":[{"id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J","last_name":"Confavreux","full_name":"Confavreux, Basile J"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"},{"full_name":"Agnes, Everton J.","last_name":"Agnes","first_name":"Everton J."},{"first_name":"Timothy","full_name":"Lillicrap, Timothy","last_name":"Lillicrap"},{"full_name":"Vogels, Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"}],"month":"12","date_updated":"2026-05-19T22:30:15Z","quality_controlled":"1","_id":"9633","type":"conference","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html","open_access":"1"}],"date_published":"2020-12-06T00:00:00Z","article_processing_charge":"No","intvolume":" 33","ec_funded":1,"related_material":{"link":[{"relation":"is_continued_by","url":"https://doi.org/10.1101/2020.10.24.353409"}],"record":[{"id":"14422","status":"public","relation":"dissertation_contains"}]},"project":[{"call_identifier":"H2020","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"},{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87"}],"publication_identifier":{"issn":["1049-5258"]},"volume":33,"day":"06","language":[{"iso":"eng"}],"publication_status":"published","publication":"Advances in Neural Information Processing Systems"},{"oa":1,"scopus_import":"1","oa_version":"Submitted Version","article_number":"100856","year":"2020","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","department":[{"_id":"ToHe"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"file_date_updated":"2022-05-16T22:30:04Z","abstract":[{"text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method.","lang":"eng"}],"date_created":"2020-02-02T23:00:59Z","article_type":"original","file":[{"creator":"dernst","file_id":"8688","content_type":"application/pdf","embargo":"2022-05-15","file_name":"2020_NAHS_GarciaSoto.pdf","file_size":818774,"access_level":"open_access","checksum":"560abfddb53f9fe921b6744f59f2cfaa","date_created":"2020-10-21T13:16:45Z","date_updated":"2022-05-16T22:30:04Z","relation":"main_file"}],"title":"Abstraction based verification of stability of polyhedral switched systems","author":[{"orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","full_name":"Garcia Soto, Miriam","last_name":"Garcia Soto"},{"first_name":"Pavithra","full_name":"Prabhakar, Pavithra","last_name":"Prabhakar"}],"citation":{"mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5). doi:10.1016/j.nahs.2020.100856","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5. Elsevier, 2020.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2020.100856"},"month":"05","doi":"10.1016/j.nahs.2020.100856","issue":"5","ddc":["000"],"_id":"7426","date_updated":"2025-04-15T06:26:15Z","quality_controlled":"1","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","date_published":"2020-05-01T00:00:00Z","article_processing_charge":"No","publisher":"Elsevier","intvolume":" 36","isi":1,"publication_identifier":{"issn":["1751-570X"]},"volume":36,"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"}],"day":"01","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000528828600003"]},"publication":"Nonlinear Analysis: Hybrid Systems","corr_author":"1"},{"scopus_import":"1","oa_version":"Submitted Version","oa":1,"has_accepted_license":"1","year":"2020","abstract":[{"text":"In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature.","lang":"eng"}],"file_date_updated":"2021-03-16T23:30:04Z","date_created":"2019-12-09T21:33:44Z","page":"877–894","department":[{"_id":"VlKo"}],"acknowledgement":"We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST).","title":"Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces","citation":{"mla":"Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.","short":"Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894.","ista":"Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894.","chicago":"Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6.","ama":"Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6","ieee":"Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020.","apa":"Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6"},"author":[{"orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","full_name":"Shehu, Yekini","last_name":"Shehu"},{"last_name":"Gibali","full_name":"Gibali, Aviv","first_name":"Aviv"},{"last_name":"Sagratella","full_name":"Sagratella, Simone","first_name":"Simone"}],"article_type":"original","file":[{"file_id":"8647","creator":"dernst","content_type":"application/pdf","file_name":"2020_JourOptimizationTheoryApplic_Shehu.pdf","embargo":"2021-03-15","date_created":"2020-10-12T10:40:27Z","checksum":"9f6dc6c6bf2b48cb3a2091a9ed5feaf2","access_level":"open_access","file_size":332641,"date_updated":"2021-03-16T23:30:04Z","relation":"main_file"}],"_id":"7161","date_updated":"2024-11-04T13:52:44Z","quality_controlled":"1","doi":"10.1007/s10957-019-01616-6","month":"03","ddc":["518","510","515"],"article_processing_charge":"No","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","date_published":"2020-03-01T00:00:00Z","publication_identifier":{"eissn":["1573-2878"],"issn":["0022-3239"]},"volume":184,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160"}],"ec_funded":1,"intvolume":" 184","publisher":"Springer Nature","isi":1,"publication_status":"published","external_id":{"isi":["000511805200009"]},"publication":"Journal of Optimization Theory and Applications","day":"01","language":[{"iso":"eng"}]},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","department":[{"_id":"MiSi"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"date_created":"2020-08-02T22:00:57Z","file_date_updated":"2021-02-02T23:30:03Z","file":[{"embargo":"2021-02-01","file_name":"2020_JCB_Sixt.pdf","date_updated":"2021-02-02T23:30:03Z","relation":"main_file","file_size":830725,"date_created":"2020-08-04T13:11:52Z","checksum":"30016d778d266b8e17d01094917873b8","access_level":"open_access","creator":"dernst","file_id":"8200","content_type":"application/pdf"}],"article_type":"letter_note","pmid":1,"title":"Zena Werb (1945-2020): Cell biology in context","citation":{"ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press, 2020.","apa":"Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202007029","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:10.1083/jcb.202007029.","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.202007029.","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020)."},"author":[{"last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Huttenlocher, Anna","last_name":"Huttenlocher","first_name":"Anna"}],"oa":1,"scopus_import":"1","oa_version":"Published Version","article_number":"e202007029","year":"2020","has_accepted_license":"1","intvolume":" 219","publisher":"Rockefeller University Press","isi":1,"volume":219,"publication_identifier":{"eissn":["1540-8140"]},"day":"22","language":[{"iso":"eng"}],"publication_status":"published","publication":"The Journal of Cell Biology","external_id":{"isi":["000573631000004"],"pmid":["32699885"]},"month":"07","doi":"10.1083/jcb.202007029","ddc":["570"],"issue":"8","date_updated":"2025-06-12T07:34:40Z","_id":"8190","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-22T00:00:00Z","article_processing_charge":"No"},{"corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD","publication_status":"published","language":[{"iso":"eng"}],"day":"28","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"date_published":"2020-02-28T00:00:00Z","type":"dissertation","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T07:27:27Z","_id":"7525","ddc":["570"],"month":"02","doi":"10.15479/AT:ISTA:7525","author":[{"last_name":"Bhandari","full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","orcid":"0000-0003-0863-4481"}],"citation":{"chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.","ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","mla":"Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525.","apa":"Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020."},"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file":[{"relation":"main_file","date_updated":"2021-03-01T23:30:04Z","file_size":9646346,"access_level":"open_access","checksum":"4589234fdb12b4ad72273b311723a7b4","date_created":"2020-02-28T08:37:53Z","embargo":"2021-02-28","file_name":"Pradeep Bhandari Thesis.pdf","content_type":"application/pdf","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","creator":"pbhandari","file_id":"7538"},{"file_id":"7539","creator":"pbhandari","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_name":"Pradeep Bhandari Thesis.docx","date_created":"2020-02-28T08:47:14Z","checksum":"aa79490553ca0a5c9b6fbcd152e93928","access_level":"closed","file_size":35252164,"date_updated":"2021-03-01T23:30:04Z","relation":"source_file","embargo_to":"open_access"}],"date_created":"2020-02-26T10:56:37Z","file_date_updated":"2021-03-01T23:30:04Z","abstract":[{"text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n","lang":"eng"}],"department":[{"_id":"RySh"}],"page":"79","has_accepted_license":"1","year":"2020","OA_place":"publisher","oa_version":"Published Version","oa":1},{"abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}],"date_created":"2020-01-28T16:14:41Z","department":[{"_id":"MaLo"}],"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","page":"407-417","author":[{"full_name":"Baranova, Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Radler","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0001-9198-2182 "},{"last_name":"Hernández-Rocamora","full_name":"Hernández-Rocamora, Víctor M.","first_name":"Víctor M."},{"first_name":"Carlos","last_name":"Alfonso","full_name":"Alfonso, Carlos"},{"full_name":"Lopez Pelegrin, Maria D","last_name":"Lopez Pelegrin","first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rivas, Germán","last_name":"Rivas","first_name":"Germán"},{"last_name":"Vollmer","full_name":"Vollmer, Waldemar","first_name":"Waldemar"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin"}],"citation":{"ieee":"N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5.","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5"},"title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","pmid":1,"article_type":"letter_note","oa_version":"Submitted Version","scopus_import":"1","oa":1,"year":"2020","publication_identifier":{"issn":["2058-5276"]},"volume":5,"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell"},{"name":"Reconstitution of bacterial cell wall synthesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","description":"News on IST Homepage"}],"record":[{"status":"public","id":"14280","relation":"dissertation_contains"}]},"isi":1,"ec_funded":1,"intvolume":" 5","publisher":"Springer Nature","publication":"Nature Microbiology","external_id":{"isi":["000508584700007"],"pmid":["31959972"]},"corr_author":"1","publication_status":"published","language":[{"iso":"eng"}],"day":"20","_id":"7387","quality_controlled":"1","date_updated":"2026-05-19T22:30:31Z","month":"01","doi":"10.1038/s41564-019-0657-5","article_processing_charge":"No","date_published":"2020-01-20T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"open_access":"1","url":"http://europepmc.org/article/PMC/7048620"}],"type":"journal_article"},{"page":"1247-1255","department":[{"_id":"FyKo"}],"acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","abstract":[{"lang":"eng","text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data."}],"date_created":"2020-10-25T23:01:20Z","pmid":1,"article_type":"original","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","author":[{"last_name":" Galan","full_name":" Galan, Silvia","first_name":"Silvia"},{"last_name":"Machnik","full_name":"Machnik, Nick N","first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6617-9742"},{"full_name":"Kruse, Kai","last_name":"Kruse","first_name":"Kai"},{"last_name":"Díaz","full_name":"Díaz, Noelia","first_name":"Noelia"},{"first_name":"Marc A","full_name":"Marti-Renom, Marc A","last_name":"Marti-Renom"},{"first_name":"Juan M","last_name":"Vaquerizas","full_name":"Vaquerizas, Juan M"}],"citation":{"short":"S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y.","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y","ieee":"S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020."},"oa":1,"scopus_import":"1","oa_version":"Submitted Version","OA_place":"repository","year":"2020","intvolume":" 52","publisher":"Springer Nature","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"18642","status":"public"}]},"volume":52,"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"day":"19","language":[{"iso":"eng"}],"publication_status":"published","publication":"Nature Genetics","external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"month":"10","doi":"10.1038/s41588-020-00712-y","_id":"8707","date_updated":"2026-05-19T22:30:32Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7610641/"}],"type":"journal_article","date_published":"2020-10-19T00:00:00Z","OA_type":"green","article_processing_charge":"No"},{"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","relation":"press_release"}],"record":[{"id":"11196","status":"public","relation":"dissertation_contains"}]},"volume":105,"publication_identifier":{"issn":["0896-6273"]},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205","call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit"}],"publisher":"Elsevier","intvolume":" 105","ec_funded":1,"isi":1,"publication_status":"published","publication":"Neuron","external_id":{"isi":["000520854700008"],"pmid":["31928842"]},"corr_author":"1","day":"18","language":[{"iso":"eng"}],"_id":"7473","date_updated":"2026-05-19T22:30:33Z","quality_controlled":"1","doi":"10.1016/j.neuron.2019.12.022","month":"03","ddc":["570"],"article_processing_charge":"No","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","date_published":"2020-03-18T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"abstract":[{"lang":"eng","text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses."}],"file_date_updated":"2020-11-20T08:58:53Z","date_created":"2020-02-10T15:59:45Z","page":"992-1006","department":[{"_id":"PeJo"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","author":[{"full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2344-1039","last_name":"Kim","full_name":"Kim, Olena"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas"}],"citation":{"apa":"Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron, vol. 105. Elsevier, pp. 992–1006, 2020.","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron, vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022."},"article_type":"original","pmid":1,"file":[{"file_name":"2020_Neuron_BorgesMerjane.pdf","file_size":9712957,"date_created":"2020-11-20T08:58:53Z","checksum":"3582664addf26859e86ac5bec3e01416","access_level":"open_access","date_updated":"2020-11-20T08:58:53Z","relation":"main_file","file_id":"8778","creator":"dernst","success":1,"content_type":"application/pdf"}],"scopus_import":"1","oa_version":"Published Version","oa":1,"has_accepted_license":"1","year":"2020"},{"day":"06","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"publication":"Journal of Cell Science","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"publisher":"The Company of Biologists","ec_funded":1,"intvolume":" 133","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"14510","status":"public"}]},"volume":133,"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","type":"journal_article","date_published":"2020-08-06T00:00:00Z","article_processing_charge":"No","month":"08","doi":"10.1242/jcs.248062","issue":"15","ddc":["575"],"_id":"8139","date_updated":"2026-05-19T22:30:37Z","quality_controlled":"1","article_type":"original","pmid":1,"file":[{"file_size":15150403,"checksum":"2d11f79a0b4e0a380fb002b933da331a","date_created":"2020-11-26T17:12:51Z","access_level":"open_access","date_updated":"2021-08-08T22:30:03Z","relation":"main_file","embargo":"2021-08-07","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","content_type":"application/pdf","file_id":"8815","creator":"ajohnson"}],"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","citation":{"ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062.","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062."},"author":[{"full_name":"Johnson, Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"},{"first_name":"G","last_name":"Vert","full_name":"Vert, G"},{"first_name":"SY","last_name":"Bednarek","full_name":"Bednarek, SY"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","file_date_updated":"2021-08-08T22:30:03Z","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.","lang":"eng"}],"date_created":"2020-07-21T08:58:19Z","article_number":"jcs248062","year":"2020","has_accepted_license":"1","oa":1,"scopus_import":"1","oa_version":"Published Version"},{"external_id":{"isi":["000565729700033"],"pmid":["32541049"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_status":"published","language":[{"iso":"eng"}],"day":"30","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"volume":117,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","call_identifier":"FWF"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"9992","status":"public"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/"}]},"isi":1,"intvolume":" 117","publisher":"National Academy of Sciences","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","date_published":"2020-06-30T00:00:00Z","OA_type":"hybrid","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"8002","date_updated":"2026-05-19T22:30:45Z","quality_controlled":"1","ddc":["580"],"issue":"26","doi":"10.1073/pnas.2003346117","month":"06","citation":{"ama":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(26). doi:10.1073/pnas.2003346117","chicago":"Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 117 (2020).","ista":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences of the United States of America. 117(26), 202003346.","mla":"Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 26, 202003346, National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.","apa":"Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., & Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2003346117","ieee":"L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 26. National Academy of Sciences, 2020."},"author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","full_name":"Montesinos López, Juan C","last_name":"Montesinos López"},{"first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","full_name":"Marhavá, Petra"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","orcid":"0000-0001-6111-9353","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots","article_type":"original","pmid":1,"file":[{"file_name":"2020_PNAS_Hoermayer.pdf","relation":"main_file","date_updated":"2020-07-14T12:48:07Z","checksum":"908b09437680181de9990915f2113aca","access_level":"open_access","date_created":"2020-06-23T11:30:53Z","file_size":2407102,"file_id":"8009","creator":"dernst","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:48:07Z","abstract":[{"text":"Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.","lang":"eng"}],"date_created":"2020-06-22T13:33:52Z","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"has_accepted_license":"1","year":"2020","article_number":"202003346","OA_place":"publisher","oa_version":"Published Version","scopus_import":"1","oa":1},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2021-02-18T10:18:43Z","file_date_updated":"2021-02-18T10:23:59Z","abstract":[{"lang":"eng","text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development."}],"acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","department":[{"_id":"EvBe"}],"title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","DOAJ_listed":"1","author":[{"last_name":"Semeradova","full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","full_name":"Montesinos López, Juan C"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"citation":{"apa":"Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048","ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.","ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048","chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.","ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048."},"file":[{"success":1,"creator":"dernst","file_id":"9161","content_type":"application/pdf","file_name":"2020_PlantComm_Semeradova.pdf","relation":"main_file","date_updated":"2021-02-18T10:23:59Z","file_size":840289,"access_level":"open_access","date_created":"2021-02-18T10:23:59Z","checksum":"785b266d82a94b007cf40dbbe7c4847e"}],"article_type":"original","pmid":1,"scopus_import":"1","oa_version":"Published Version","oa":1,"has_accepted_license":"1","OA_place":"publisher","article_number":"100048","year":"2020","related_material":{"record":[{"relation":"dissertation_contains","id":"10135","status":"public"}]},"project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","grant_number":"24746"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"volume":1,"publication_identifier":{"issn":["2590-3462"]},"publisher":"Elsevier","intvolume":" 1","isi":1,"publication_status":"published","corr_author":"1","publication":"Plant Communications","external_id":{"pmid":["33367243"],"isi":["000654052800010"]},"day":"11","language":[{"iso":"eng"}],"date_updated":"2026-05-19T22:30:45Z","quality_controlled":"1","_id":"9160","month":"05","doi":"10.1016/j.xplc.2020.100048","issue":"3","ddc":["580"],"article_processing_charge":"No","type":"journal_article","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","status":"public","OA_type":"gold","date_published":"2020-05-11T00:00:00Z"},{"month":"12","doi":"10.48550/arXiv.2012.00322","arxiv":1,"ddc":["530"],"date_updated":"2026-05-19T22:30:46Z","_id":"8831","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2020-12-02T00:00:00Z","article_processing_charge":"No","ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"10559","status":"public"},{"status":"public","id":"8834","relation":"research_data"},{"status":"public","id":"10058","relation":"dissertation_contains"}]},"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"day":"02","language":[{"iso":"eng"}],"publication_status":"draft","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"corr_author":"1","publication":"arXiv","external_id":{"arxiv":["2012.00322"]},"oa":1,"oa_version":"Submitted Version","article_number":"2012.00322","year":"2020","has_accepted_license":"1","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO).","department":[{"_id":"GeKa"}],"date_created":"2020-12-02T10:42:53Z","file_date_updated":"2020-12-02T10:42:31Z","abstract":[{"lang":"eng","text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip."}],"file":[{"file_name":"Superconducting_2D_Ge.pdf","file_size":1697939,"checksum":"22a612e206232fa94b138b2c2f957582","access_level":"open_access","date_created":"2020-12-02T10:42:31Z","date_updated":"2020-12-02T10:42:31Z","relation":"main_file","file_id":"8832","creator":"gkatsaro","content_type":"application/pdf"}],"title":"Enhancement of proximity induced superconductivity in planar Germanium","citation":{"mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, 2012.00322, doi:10.48550/arXiv.2012.00322.","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.).","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2012.00322.","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. arXiv. doi:10.48550/arXiv.2012.00322","ieee":"K. Aggarwal et al., “Enhancement of proximity induced superconductivity in planar Germanium,” arXiv. .","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. arXiv. https://doi.org/10.48550/arXiv.2012.00322"},"author":[{"last_name":"Aggarwal","full_name":"Aggarwal, Kushagra","first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293"},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"orcid":"0000-0002-7197-4801","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","last_name":"Jirovec"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357"},{"full_name":"Sammak, Amir","last_name":"Sammak","first_name":"Amir"},{"first_name":"Marc","last_name":"Botifoll","full_name":"Botifoll, Marc"},{"first_name":"Sara","full_name":"Marti-Sanchez, Sara","last_name":"Marti-Sanchez"},{"first_name":"Menno","full_name":"Veldhorst, Menno","last_name":"Veldhorst"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Scappucci","full_name":"Scappucci, Giordano","first_name":"Giordano"},{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros"}]}]