[{"abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. "}],"oa_version":"Published Version","acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. 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Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.","short":"F.R. Klausen, A.B. Lauritsen, (2023).","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869","ama":"Klausen FR, Lauritsen AB. 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Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","author":[{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","short":"F.K. Schur, (2023).","mla":"Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562."},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"doi":"10.15479/AT:ISTA:14562","date_published":"2023-11-21T00:00:00Z","date_created":"2023-11-20T09:22:33Z","day":"21","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R."},{"author":[{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"article_processing_charge":"No","department":[{"_id":"AnSa"}],"file_date_updated":"2023-10-31T08:57:50Z","title":"Stress granules plug and stabilize damaged endolysosomal membranes","date_updated":"2023-11-27T09:05:07Z","citation":{"ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.","chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.","ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472","apa":"Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472","short":"C.E. Vanhille-Campos, A. Šarić, (2023).","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","_id":"14472","date_published":"2023-10-31T00:00:00Z","doi":"10.15479/AT:ISTA:14472","related_material":{"record":[{"relation":"used_in_publication","id":"14610","status":"public"}]},"date_created":"2023-10-30T16:38:32Z","has_accepted_license":"1","year":"2023","day":"31","file":[{"success":1,"checksum":"a18706e952e8660c51ede52a167270b7","file_id":"14473","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"SGporecondensation-main.zip","date_created":"2023-10-30T16:31:08Z","creator":"ipalaia","file_size":62821432,"date_updated":"2023-10-30T16:31:08Z"},{"date_updated":"2023-10-31T08:57:50Z","file_size":1697,"creator":"dernst","date_created":"2023-10-31T08:57:50Z","file_name":"README.txt","content_type":"text/plain","access_level":"open_access","relation":"main_file","file_id":"14474","checksum":"389eab31c6509dbc05795017fb618758","success":1}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"10","abstract":[{"lang":"eng","text":"Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w."}],"oa_version":"Published Version"},{"has_accepted_license":"1","year":"2023","day":"28","file":[{"file_size":77070,"date_updated":"2023-02-28T06:34:08Z","creator":"scremer","file_name":"Metzler_ReadMe.pdf","date_created":"2023-02-28T06:34:08Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12694","checksum":"c1565d655ca05601acfd84e0d12b8563"},{"success":1,"file_id":"12695","checksum":"75c4c4948563d6261cb7548f80d909f1","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","access_level":"open_access","file_name":"Metzler_RepositoryData.xlsx","date_created":"2023-02-28T06:34:12Z","file_size":88001,"date_updated":"2023-02-28T06:34:12Z","creator":"scremer"}],"date_published":"2023-02-28T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12696"}]},"doi":"10.15479/AT:ISTA:12693","contributor":[{"contributor_type":"data_collector","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","last_name":"Metzler"},{"last_name":"Kirchner","contributor_type":"data_collector","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","first_name":"Jessica"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","contributor_type":"data_collector","last_name":"Grasse"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2023-02-28T06:38:37Z","abstract":[{"text":"See Readme File for further information.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","date_updated":"2023-12-13T11:13:13Z","citation":{"ista":"Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12693.","chicago":"Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12693.","ama":"Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:10.15479/AT:ISTA:12693","apa":"Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12693","short":"S. Cremer, (2023).","ieee":"S. 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However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"oa_version":"Published Version","acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. ","author":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"JoDa"}],"file_date_updated":"2023-05-18T19:51:52Z","title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","citation":{"mla":"Danzl, Johann G. Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12817.","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12817","ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:10.15479/AT:ISTA:12817","short":"J.G. Danzl, (2023).","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12817.","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817."},"date_updated":"2024-01-10T08:37:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","_id":"12817"},{"file":[{"file_size":87018103,"date_updated":"2023-03-24T09:34:20Z","creator":"lbecker","file_name":"Research_Data.zip","date_created":"2023-03-23T10:03:16Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"fd9a28620a81a82991fb70f4fd6591d9","file_id":"12743"},{"file_name":"README.txt","date_created":"2023-03-24T07:13:55Z","creator":"dernst","file_size":747,"date_updated":"2023-03-24T09:42:03Z","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","file_id":"12755","relation":"main_file","access_level":"open_access","content_type":"text/plain"}],"day":"23","has_accepted_license":"1","year":"2023","date_published":"2023-03-23T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12675"}]},"doi":"10.15479/AT:ISTA:12497","date_created":"2023-02-03T08:08:02Z","contributor":[{"last_name":"Berbon","contributor_type":"researcher","first_name":"Mélanie"},{"first_name":"Alicia","contributor_type":"researcher","last_name":"Vallet"},{"first_name":"Axelle","contributor_type":"researcher","last_name":"Grelard"},{"first_name":"Estelle","contributor_type":"researcher","last_name":"Morvan"},{"last_name":"Bardiaux","contributor_type":"researcher","first_name":"Benjamin"},{"last_name":"Lichtenecker","contributor_type":"researcher","first_name":"Roman"},{"last_name":"Ernst","first_name":"Matthias","contributor_type":"researcher"},{"last_name":"Loquet","contributor_type":"researcher","first_name":"Antoine"},{"first_name":"Paul","contributor_type":"contact_person","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","contributor_type":"researcher","last_name":"Becker","orcid":"0000-0002-6401-5151"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture."}],"month":"03","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["572"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497","apa":"Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.","short":"L.M. Becker, P. Schanda, (2023).","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.","ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497."},"date_updated":"2024-02-21T12:14:06Z","file_date_updated":"2023-03-24T09:42:03Z","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","author":[{"first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151"},{"last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_processing_charge":"No","_id":"12497","status":"public","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"}},{"project":[{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"article_processing_charge":"No","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"}],"title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","citation":{"mla":"Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.","short":"J.G. Danzl, (2023).","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13126."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","date_created":"2023-06-07T07:15:12Z","date_published":"2023-08-04T00:00:00Z","doi":"10.15479/AT:ISTA:13126","year":"2023","has_accepted_license":"1","day":"04","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"research_data","status":"public","_id":"13126","department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"file_date_updated":"2023-08-04T13:19:47Z","date_updated":"2024-02-21T12:18:19Z","ddc":["610"],"month":"08","abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"oa_version":"Published Version","contributor":[{"last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","orcid":"0000-0002-2340-7431"},{"id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana","last_name":"Stefanickova"},{"orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","last_name":"Cenameri"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","orcid":"0000-0002-3183-8207"},{"orcid":"0000-0003-2356-9403","last_name":"Venturino","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","last_name":"Roessler"},{"last_name":"Czech","first_name":"Thomas"},{"first_name":"Romana","last_name":"Höftberger"},{"last_name":"Siegert","orcid":"0000-0001-8635-0877","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"related_material":{"link":[{"description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. 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emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. "}],"oa_version":"Published Version","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). 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Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116","mla":"Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116.","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13116."},"ddc":["539"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Dunajova","full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"first_name":"Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","last_name":"Prats Mateu","full_name":"Prats Mateu, Batirtze"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"first_name":"Dörte","last_name":"Brandis","full_name":"Brandis, Dörte"},{"full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"last_name":"Wong","full_name":"Wong, Richard W.","first_name":"Richard W."},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"article_processing_charge":"No","department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"title":"Chiral and nematic phases of flexible active filaments","file_date_updated":"2023-08-08T11:17:28Z"},{"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14614.","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14614.","mla":"Lasne, Clementine, and Marwan N. Elkrewi. The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14614.","ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023.","short":"C. Lasne, M.N. Elkrewi, (2023).","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:10.15479/AT:ISTA:14614","apa":"Lasne, C., & Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14614"},"date_updated":"2024-02-21T12:18:35Z","file_date_updated":"2023-11-30T14:16:59Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","department":[{"_id":"BeVi"}],"author":[{"id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine","last_name":"Lasne","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616"},{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"article_processing_charge":"No","_id":"14614","status":"public","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"type":"research_data","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)"},"file":[{"date_created":"2023-11-28T13:15:26Z","file_name":"panorpaX.zip","date_updated":"2023-11-28T13:15:26Z","file_size":404968272,"creator":"clasne","file_id":"14625","checksum":"cd0f13322b5156819ecaebd2bc8e7d12","success":1,"content_type":"application/zip","access_level":"open_access","relation":"main_file"},{"date_created":"2023-11-30T14:16:59Z","file_name":"panorpa_readme.txt","creator":"clasne","date_updated":"2023-11-30T14:16:59Z","file_size":2625,"checksum":"9ff600416577687a737cb3c96dfcb26c","file_id":"14634","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/plain"}],"day":"01","has_accepted_license":"1","year":"2023","date_published":"2023-12-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"14613","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:14614","contributor":[{"contributor_type":"researcher","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"}],"date_created":"2023-11-27T16:39:19Z","oa_version":"Published Version","abstract":[{"text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"month":"12","publisher":"Institute of Science and Technology Austria","oa":1},{"month":"07","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"date_created":"2023-06-29T13:16:42Z","date_published":"2023-07-29T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"15084","status":"public"}]},"doi":"10.15479/AT:ISTA:13173","day":"29","file":[{"title":"Outdated Version","date_created":"2023-06-29T13:11:22Z","file_name":"Raw data for Koppensteiner et al.zip","creator":"shigemot","date_updated":"2023-11-17T14:30:44Z","file_size":542873672,"file_id":"13174","checksum":"ed59170869ba621f89f7c1894092192f","access_level":"closed","relation":"main_file","description":"After review an updated version of the data is provided","content_type":"application/x-zip-compressed"},{"file_name":"11-17-23 Updated Koppensteiner et al. raw data.xlsx","date_created":"2023-11-17T14:13:02Z","creator":"patrickd","file_size":915079,"date_updated":"2023-11-17T14:13:02Z","success":1,"file_id":"14550","checksum":"c07860eb82b4d367245f1b589fe5c250","relation":"main_file","access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"},{"creator":"dernst","file_size":544868924,"date_updated":"2024-02-06T07:21:43Z","file_name":"EM_Images.zip","date_created":"2024-02-06T07:21:43Z","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"file_id":"14942","checksum":"abf84b1699edac4349dc3a92d466fb7b"}],"year":"2023","has_accepted_license":"1","keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","_id":"13173","title":"Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals","file_date_updated":"2024-02-06T07:21:43Z","department":[{"_id":"RySh"}],"article_processing_charge":"No","author":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["571"],"date_updated":"2024-03-12T13:44:18Z","citation":{"mla":"Shigemoto, Ryuichi. Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13173.","apa":"Shigemoto, R. (2023). Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13173","ama":"Shigemoto R. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. 2023. doi:10.15479/AT:ISTA:13173","short":"R. Shigemoto, (2023).","ieee":"R. Shigemoto, “Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals.” Institute of Science and Technology Austria, 2023.","chicago":"Shigemoto, Ryuichi. “Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13173.","ista":"Shigemoto R. 2023. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13173."}},{"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"author":[{"orcid":" 0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"In vitro reconstitution of Escherichia coli divisome activation","citation":{"chicago":"Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10934.","ista":"Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:10934.","mla":"Radler, Philipp. In Vitro Reconstitution of Escherichia Coli Divisome Activation. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10934.","apa":"Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10934","ama":"Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:10.15479/AT:ISTA:10934","short":"P. Radler, (2022).","ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","doi":"10.15479/AT:ISTA:10934","date_published":"2022-04-05T00:00:00Z","date_created":"2022-03-31T11:32:32Z","has_accepted_license":"1","year":"2022","day":"05","type":"research_data","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":["Bacterial cell division","in vitro reconstitution","FtsZ","FtsN","FtsA"],"_id":"10934","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"file_date_updated":"2022-04-22T10:15:19Z","date_updated":"2024-02-21T12:35:18Z","ddc":["572"],"month":"04","abstract":[{"lang":"eng","text":"FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. 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Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321","mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321."}},{"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","file_date_updated":"2022-08-08T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"article_processing_charge":"No","author":[{"last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","short":"M.N. Elkrewi, (2022).","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653","mla":"Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653."},"date_updated":"2024-02-21T12:35:53Z","status":"public","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)"},"type":"research_data","_id":"11653","contributor":[{"orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","last_name":"Mrnjavac"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075"},{"last_name":"Sax","first_name":"Luca"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"first_name":"Francisco","last_name":"Hontoria "},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"date_created":"2022-07-26T11:01:47Z","date_published":"2022-08-05T00:00:00Z","doi":"10.15479/AT:ISTA:11653","related_material":{"record":[{"status":"public","id":"12248","relation":"used_in_publication"}]},"file":[{"checksum":"5f1d7c6d7ab5375ed2564521432bed0c","file_id":"11655","embargo":"2022-08-07","access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","title":"Supplementary Datasets","date_created":"2022-07-26T12:37:52Z","file_name":"Data.zip","creator":"melkrewi","date_updated":"2022-08-08T22:30:04Z","file_size":2209382998}],"day":"05","year":"2022","has_accepted_license":"1","month":"08","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}]},{"date_created":"2021-03-27T13:47:49Z","doi":"10.15479/AT:ISTA:9291","date_published":"2021-03-29T00:00:00Z","day":"29","file":[{"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","file_id":"9292","checksum":"635df3c08fc13c3dac008cd421aefbe4","success":1,"date_updated":"2021-03-27T13:46:17Z","file_size":10616071,"creator":"gkatsaro","date_created":"2021-03-27T13:46:17Z","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip"},{"date_updated":"2021-04-01T07:52:56Z","file_size":470,"creator":"dernst","date_created":"2021-04-01T07:52:56Z","file_name":"README.txt","content_type":"text/plain","access_level":"open_access","relation":"main_file","checksum":"12b3ca69ae7509a346711baae0b02a75","file_id":"9302","success":1}],"year":"2021","has_accepted_license":"1","month":"03","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for figures presented in the main text and supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html)."}],"title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","file_date_updated":"2021-04-01T07:52:56Z","department":[{"_id":"GeKa"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9291.","ista":"Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9291.","mla":"Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9291.","ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","short":"G. Katsaros, (2021).","apa":"Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9291","ama":"Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi:10.15479/AT:ISTA:9291"},"date_updated":"2024-02-21T12:37:14Z","status":"public","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)"},"type":"research_data","_id":"9291"},{"_id":"9636","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","status":"public","date_updated":"2024-02-21T12:36:52Z","citation":{"mla":"Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","department":[{"_id":"AnHi"}],"file_date_updated":"2021-07-07T20:37:28Z","oa_version":"Submitted Version","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","file":[{"success":1,"checksum":"18e90687ec7bbd75f8bfea4d8293fb30","file_id":"9637","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"figures_data.zip","date_created":"2021-07-07T20:37:28Z","file_size":3345244,"date_updated":"2021-07-07T20:37:28Z","creator":"ahigginb"}],"date_created":"2021-07-07T20:43:10Z","related_material":{"record":[{"status":"public","id":"10029","relation":"used_in_publication"}]},"date_published":"2021-01-01T00:00:00Z"},{"status":"public","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)"},"_id":"9323","title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"file_date_updated":"2021-04-14T09:49:30Z","author":[{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"date_updated":"2024-02-21T12:39:15Z","citation":{"apa":"Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323","short":"D. Jirovec, (2021).","ieee":"D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021.","mla":"Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323.","ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323.","chicago":"Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323."},"month":"04","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"text":"This .zip File contains the data for figures presented in the main text and supplementary material of \"A singlet triplet hole spin qubit in planar Ge\" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python.","lang":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","id":"8909","status":"public"}]},"date_published":"2021-04-14T00:00:00Z","doi":"10.15479/AT:ISTA:9323","contributor":[{"last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"}],"date_created":"2021-04-14T09:50:22Z","file":[{"file_size":221832287,"date_updated":"2021-04-14T09:48:47Z","creator":"djirovec","file_name":"DataRepositorySTqubit.zip","date_created":"2021-04-14T09:48:47Z","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","success":1,"checksum":"c569d2a2ce1694445cdbca19cf8ae023","file_id":"9324"},{"file_name":"ReadMe","date_created":"2021-04-14T09:49:30Z","file_size":4323,"date_updated":"2021-04-14T09:49:30Z","creator":"djirovec","success":1,"file_id":"9325","checksum":"845bdf87430718ad6aff47eda7b5fc92","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access"}],"day":"14","has_accepted_license":"1","year":"2021"},{"abstract":[{"text":"This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\".","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9390","checksum":"80a905c4eef24dab6fb247e81a3d67f5","creator":"mvalenti","file_size":10572981,"date_updated":"2021-05-14T11:42:23Z","file_name":"Notebook_Valentini.pdf","date_created":"2021-05-14T11:42:23Z"},{"creator":"mvalenti","date_updated":"2021-05-14T11:56:48Z","file_size":99076111,"date_created":"2021-05-14T11:56:48Z","file_name":"Experimental_data.zip","access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","checksum":"1e61a7e63949448a8db0091cdac23570","file_id":"9391"}],"contributor":[{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","contributor_type":"contact_person","first_name":"Marco"}],"date_created":"2021-05-14T12:07:53Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8910"}]},"doi":"10.15479/AT:ISTA:9389","date_published":"2021-01-01T00:00:00Z","_id":"9389","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)"},"type":"research_data","status":"public","date_updated":"2024-02-21T12:40:09Z","citation":{"ista":"Valentini M. 2021. 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Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology.","lang":"eng"}],"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"08","has_accepted_license":"1","year":"2020","day":"18","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"checksum":"4f1382ed4384751b6013398c11557bf6","file_id":"8280","creator":"dernst","file_size":5778420,"date_updated":"2020-08-18T08:03:23Z","file_name":"Data_Rcode_MathematicaNB.zip","date_created":"2020-08-18T08:03:23Z"}],"doi":"10.15479/AT:ISTA:8254","date_published":"2020-08-18T00:00:00Z","related_material":{"record":[{"relation":"later_version","id":"11321","status":"public"},{"status":"public","id":"9192","relation":"later_version"}]},"date_created":"2020-08-12T12:49:23Z","contributor":[{"contributor_type":"data_collector","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon"},{"last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Parvathy"},{"contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","last_name":"Pickup","contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett"}],"_id":"8254","type":"research_data","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","date_updated":"2024-02-21T12:41:09Z","citation":{"mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","short":"L.S. Arathoon, (2020).","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"author":[{"orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"}],"article_processing_charge":"No","file_date_updated":"2020-08-18T08:03:23Z","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","department":[{"_id":"NiBa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","short":"B. Kavcic, (2020).","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930."},"date_updated":"2024-02-21T12:41:42Z","file_date_updated":"2020-12-09T15:00:19Z","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","department":[{"_id":"GaTk"}],"author":[{"last_name":"Kavcic","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","_id":"8930","status":"public","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"type":"research_data","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)"},"day":"10","file":[{"file_name":"PLoSCompBiol2020_datarep.zip","date_created":"2020-12-09T15:00:19Z","creator":"bkavcic","file_size":315494370,"date_updated":"2020-12-09T15:00:19Z","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_id":"8932","relation":"main_file","access_level":"open_access","content_type":"application/zip"}],"has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:8930","related_material":{"record":[{"status":"public","id":"8997","relation":"used_in_publication"}]},"date_published":"2020-12-10T00:00:00Z","contributor":[{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","contributor_type":"supervisor","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Tobias"}],"date_created":"2020-12-09T15:04:02Z","oa_version":"Published Version","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"month":"12","publisher":"Institute of Science and Technology Austria","oa":1},{"month":"12","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"date_created":"2020-12-20T10:00:26Z","contributor":[{"contributor_type":"project_member","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Kathrin","last_name":"Tomasek"},{"contributor_type":"project_member","first_name":"Caroline","last_name":"Caruso Carter"},{"last_name":"Sonnleitner","contributor_type":"project_member","first_name":"Elisabeth"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic"},{"first_name":"Tiago","contributor_type":"project_member","last_name":"Paixão"},{"contributor_type":"project_manager","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"doi":"10.15479/AT:ISTA:8951","related_material":{"record":[{"relation":"used_in_publication","id":"9283","status":"public"}]},"date_published":"2020-12-21T00:00:00Z","file":[{"file_name":"readme.txt","date_created":"2020-12-20T09:52:52Z","file_size":523,"date_updated":"2020-12-20T09:52:52Z","creator":"bkavcic","success":1,"checksum":"f57862aeee1690c7effd2b1117d40ed1","file_id":"8952","content_type":"text/plain","relation":"main_file","access_level":"open_access"},{"success":1,"checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_id":"8954","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","file_name":"GRNs Research depository.gb","date_created":"2020-12-20T22:01:44Z","creator":"bkavcic","file_size":379228,"date_updated":"2020-12-20T22:01:44Z"}],"day":"21","year":"2020","has_accepted_license":"1","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"status":"public","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)"},"type":"research_data","_id":"8951","department":[{"_id":"CaGu"}],"file_date_updated":"2020-12-20T22:01:44Z","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","article_processing_charge":"No","author":[{"first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:41:57Z","citation":{"mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","short":"A.A. Nagy-Staron, (2020).","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951."}},{"article_processing_charge":"No","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","file_date_updated":"2020-07-14T12:47:57Z","citation":{"short":"R. Grah, (2020).","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383."},"date_updated":"2024-02-21T12:42:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"status":"public","_id":"7383","contributor":[{"first_name":"Calin C","contributor_type":"project_leader","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"date_created":"2020-01-28T10:41:49Z","date_published":"2020-01-28T00:00:00Z","doi":"10.15479/AT:ISTA:7383","related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"year":"2020","has_accepted_license":"1","day":"28","file":[{"checksum":"9d292cf5207b3829225f44c044cdb3fd","file_id":"7384","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2020-01-28T10:39:40Z","file_name":"Scripts.zip","creator":"rgrah","date_updated":"2020-07-14T12:47:57Z","file_size":73363365},{"file_size":962,"date_updated":"2020-07-14T12:47:57Z","creator":"rgrah","file_name":"READ_ME_MAIN.txt","date_created":"2020-01-28T10:39:30Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"7385","checksum":"4076ceab32ef588cc233802bab24c1ab"}],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"01","abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"oa_version":"Published Version"},{"contributor":[{"contributor_type":"research_group","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"date_created":"2021-03-05T18:00:47Z","doi":"10.15479/AT:ISTA:9222","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7541"}]},"date_published":"2020-03-16T00:00:00Z","file":[{"checksum":"41b66e195ed3dbd73077feee77b05652","file_id":"9223","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","file_name":"DOI_SiteControlledHWs.zip","date_created":"2021-03-05T17:50:45Z","file_size":13317557,"date_updated":"2021-03-05T17:50:45Z","creator":"gkatsaro"},{"file_id":"9233","checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/plain","date_created":"2021-03-10T07:31:50Z","file_name":"Readme.txt","creator":"dernst","date_updated":"2021-03-10T07:31:50Z","file_size":3515}],"day":"16","year":"2020","has_accepted_license":"1","month":"03","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","file_date_updated":"2021-03-10T07:31:50Z","department":[{"_id":"GeKa"}],"article_processing_charge":"No","author":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222.","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","short":"G. Katsaros, (2020)."},"date_updated":"2024-02-21T12:42:13Z","status":"public","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)"},"type":"research_data","_id":"9222"},{"publisher":"Institute of Science and Technology Austria","oa":1,"month":"09","abstract":[{"lang":"eng","text":"Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8366"}]},"date_published":"2020-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:8375","ec_funded":1,"contributor":[{"first_name":"Ruslan","contributor_type":"researcher","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","orcid":"0000-0001-9819-5077"},{"last_name":"McMahan","first_name":"Connor","contributor_type":"researcher"},{"contributor_type":"researcher","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez"},{"last_name":"Daraio","contributor_type":"researcher","first_name":"Chiara"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","contributor_type":"researcher","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-09-11T09:52:54Z","has_accepted_license":"1","year":"2020","day":"21","file":[{"date_updated":"2020-09-11T09:45:21Z","file_size":29214988,"creator":"rguseino","date_created":"2020-09-11T09:45:21Z","file_name":"supplementary_movie_1.mp4","content_type":"video/mp4","access_level":"open_access","relation":"main_file","checksum":"4029ffd65fb82ef2366b2fc2a4908e16","file_id":"8376","success":1},{"content_type":"video/mp4","relation":"main_file","access_level":"open_access","success":1,"file_id":"8377","checksum":"8ed03b04d80f1a4e622cb22e6100afd8","file_size":28449475,"date_updated":"2020-09-11T09:45:25Z","creator":"rguseino","file_name":"supplementary_movie_2.mp4","date_created":"2020-09-11T09:45:25Z"},{"success":1,"file_id":"8378","checksum":"ad6864afb5e694e5c52a88fba4e02eea","relation":"main_file","access_level":"open_access","content_type":"video/mp4","file_name":"supplementary_movie_3.mp4","date_created":"2020-09-11T09:45:28Z","creator":"rguseino","file_size":26315853,"date_updated":"2020-09-11T09:45:28Z"},{"file_id":"8379","checksum":"b079cef7871fe1afb69af0e2b099f3b1","success":1,"access_level":"open_access","relation":"main_file","content_type":"video/mp4","date_created":"2020-09-11T09:45:33Z","file_name":"supplementary_movie_4.mp4","creator":"rguseino","date_updated":"2020-09-11T09:45:33Z","file_size":25198755},{"date_updated":"2020-09-11T09:45:36Z","file_size":29011354,"creator":"rguseino","date_created":"2020-09-11T09:45:36Z","file_name":"supplementary_movie_5.mp4","content_type":"video/mp4","access_level":"open_access","relation":"main_file","file_id":"8380","checksum":"9d1d48a8ed5c109a999c51b044ee523d","success":1},{"content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"checksum":"d414d0059e982d752d218756b3c3ce05","file_id":"8381","file_size":586,"date_updated":"2020-09-11T09:52:36Z","creator":"rguseino","file_name":"readme.txt","date_created":"2020-09-11T09:52:36Z"}],"type":"research_data","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","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"8375","author":[{"first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077"}],"article_processing_charge":"No","title":"Supplementary data for \"Computational design of curved thin shells: from glass façades to programmable matter\"","file_date_updated":"2020-09-11T09:52:36Z","department":[{"_id":"BeBi"}],"date_updated":"2024-02-21T12:44:29Z","citation":{"chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8375.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8375.","mla":"Guseinov, Ruslan. Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8375.","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.","short":"R. Guseinov, (2020).","ama":"Guseinov R. Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” 2020. doi:10.15479/AT:ISTA:8375","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8375"},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","project":[{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"}],"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)"},"type":"research_data","_id":"7689","file_date_updated":"2020-07-14T12:48:02Z","title":"Supplementary data for \"Zero field splitting of heavy-hole states in quantum dots\"","department":[{"_id":"GeKa"}],"article_processing_charge":"No","author":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Katsaros, Georgios. Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7689.","apa":"Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7689","ama":"Katsaros G. Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:10.15479/AT:ISTA:7689","short":"G. Katsaros, (2020).","ieee":"G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020.","chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","ista":"Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7689."},"date_updated":"2024-02-21T12:44:02Z","month":"05","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n"}],"contributor":[{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","contributor_type":"contact_person"}],"date_created":"2020-05-01T15:14:46Z","ec_funded":1,"related_material":{"record":[{"id":"8203","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:7689","date_published":"2020-05-01T00:00:00Z","file":[{"checksum":"d23c0cb9e2d19e14e2f902b88b97c05d","file_id":"7786","access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2020-05-01T15:13:28Z","file_name":"DOI_ZeroFieldSplitting.zip","creator":"gkatsaro","date_updated":"2020-07-14T12:48:02Z","file_size":5514403}],"day":"01","year":"2020","has_accepted_license":"1"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"11","year":"2020","has_accepted_license":"1","file":[{"success":1,"file_id":"8762","checksum":"f5ae57b97017b9f61081032703361233","relation":"main_file","access_level":"open_access","content_type":"application/x-gzip","file_name":"mdn_model.tar.gz","date_created":"2020-11-16T10:31:29Z","creator":"rguseino","file_size":15378270,"date_updated":"2020-11-16T10:31:29Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/x-gzip","file_id":"8763","checksum":"b0d25e04060ee78c585ee2f23542c744","success":1,"creator":"rguseino","date_updated":"2020-11-16T10:43:23Z","file_size":615387734,"date_created":"2020-11-16T10:43:23Z","file_name":"optimal_panels_data.tar.gz"},{"date_created":"2020-11-18T10:04:59Z","file_name":"readme.txt","creator":"rguseino","date_updated":"2020-11-18T10:04:59Z","file_size":1228,"file_id":"8770","checksum":"69c1dde3434ada86d125e0c2588caf1e","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/plain"}],"day":"23","contributor":[{"last_name":"Gavriil","first_name":"Konstantinos","contributor_type":"researcher"},{"last_name":"Guseinov","orcid":"0000-0001-9819-5077","contributor_type":"researcher","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan"},{"contributor_type":"researcher","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez"},{"contributor_type":"researcher","first_name":"Davide","last_name":"Pellis"},{"contributor_type":"researcher","id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","orcid":"0000-0002-5198-7445","last_name":"Henderson"},{"first_name":"Florian","contributor_type":"researcher","last_name":"Rist"},{"first_name":"Helmut","contributor_type":"researcher","last_name":"Pottmann"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","contributor_type":"researcher","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"date_created":"2020-11-16T10:47:18Z","ec_funded":1,"related_material":{"record":[{"relation":"used_in_publication","id":"8562","status":"public"}],"link":[{"url":"https://github.com/russelmann/cold-glass-acm","relation":"software"}]},"doi":"10.15479/AT:ISTA:8761","date_published":"2020-11-23T00:00:00Z","_id":"8761","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)"},"type":"research_data","status":"public","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"date_updated":"2024-02-21T12:43:22Z","citation":{"chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8761.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8761.","mla":"Guseinov, Ruslan. Supplementary Data for “Computational Design of Cold Bent Glass Façades.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8761.","ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:10.15479/AT:ISTA:8761","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8761","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","short":"R. Guseinov, (2020)."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","last_name":"Guseinov"}],"title":"Supplementary data for \"Computational design of cold bent glass façades\"","department":[{"_id":"BeBi"}],"file_date_updated":"2020-11-18T10:04:59Z"},{"date_updated":"2024-02-21T12:43:41Z","citation":{"mla":"Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8563.","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","author":[{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929"},{"full_name":"Schönenberger, Philipp","last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"}],"file_date_updated":"2020-10-19T10:12:29Z","department":[{"_id":"JoCs"}],"title":"Optogenetic alteration of hippocampal network activity","_id":"8563","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"research_data","status":"public","year":"2020","has_accepted_license":"1","day":"19","file":[{"date_created":"2020-09-23T14:36:17Z","file_name":"upload.tgz","date_updated":"2020-09-23T14:36:17Z","file_size":145243906,"creator":"jozsef","checksum":"a16098a6d172f9c42ab5af5f6991668c","file_id":"8564","success":1,"content_type":"application/x-compressed","access_level":"open_access","relation":"main_file"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"open_access","relation":"main_file","file_id":"8675","checksum":"0bfc54b7e14c0694cd081617318ba606","success":1,"date_updated":"2020-10-19T10:12:29Z","file_size":11648,"creator":"jozsef","date_created":"2020-10-19T10:12:29Z","file_name":"redme.docx"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","contributor":[{"contributor_type":"project_leader","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"}],"date_created":"2020-09-23T14:39:54Z","doi":"10.15479/AT:ISTA:8563","related_material":{"record":[{"status":"public","id":"8740","relation":"used_in_publication"}]},"date_published":"2020-10-19T00:00:00Z","abstract":[{"text":"Supplementary data provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"10"},{"citation":{"apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","short":"F.K. Schur, (2020).","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592."},"date_updated":"2024-02-21T12:44:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"author":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"FlSc"}],"file_date_updated":"2023-12-01T10:39:59Z","title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","_id":"14592","type":"research_data","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"has_accepted_license":"1","year":"2020","day":"01","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"0108616e2a59e51879ea51299a29b091","file_id":"14593","success":1,"creator":"fschur","date_updated":"2023-11-22T14:58:44Z","file_size":49297,"date_created":"2023-11-22T14:58:44Z","file_name":"3Dprint-files_download_v2.zip"},{"creator":"cchlebak","date_updated":"2023-12-01T10:39:59Z","file_size":641,"date_created":"2023-12-01T10:39:59Z","file_name":"readme.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"4c66ddedee4d01c1c4a7978208350cfc","file_id":"14637","success":1}],"related_material":{"record":[{"id":"8586","status":"public","relation":"research_data"}]},"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","date_created":"2023-11-22T15:00:57Z","contributor":[{"first_name":"Florian","contributor_type":"researcher","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Bettina","last_name":"Zens"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Robert"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"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"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"12"},{"file_date_updated":"2020-07-14T12:47:47Z","department":[{"_id":"CaGu"}],"title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","article_processing_charge":"No","author":[{"last_name":"Tomanek","orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella","first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"citation":{"mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","short":"I. Tomanek, (2019).","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016."},"date_updated":"2024-02-21T12:45:25Z","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"status":"public","type":"research_data","_id":"7016","date_created":"2019-11-13T09:07:31Z","contributor":[{"orcid":"0000-0001-6220-2052","last_name":"Guet","contributor_type":"project_leader","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"date_published":"2019-11-13T00:00:00Z","doi":"10.15479/AT:ISTA:7016","related_material":{"record":[{"status":"public","id":"7652","relation":"used_in_publication"}]},"day":"13","file":[{"file_size":2456192500,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","file_name":"D8_S35_R2_001.fastq","title":"Locus1_amplified","date_created":"2019-11-13T08:52:21Z","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - 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However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}]},{"oa_version":"Published Version","month":"12","oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","file_id":"7155","checksum":"155133e6e188e85b3c0676a5e70b9341","file_size":65307107,"date_updated":"2020-07-14T12:47:50Z","creator":"dernst","file_name":"temporal_morphing_supp_data.zip","date_created":"2019-12-09T07:52:17Z"}],"day":"06","year":"2019","has_accepted_license":"1","date_created":"2019-12-09T07:52:46Z","ec_funded":1,"contributor":[{"last_name":"Guseinov","orcid":"0000-0001-9819-5077","first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Connor","last_name":"McMahan"},{"last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus"},{"last_name":"Daraio","first_name":"Chiara"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"date_published":"2019-12-06T00:00:00Z","doi":"10.15479/AT:ISTA:7154","related_material":{"record":[{"relation":"used_in_publication","id":"8433","status":"deleted"},{"relation":"used_in_publication","status":"public","id":"7262"}]},"_id":"7154","status":"public","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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)"},"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"ista":"Guseinov R. 2019. 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Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060."},"file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"BeVi"}],"title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","article_processing_charge":"No","author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"_id":"6060","status":"public","type":"research_data","day":"28","file":[{"checksum":"a338a622d728af0e3199cb07e6dd64d3","file_id":"6061","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"SupData.zip","date_created":"2019-02-28T10:54:27Z","file_size":36646050,"date_updated":"2020-07-14T12:47:17Z","creator":"bvicoso"}],"year":"2019","has_accepted_license":"1","date_created":"2019-02-28T10:55:15Z","date_published":"2019-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:6060","related_material":{"record":[{"relation":"research_paper","id":"6418","status":"public"}]},"oa_version":"Published Version","month":"02","oa":1,"publisher":"Institute of Science and Technology Austria"},{"status":"public","type":"research_data","_id":"6074","file_date_updated":"2020-07-14T12:47:18Z","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","department":[{"_id":"GaNo"}],"author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","last_name":"Dotter"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","short":"C. Dotter, G. Novarino, (2019).","chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074."},"date_updated":"2024-02-21T13:41:01Z","month":"01","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS."}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"date_published":"2019-01-09T00:00:00Z","doi":"10.15479/AT:ISTA:6074","date_created":"2019-03-07T13:32:35Z","day":"09","file":[{"date_created":"2019-03-07T13:37:19Z","file_name":"Setd5_paper.zip","date_updated":"2020-07-14T12:47:18Z","file_size":33202743,"creator":"dernst","file_id":"6084","checksum":"bc1b285edca9e98a2c63d153c79bb75b","content_type":"application/zip","access_level":"open_access","relation":"supplementary_material"}],"has_accepted_license":"1","year":"2019"},{"_id":"6062","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","date_updated":"2024-02-21T12:46:04Z","citation":{"ista":"Nardin M. 2019. 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