[{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2023","day":"10","page":"180","date_published":"2023-11-10T00:00:00Z","doi":"10.15479/at:ista:14510","date_created":"2023-11-10T09:10:06Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"citation":{"ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509"}],"article_processing_charge":"No","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_created":"2023-11-20T09:18:51Z","creator":"ngnyliuk","file_size":20824903,"date_updated":"2023-11-20T09:18:51Z","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_id":"14567","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_created":"2023-11-20T09:23:11Z","file_size":24871844,"date_updated":"2023-11-23T13:10:55Z","creator":"ngnyliuk","embargo":"2024-11-23","file_id":"14568","checksum":"bfc96d47fc4e7e857dd71656097214a4","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14591"},{"relation":"part_of_dissertation","id":"9887","status":"public"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"_id":"14510","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-27T23:30:45Z","ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"file_date_updated":"2023-11-23T13:10:55Z"},{"keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"status":"public","type":"journal_article","article_type":"original","_id":"10406","department":[{"_id":"CaHe"}],"date_updated":"2023-08-14T13:05:13Z","intvolume":" 55","month":"08","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future.","lang":"eng"}],"ec_funded":1,"volume":55,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","article_processing_charge":"No","external_id":{"isi":["000747220900010"],"pmid":["34460295"]},"author":[{"full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","last_name":"Mishra","first_name":"Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233.","chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021.","apa":"Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748."},"publisher":"Annual Reviews","quality_controlled":"1","acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","date_created":"2021-12-05T23:01:41Z","date_published":"2021-08-30T00:00:00Z","doi":"10.1146/annurev-genet-071819-103748","page":"209-233","publication":"Annual Review of Genetics","day":"30","year":"2021","isi":1},{"acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","quality_controlled":"1","publisher":"Humana","has_accepted_license":"1","year":"2021","day":"27","publication":" Receptor and Ion Channel Detection in the Brain","page":"267-283","doi":"10.1007/978-1-0716-1522-5_19","date_published":"2021-07-27T00:00:00Z","date_created":"2021-07-30T09:34:56Z","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"}],"citation":{"ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection in the Brain, 169:267–83. Neuromethods. New York: Humana, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain (Vol. 169, pp. 267–283). New York: Humana. https://doi.org/10.1007/978-1-0716-1522-5_19","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the Brain, vol. 169, New York: Humana, 2021, pp. 267–283.","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” Receptor and Ion Channel Detection in the Brain, vol. 169, Humana, 2021, pp. 267–83, doi:10.1007/978-1-0716-1522-5_19."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi","full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","last_name":"Harada"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"article_processing_charge":"No","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","abstract":[{"lang":"eng","text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms."}],"oa_version":"None","alternative_title":["Neuromethods"],"place":"New York","month":"07","intvolume":" 169","publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"9562","status":"public"}]},"volume":169,"ec_funded":1,"series_title":"Neuromethods","_id":"9756","type":"book_chapter","status":"public","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"date_updated":"2024-03-27T23:30:30Z","ddc":["573"],"department":[{"_id":"RySh"},{"_id":"EM-Fac"}]},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"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.","doi":"10.1016/j.jsb.2020.107633","date_published":"2020-12-01T00:00:00Z","date_created":"2020-09-29T13:24:06Z","day":"01","publication":"Journal of Structural Biology","has_accepted_license":"1","isi":1,"year":"2020","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"article_number":"107633","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"last_name":"Zens","full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000600997800008"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","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.","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."},"month":"12","intvolume":" 212","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","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."}],"issue":"3","related_material":{"record":[{"relation":"used_in_publication","id":"14592","status":"public"},{"id":"12491","status":"public","relation":"dissertation_contains"}]},"volume":212,"file":[{"file_name":"2020_JourStrucBiology_Faessler.pdf","date_created":"2020-12-10T14:01:10Z","creator":"dernst","file_size":7076870,"date_updated":"2020-12-10T14:01:10Z","success":1,"checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_id":"8937","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1047-8477"]},"publication_status":"published","status":"public","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8586","file_date_updated":"2020-12-10T14:01:10Z","department":[{"_id":"FlSc"}],"ddc":["570"],"date_updated":"2024-03-27T23:30:05Z"},{"article_number":"A3.27","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497","call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society vol. 7, A3.27.","chicago":"Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” In Intrinsic Activity, Vol. 7. Austrian Pharmacological Society, 2019. https://doi.org/10.25006/ia.7.s1-a3.27.","ama":"Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In: Intrinsic Activity. Vol 7. Austrian Pharmacological Society; 2019. doi:10.25006/ia.7.s1-a3.27","apa":"Kim, O., Borges Merjane, C., & Jonas, P. M. (2019). Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In Intrinsic Activity (Vol. 7). Innsbruck, Austria: Austrian Pharmacological Society. https://doi.org/10.25006/ia.7.s1-a3.27","ieee":"O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in Intrinsic Activity, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.","short":"O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian Pharmacological Society, 2019.","mla":"Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” Intrinsic Activity, vol. 7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:10.25006/ia.7.s1-a3.27."},"title":"Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy","author":[{"last_name":"Kim","full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"},{"first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","acknowledgement":"This work was supported by the ERC and EU Horizon 2020 (ERC 692692; MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).","quality_controlled":"1","publisher":"Austrian Pharmacological Society","oa":1,"day":"11","publication":"Intrinsic Activity","year":"2019","doi":"10.25006/ia.7.s1-a3.27","date_published":"2019-09-11T00:00:00Z","date_created":"2022-04-20T15:06:05Z","_id":"11222","status":"public","keyword":["hippocampus","mossy fibers","readily releasable pool","electron microscopy"],"type":"conference_abstract","conference":{"name":"ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society","start_date":"2019-09-25","end_date":"2019-09-27","location":"Innsbruck, Austria"},"date_updated":"2024-03-27T23:30:07Z","department":[{"_id":"PeJo"}],"oa_version":"Published Version","month":"09","intvolume":" 7","main_file_link":[{"url":"https://www.intrinsicactivity.org/2019/7/S1/A3.27/","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2309-8503"]},"publication_status":"published","related_material":{"record":[{"id":"11196","status":"public","relation":"dissertation_contains"}]},"issue":"Suppl. 1","volume":7,"ec_funded":1},{"date_updated":"2024-02-21T13:44:45Z","citation":{"chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74","short":"T. Bergmiller, N. Nikolic, (2018).","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["579"],"publist_id":"7385","author":[{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nikolic","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:04Z","department":[{"_id":"CaGu"}],"title":"Time-lapse microscopy data","_id":"5569","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["microscopy","microfluidics"],"has_accepted_license":"1","datarep_id":"74","year":"2018","day":"07","file":[{"date_created":"2018-12-12T13:04:39Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":3558703796,"checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637","access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"bf26649af310ef6892d68576515cde6d","file_id":"5638","creator":"system","file_size":1830422606,"date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","date_created":"2018-12-12T13:04:55Z"},{"creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":2140849248,"date_created":"2018-12-12T13:05:11Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","file_id":"5639"}],"doi":"10.15479/AT:ISTA:74","date_published":"2018-02-07T00:00:00Z","related_material":{"record":[{"status":"public","id":"438","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:35Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02"},{"page":"103","date_created":"2022-01-25T14:54:14Z","date_published":"2017-09-18T00:00:00Z","publication_status":"published","year":"2017","degree_awarded":"PhD","language":[{"iso":"eng"}],"day":"18","oa":1,"main_file_link":[{"url":"http://hdl.handle.net/2142/99178","open_access":"1"}],"alternative_title":["Graduate Dissertations and Theses at Illinois"],"publisher":"University of Illinois at Urbana-Champaign","month":"09","abstract":[{"lang":"eng","text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy"}],"title":"Magnetic force microscopy studies of mesoscopic superconducting structures","citation":{"chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017.","ista":"Polshyn H. 2017. 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University of Illinois at Urbana-Champaign."},"date_updated":"2022-01-25T15:00:26Z","supervisor":[{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","type":"dissertation","keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"status":"public","_id":"10663"},{"date_created":"2018-12-12T12:31:32Z","doi":"10.15479/AT:ISTA:53","related_material":{"record":[{"relation":"research_paper","status":"public","id":"665"}]},"date_published":"2017-03-10T00:00:00Z","datarep_id":"53","year":"2017","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5603","checksum":"d77859af757ac8025c50c7b12b52eaf3","creator":"system","file_size":6773204,"date_updated":"2020-07-14T12:47:03Z","file_name":"IST-2017-53-v1+1_Data_MDE.zip","date_created":"2018-12-12T13:02:38Z"}],"day":"10","oa":1,"publisher":"Institute of Science and Technology Austria","month":"03","abstract":[{"lang":"eng","text":"This repository contains the data collected for the manuscript \"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.\r\nData is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic \"mother machine\" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","first_name":"Anna M","last_name":"Andersson","full_name":"Andersson, Anna M","orcid":"0000-0003-2912-6769"},{"full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Enrique","last_name":"Balleza","full_name":"Balleza, Enrique"},{"first_name":"Daniel","full_name":"Kiviet, Daniel","last_name":"Kiviet"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"file_date_updated":"2020-07-14T12:47:03Z","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"title":"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","citation":{"apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:53","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).","ieee":"T. Bergmiller et al., “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.","mla":"Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. 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Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:69.","ieee":"R. Hauschild, “Live tracking of moving samples in confocal microscopy for vertically grown roots.” Institute of Science and Technology Austria, 2017.","short":"R. Hauschild, (2017).","ama":"Hauschild R. Live tracking of moving samples in confocal microscopy for vertically grown roots. 2017. doi:10.15479/AT:ISTA:69","apa":"Hauschild, R. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:69","chicago":"Hauschild, Robert. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:69.","ista":"Hauschild R. 2017. 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Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:44.","mla":"Hauschild, Robert. Fiji Script to Determine Average Speed and Direction of Migration of Cells. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:44.","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016.","short":"R. Hauschild, (2016).","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:44","ama":"Hauschild R. 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