[{"scopus_import":"1","type":"journal_article","date_published":"2026-04-16T00:00:00Z","publication":"Science","ec_funded":1,"title":"Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape","OA_type":"closed access","doi":"10.1126/science.aea6343","citation":{"short":"B.L. Springstein, M. Javoor, D. Megrian, R. Hajdu, D.M. Hanke, B. Zens, G.L. Weiss, F.K. Schur, M. Loose, Science 392 (2026).","mla":"Springstein, Benjamin L., et al. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” <i>Science</i>, vol. 392, no. 6795, eaea6343, AAAS, 2026, doi:<a href=\"https://doi.org/10.1126/science.aea6343\">10.1126/science.aea6343</a>.","ieee":"B. L. Springstein <i>et al.</i>, “Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape,” <i>Science</i>, vol. 392, no. 6795. AAAS, 2026.","apa":"Springstein, B. L., Javoor, M., Megrian, D., Hajdu, R., Hanke, D. M., Zens, B., … Loose, M. (2026). Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aea6343\">https://doi.org/10.1126/science.aea6343</a>","chicago":"Springstein, Benjamin L, Manjunath Javoor, Daniela Megrian, Roman Hajdu, Dustin M. Hanke, Bettina Zens, Gregor L. Weiss, Florian KM Schur, and Martin Loose. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.aea6343\">https://doi.org/10.1126/science.aea6343</a>.","ista":"Springstein BL, Javoor M, Megrian D, Hajdu R, Hanke DM, Zens B, Weiss GL, Schur FK, Loose M. 2026. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. Science. 392(6795), eaea6343.","ama":"Springstein BL, Javoor M, Megrian D, et al. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. <i>Science</i>. 2026;392(6795). doi:<a href=\"https://doi.org/10.1126/science.aea6343\">10.1126/science.aea6343</a>"},"volume":392,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"abstract":[{"text":"Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low–copy number plasmids. In multicellular cyanobacteria such as Anabaena sp., we found that a chromosomally encoded ParMR system has evolved into a cytoskeletal system named CorMR with a function in cell shape control rather than DNA segregation. Live-cell imaging, in vitro reconstitution, and cryo–electron microscopy revealed that CorM formed dynamically unstable, antiparallel double-stranded filaments that were recruited to the membrane by CorR through an amphipathic helix conserved in multicellular cyanobacteria. CorMR filaments were regulated by MinC, which excluded them from the poles and division plane. Comparative genomics indicated that the repurposing of ParMR and Min systems coevolved with cyanobacterial multicellularity, highlighting the evolutionary plasticity of cytoskeletal systems in bacteria.","lang":"eng"}],"date_updated":"2026-04-28T13:29:05Z","day":"16","publisher":"AAAS","_id":"21762","corr_author":"1","date_created":"2026-04-26T22:01:46Z","status":"public","acknowledgement":"We thank all members of the Loose lab at ISTA for helpful discussions; M. Kojic for critical reading of the manuscript; A. Herrero (Sevilla University) for sharing her extensive BACTH plasmid library and other plasmids, as well as cyanobacterial strains; T. Dagan and F. Nies (both Kiel University) for sharing cyanobacterial strains and plasmids and for valuable discussions; N. Sapay and A. Michon for providing the Amphipaseek code, which enabled us to perform our large-scale amphipathic helix screen of cyanobacterial CorR proteins; V.-V. Hodirnau for support in cryo-ET data collection; and J. Hansen for advice about cryo-EM data processing.\r\nThis work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF), the Scientific Computing (SciComp), the Electron Microscopy Facility (EMF), and the Lab Support Facility (LSF). This work was funded by the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant 101034413 to B.L.S.); the European Research Council (ERC) of the European Union (grant ActinID 101076260 to F.K.M.S.); the Swiss National Science Foundation (starting grant TMSGI3_226208 to G.L.W.); and the Jean-Jacques et Letitia Lopez-Loreta Foundation (G.L.W.).","article_processing_charge":"No","department":[{"_id":"MaLo"},{"_id":"FlSc"},{"_id":"GradSch"},{"_id":"EM-Fac"}],"article_type":"original","article_number":"eaea6343","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"quality_controlled":"1","year":"2026","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6795","author":[{"full_name":"Springstein, Benjamin L","first_name":"Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","last_name":"Springstein","orcid":"0000-0002-3461-5391"},{"last_name":"Javoor","orcid":"0000-0003-2311-2112","full_name":"Javoor, Manjunath","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"last_name":"Megrian","first_name":"Daniela","full_name":"Megrian, Daniela"},{"full_name":"Hajdu, Roman","first_name":"Roman","id":"ffab949d-133f-11ed-8f02-94de21ace503","last_name":"Hajdu"},{"last_name":"Hanke","first_name":"Dustin M.","full_name":"Hanke, Dustin M."},{"full_name":"Zens, Bettina","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","last_name":"Zens"},{"last_name":"Weiss","full_name":"Weiss, Gregor L.","first_name":"Gregor L."},{"last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km","full_name":"Schur, Florian Km"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"}],"external_id":{"pmid":["41990175"]},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413"},{"name":"A molecular atlas of Actin filament IDentities in the cell motility machinery","_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","grant_number":"101076260"}],"intvolume":"       392","publication_status":"published","oa_version":"None"},{"author":[{"last_name":"Vorlaufer","orcid":"0009-0000-7590-3501","full_name":"Vorlaufer, Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob"},{"id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","first_name":"Nikolai","full_name":"Semenov, Nikolai","last_name":"Semenov"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Javoor, Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","last_name":"Javoor","orcid":"0000-0003-2311-2112"},{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","last_name":"Zens"},{"first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas"},{"first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854"},{"last_name":"Suplata","full_name":"Suplata, Marek","first_name":"Marek","id":"EE8452B8-C26A-11E9-B157-E80CE6697425"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","full_name":"Jahr, Wiebke","orcid":"0000-0003-0201-2315","last_name":"Jahr"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia"},{"last_name":"Wartak","full_name":"Wartak, Andreas","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","first_name":"Andreas"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km","full_name":"Schur, Florian Km"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"project":[{"name":"CryoMinflux-guided in-situ molecular census and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057"}],"intvolume":"         5","publication_status":"published","oa_version":"Published Version","file":[{"file_id":"19802","access_level":"open_access","creator":"dernst","success":1,"file_size":7238179,"relation":"main_file","file_name":"2025_BiophysicalReports_Vorlaufer.pdf","checksum":"4018c833f25a3ad3b57e3577fed70334","date_created":"2025-06-10T07:24:46Z","date_updated":"2025-06-10T07:24:46Z","content_type":"application/pdf"}],"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"article_type":"original","article_number":"100211","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","year":"2025","month":"06","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-06-10T07:24:46Z","doi":"10.1016/j.bpr.2025.100211","citation":{"mla":"Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no. 2, 100211, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>.","short":"J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025).","ama":"Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2). doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>","ista":"Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211.","chicago":"Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>.","apa":"Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>","ieee":"J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol. 5, no. 2. Elsevier, 2025."},"volume":5,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2667-0747"]},"date_updated":"2026-04-07T11:48:07Z","abstract":[{"lang":"eng","text":"Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases."}],"_id":"19795","day":"11","publisher":"Elsevier","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2025-06-08T22:01:22Z","corr_author":"1","article_processing_charge":"Yes","acknowledgement":"We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).","status":"public","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20206"}]},"scopus_import":"1","type":"journal_article","date_published":"2025-06-11T00:00:00Z","ec_funded":1,"publication":"Biophysical Reports","OA_place":"publisher","ddc":["570"],"DOAJ_listed":"1","has_accepted_license":"1","title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","OA_type":"gold"},{"status":"public","acknowledgement":"This project has received financing from the European Research Council grant agreement no. 949120 under the European Union’s Horizon 2020 research and innovation programme. The Analytical Instrumentation Center of the TU Wien acknowledges support by the FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state of Lower Austria and the European Regional Development Fund under grant no. WST3-F-542638/004-2021. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing facility, Electron Microscopy Facility and Lab Support Facility. We thank J. Garcia-Suarez and G. Anciaux for the suggestion to look into the roughness power spectral density. We thank I.-M. Strugaru for help with testing the device for Young’s modulus measurements. Open access funding provided by Institute of Science and Technology (IST Austria).","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","day":"20","_id":"19278","corr_author":"1","oa":1,"date_created":"2025-03-02T23:01:52Z","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"abstract":[{"text":"When two insulating, neutral materials are contacted and separated, they exchange electrical charge1. Experiments have long suggested that this ‘contact electrification’ is transitive, with different materials ordering into ‘triboelectric series’ based on the sign of charge acquired2. At the same time, the effect is plagued by unpredictability, preventing consensus on the mechanism and casting doubt on the rhyme and reason that series imply3. Here we expose an unanticipated connection between the unpredictability and order in contact electrification: nominally identical materials initially exchange charge randomly and intransitively, but—over repeated experiments—order into triboelectric series. We find that this evolution is driven by the act of contact itself—samples with more contacts in their history charge negatively to ones with fewer contacts. Capturing this ‘contact bias’ in a minimal model, we recreate both the initial randomness and ultimate order in numerical simulations and use it experimentally to force the appearance of a triboelectric series of our choosing. With a set of surface-sensitive techniques to search for the underlying alterations contact creates, we only find evidence of nanoscale morphological changes, pointing to a mechanism strongly coupled with mechanics. Our results highlight the centrality of contact history in contact electrification and suggest that focusing on the unpredictability that has long plagued the effect may hold the key to understanding it.","lang":"eng"}],"date_updated":"2026-07-29T13:11:24Z","file_date_updated":"2025-03-04T10:05:18Z","doi":"10.1038/s41586-024-08530-6","citation":{"ieee":"J. C. A. Sobarzo Ponce <i>et al.</i>, “Spontaneous ordering of identical materials into a triboelectric series,” <i>Nature</i>, vol. 638, no. 8051. Springer Nature, 2025.","apa":"Sobarzo Ponce, J. C. A., Pertl, F., Balazs, D., Costanzo, T., Sauer, M., Foelske, A., … Waitukaitis, S. R. (2025). Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>","chicago":"Sobarzo Ponce, Juan Carlos A, Felix Pertl, Daniel Balazs, Tommaso Costanzo, Markus Sauer, Annette Foelske, Markus Ostermann, et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>.","ama":"Sobarzo Ponce JCA, Pertl F, Balazs D, et al. Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. 2025;638(8051). doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>","ista":"Sobarzo Ponce JCA, Pertl F, Balazs D, Costanzo T, Sauer M, Foelske A, Ostermann M, Pichler CM, Wang Y, Nagata Y, Bonn M, Waitukaitis SR. 2025. Spontaneous ordering of identical materials into a triboelectric series. Nature. 638(8051), 664–669.","short":"J.C.A. Sobarzo Ponce, F. Pertl, D. Balazs, T. Costanzo, M. Sauer, A. Foelske, M. Ostermann, C.M. Pichler, Y. Wang, Y. Nagata, M. Bonn, S.R. Waitukaitis, Nature 638 (2025).","mla":"Sobarzo Ponce, Juan Carlos A., et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>, vol. 638, no. 8051, 664–669, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>."},"volume":638,"language":[{"iso":"eng"}],"OA_type":"hybrid","ddc":["530"],"OA_place":"publisher","title":"Spontaneous ordering of identical materials into a triboelectric series","has_accepted_license":"1","date_published":"2025-02-20T00:00:00Z","publication":"Nature","ec_funded":1,"scopus_import":"1","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/an-electrifying-turn-in-an-age-old-quest/","relation":"press_release"}],"record":[{"status":"public","relation":"dissertation_contains","id":"20203"}]},"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"19289","access_level":"open_access","creator":"dernst","success":1,"file_size":3807415,"relation":"main_file","checksum":"fecf302274dd3218d3e7dd22f39a6c0c","file_name":"2025_Nature_Sobarzo.pdf","date_created":"2025-03-04T10:05:18Z","date_updated":"2025-03-04T10:05:18Z","content_type":"application/pdf"}],"publication_status":"published","project":[{"grant_number":"949120","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"intvolume":"       638","author":[{"last_name":"Sobarzo Ponce","full_name":"Sobarzo Ponce, Juan Carlos A","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"orcid":"0000-0003-0463-5794","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix","full_name":"Pertl, Felix"},{"full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"full_name":"Costanzo, Tommaso","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","last_name":"Costanzo"},{"full_name":"Sauer, Markus","first_name":"Markus","last_name":"Sauer"},{"full_name":"Foelske, Annette","first_name":"Annette","last_name":"Foelske"},{"last_name":"Ostermann","full_name":"Ostermann, Markus","first_name":"Markus"},{"full_name":"Pichler, Christian M.","first_name":"Christian M.","last_name":"Pichler"},{"last_name":"Wang","first_name":"Yongkang","full_name":"Wang, Yongkang"},{"full_name":"Nagata, Yuki","first_name":"Yuki","last_name":"Nagata"},{"last_name":"Bonn","first_name":"Mischa","full_name":"Bonn, Mischa"},{"full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis"}],"external_id":{"pmid":["39972227"],"isi":["001428076100015"]},"month":"02","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","issue":"8051","quality_controlled":"1","year":"2025","article_number":"664-669","article_type":"original","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"department":[{"_id":"ScWa"},{"_id":"LifeSc"},{"_id":"EM-Fac"}]},{"doi":"10.1038/s41567-023-02302-1","citation":{"mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 310–21, doi:<a href=\"https://doi.org/10.1038/s41567-023-02302-1\">10.1038/s41567-023-02302-1</a>.","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics 20 (2024) 310–321.","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. <i>Nature Physics</i>. 2024;20:310-321. doi:<a href=\"https://doi.org/10.1038/s41567-023-02302-1\">10.1038/s41567-023-02302-1</a>","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 20, 310–321.","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02302-1\">https://doi.org/10.1038/s41567-023-02302-1</a>","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-023-02302-1\">https://doi.org/10.1038/s41567-023-02302-1</a>.","ieee":"S. Caballero Mancebo <i>et al.</i>, “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 310–321, 2024."},"file_date_updated":"2024-07-16T12:12:43Z","language":[{"iso":"eng"}],"volume":20,"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"abstract":[{"lang":"eng","text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces."}],"date_updated":"2025-09-04T11:48:28Z","day":"01","publisher":"Springer Nature","_id":"14846","corr_author":"1","date_created":"2024-01-21T23:00:57Z","oa":1,"status":"public","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/","relation":"press_release"}]},"type":"journal_article","date_published":"2024-02-01T00:00:00Z","publication":"Nature Physics","ddc":["530"],"has_accepted_license":"1","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","author":[{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo"},{"last_name":"Shinde","full_name":"Shinde, Rushikesh","first_name":"Rushikesh"},{"last_name":"Bolger-Munro","orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","first_name":"Madison"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo"},{"first_name":"Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Gregory","last_name":"Szep"},{"full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene","last_name":"Steccari"},{"last_name":"Labrousse Arias","first_name":"David","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","full_name":"Labrousse Arias, David"},{"orcid":"0000-0002-9438-4783","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Zheden, Vanessa"},{"full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Andrew","full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones"},{"last_name":"Voituriez","first_name":"Raphaël","full_name":"Voituriez, Raphaël"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"external_id":{"pmid":["38370025"],"isi":["001138880800005"]},"project":[{"call_identifier":"FWF","grant_number":"I03601","name":"Control of embryonic cleavage pattern","_id":"2646861A-B435-11E9-9278-68D0E5697425"}],"intvolume":"        20","publication_status":"published","page":"310-321","oa_version":"Published Version","file":[{"content_type":"application/pdf","date_updated":"2024-07-16T12:12:43Z","date_created":"2024-07-16T12:12:43Z","file_name":"2024_NaturePhysics_CaballeroMancebo.pdf","checksum":"7891ebe7c900ae47469ab127031dd1ec","relation":"main_file","file_size":9897883,"success":1,"creator":"dernst","access_level":"open_access","file_id":"17267"}],"department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"article_type":"original","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"quality_controlled":"1","year":"2024","month":"02","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"year":"2024","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","keyword":["Molecular Biology","Structural Biology"],"month":"07","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"pmid":1,"article_type":"original","page":"1114-1123","publication_status":"published","file":[{"date_updated":"2024-07-22T11:27:22Z","content_type":"application/pdf","date_created":"2024-07-22T11:27:22Z","checksum":"bda7bf65d81455480efaed8ca293b0db","file_name":"2024_NatureStrucBio_Datler.pdf","creator":"dernst","access_level":"open_access","file_id":"17307","relation":"main_file","file_size":17485494,"success":1}],"oa_version":"Published Version","external_id":{"isi":["001158144600002"],"pmid":["38316877"]},"author":[{"orcid":"0000-0002-3616-8580","last_name":"Datler","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"full_name":"Hansen, Jesse","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","orcid":"0000-0001-7967-2085"},{"last_name":"Thader","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"full_name":"Bauer, Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W","last_name":"Bauer"},{"orcid":"0000-0003-3904-947X","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"intvolume":"        31","project":[{"call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"has_accepted_license":"1","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","OA_place":"publisher","ddc":["570"],"OA_type":"hybrid","APC_amount":"11700 EUR","type":"journal_article","scopus_import":"1","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website"}],"record":[{"status":"public","id":"18766","relation":"dissertation_contains"}]},"publication":"Nature Structural & Molecular Biology","date_published":"2024-07-01T00:00:00Z","oa":1,"date_created":"2024-02-12T09:59:45Z","corr_author":"1","_id":"14979","publisher":"Springer Nature","day":"01","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","status":"public","volume":31,"language":[{"iso":"eng"}],"file_date_updated":"2024-07-22T11:27:22Z","doi":"10.1038/s41594-023-01201-6","citation":{"ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>."},"date_updated":"2026-04-07T12:59:44Z","abstract":[{"lang":"eng","text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses."}],"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]}},{"type":"journal_article","scopus_import":"1","publication":"Journal of Cell Biology","ec_funded":1,"date_published":"2024-03-20T00:00:00Z","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","has_accepted_license":"1","ddc":["570"],"volume":223,"language":[{"iso":"eng"}],"citation":{"ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>.","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024.","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024)."},"file_date_updated":"2024-03-25T12:52:04Z","doi":"10.1083/jcb.202309125","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"date_updated":"2025-09-04T13:17:16Z","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"corr_author":"1","date_created":"2024-03-21T06:45:51Z","oa":1,"publisher":"Rockefeller University Press","day":"20","_id":"15146","status":"public","acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"article_number":"e202309125","article_type":"original","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"year":"2024","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"6","month":"03","external_id":{"pmid":["38506714"],"isi":["001264190100001"]},"author":[{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","last_name":"Zens"},{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse","last_name":"Hansen","orcid":"0000-0001-7967-2085"},{"full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia","last_name":"Datler","orcid":"0000-0002-3616-8580"},{"last_name":"Hodirnau","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Zheden","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alanko, Jonna H","first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","orcid":"0000-0002-7698-3061"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"intvolume":"       223","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"_id":"7bd318a1-9f16-11ee-852c-cc9217763180","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","grant_number":"E435"},{"grant_number":"724373","call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2615199A-B435-11E9-9278-68D0E5697425","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","grant_number":"21317"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ visual proteomics and structure determination","grant_number":"CZI01"}],"publication_status":"published","file":[{"date_updated":"2024-03-25T12:52:04Z","content_type":"application/pdf","date_created":"2024-03-25T12:52:04Z","file_name":"2024_JCB_Zens.pdf","checksum":"90d1984a93660735e506c2a304bc3f73","creator":"dernst","file_id":"15188","access_level":"open_access","file_size":11907016,"relation":"main_file","success":1}],"oa_version":"Published Version"},{"APC_amount":"6248,82 EUR","OA_type":"gold","ddc":["570"],"OA_place":"publisher","DOAJ_listed":"1","title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","has_accepted_license":"1","date_published":"2024-11-18T00:00:00Z","publication":"PLoS Biology","ec_funded":1,"scopus_import":"1","related_material":{"record":[{"relation":"research_data","id":"18296","status":"public"}]},"type":"journal_article","status":"public","acknowledgement":"We thank Carolina Borges-Merjane, Jing-Jing Chen, Katharina Lichter, and Samuel Young for critically reading the manuscript; the Electron Microscopy Facility of ISTA, in particular Vanessa Zheden, for extensive support, advice, and experimental assistance; the Preclinical Facility of ISTA, in particular Victoria Wimmer and Michael Schunn, for experimental assistance; Florian Marr and Christina Altmutter for technical support; Alois Schlögl for help with analysis; and Eleftheria Kralli-Beller for manuscript editing. We also thank Cordelia Imig for providing Munc13-1cKO-Munc13-2/3(−/−) mutant mice. Part of the work has been published in O.K.’s thesis in partial fulfillment of the requirements for the degree of Doctor of Philosophy.\r\nThis project received funding from the European Research Council and European Union’s Horizon 2020 research and innovation programme (ERC 692692 to P.J.; https://cordis.europa.eu/project/id/692692/de) and from the Fond zur Förderung der Wissenschaftlichen Forschung (Z312-B27 Wittgenstein award to P.J., https://www.fwf.ac.at/en/funding/portfolio/projects/fwf-wittgenstein-award; W1205-B09 and P36232-B to P.J., https://www.fwf.ac.at/en/funding; I6166-B to R.S.; https://www.fwf.ac.at/en/funding). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","article_processing_charge":"Yes","day":"18","publisher":"Public Library of Science","_id":"18603","corr_author":"1","oa":1,"date_created":"2024-12-01T23:01:54Z","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"abstract":[{"text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the rodent hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.","lang":"eng"}],"date_updated":"2026-04-16T12:20:34Z","doi":"10.1371/journal.pbio.3002879","citation":{"mla":"Kim, Olena, et al. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” <i>PLoS Biology</i>, vol. 22, no. 11, e3002879, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002879\">10.1371/journal.pbio.3002879</a>.","short":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, P.M. Jonas, PLoS Biology 22 (2024).","apa":"Kim, O., Okamoto, Y., Kaufmann, W., Brose, N., Shigemoto, R., &#38; Jonas, P. M. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002879\">https://doi.org/10.1371/journal.pbio.3002879</a>","chicago":"Kim, Olena, Yuji Okamoto, Walter Kaufmann, Nils Brose, Ryuichi Shigemoto, and Peter M Jonas. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002879\">https://doi.org/10.1371/journal.pbio.3002879</a>.","ama":"Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. <i>PLoS Biology</i>. 2024;22(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002879\">10.1371/journal.pbio.3002879</a>","ista":"Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. PLoS Biology. 22(11), e3002879.","ieee":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, and P. M. Jonas, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons,” <i>PLoS Biology</i>, vol. 22, no. 11. Public Library of Science, 2024."},"file_date_updated":"2024-12-03T08:56:53Z","language":[{"iso":"eng"}],"volume":22,"month":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"11","quality_controlled":"1","year":"2024","article_number":"e3002879","article_type":"original","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"oa_version":"Published Version","file":[{"content_type":"application/pdf","date_updated":"2024-12-03T08:56:53Z","date_created":"2024-12-03T08:56:53Z","checksum":"7de2dcb50deb65dde05c80082bb85a82","file_name":"2024_PloSBio_Kim.pdf","relation":"main_file","file_size":3057631,"success":1,"creator":"dernst","file_id":"18608","access_level":"open_access"}],"publication_status":"published","project":[{"grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"grant_number":"I06166","name":"Structural & functional basis of presynaptic plasticity","_id":"b1b85715-d554-11ed-a5ad-84a07fc9f18e"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","grant_number":"W01205"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"intvolume":"        22","author":[{"full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","last_name":"Kim","orcid":"0000-0003-2344-1039"},{"full_name":"Okamoto, Yuji","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","orcid":"0000-0003-0408-6094"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"external_id":{"isi":["001358568700003"],"pmid":["39556620"]}},{"file":[{"file_size":40623405,"relation":"main_file","success":1,"creator":"dernst","access_level":"open_access","file_id":"18921","date_created":"2025-01-27T14:40:08Z","checksum":"291dd7ceccbe6bfd8e0a9157584f88e9","file_name":"2024_ScienceAdv_Homola.pdf","content_type":"application/pdf","date_updated":"2025-01-27T14:40:08Z"}],"oa_version":"Published Version","publication_status":"published","intvolume":"        10","external_id":{"pmid":["38598627"]},"author":[{"last_name":"Homola","full_name":"Homola, Miroslav","first_name":"Miroslav"},{"full_name":"Büttner, Renate Carina","id":"3b7984c9-17ff-11ed-b6fe-f943c4a5b626","first_name":"Renate Carina","last_name":"Büttner"},{"first_name":"Tibor","full_name":"Füzik, Tibor","last_name":"Füzik"},{"first_name":"Pavel","full_name":"Křepelka, Pavel","last_name":"Křepelka"},{"full_name":"Holbová, Radka","first_name":"Radka","last_name":"Holbová"},{"first_name":"Jiří","full_name":"Nováček, Jiří","last_name":"Nováček"},{"first_name":"Marten L.","full_name":"Chaillet, Marten L.","last_name":"Chaillet"},{"last_name":"Žák","first_name":"Jakub","full_name":"Žák, Jakub"},{"last_name":"Grybchuk","first_name":"Danyil","full_name":"Grybchuk, Danyil"},{"last_name":"Förster","first_name":"Friedrich","full_name":"Förster, Friedrich"},{"last_name":"Wilson","full_name":"Wilson, William H.","first_name":"William H."},{"last_name":"Schroeder","first_name":"Declan C.","full_name":"Schroeder, Declan C."},{"last_name":"Plevka","first_name":"Pavel","full_name":"Plevka, Pavel"}],"issue":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","year":"2024","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"article_number":"eadk1954 ","article_type":"original","department":[{"_id":"EM-Fac"}],"article_processing_charge":"Yes","acknowledgement":"We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core Facility and Proteomics Core Facility of the Central European Institute of Technology (CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR); and (iii) Plant Sciences Core Facility for support with obtaining scientific data presented here. We acknowledge support from the project National Institute of Virology and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European Union - Next Generation EU. This work received funding from the Czech Science Foundation grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI” (no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship funded by Brno city municipality to M.H.","status":"public","date_created":"2025-01-27T14:32:34Z","oa":1,"_id":"18920","publisher":"American Association for the Advancement of Science","day":"01","date_updated":"2025-05-14T09:29:04Z","abstract":[{"text":"The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.","lang":"eng"}],"publication_identifier":{"eissn":["2375-2548"]},"volume":10,"language":[{"iso":"eng"}],"file_date_updated":"2025-01-27T14:40:08Z","citation":{"ama":"Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. 2024;10(15). doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>","ista":"Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 10(15), eadk1954.","chicago":"Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>.","apa":"Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>","ieee":"M. Homola <i>et al.</i>, “Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi,” <i>Science Advances</i>, vol. 10, no. 15. American Association for the Advancement of Science, 2024.","mla":"Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>, vol. 10, no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>.","short":"M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L. Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka, Science Advances 10 (2024)."},"doi":"10.1126/sciadv.adk1954","OA_type":"gold","title":"Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","has_accepted_license":"1","DOAJ_listed":"1","OA_place":"publisher","ddc":["570"],"publication":"Science Advances","date_published":"2024-04-01T00:00:00Z","type":"journal_article","related_material":{"link":[{"relation":"software","url":" https://github.com/fuzikt/tomostarpy."}]},"scopus_import":"1"},{"type":"journal_article","related_material":{"link":[{"url":"https://github.com/heiniglab/gaertner_megakaryocytes","relation":"software"}]},"scopus_import":"1","publication":"Nature","ec_funded":1,"date_published":"2024-07-18T00:00:00Z","title":"Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis","has_accepted_license":"1","ddc":["570"],"language":[{"iso":"eng"}],"volume":631,"file_date_updated":"2024-07-22T06:16:11Z","doi":"10.1038/s41586-024-07671-y","citation":{"ieee":"F. R. Gärtner <i>et al.</i>, “Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis,” <i>Nature</i>, vol. 631. Springer Nature, pp. 645–653, 2024.","apa":"Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck, A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07671-y\">https://doi.org/10.1038/s41586-024-07671-y</a>","chicago":"Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu, Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07671-y\">https://doi.org/10.1038/s41586-024-07671-y</a>.","ama":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. <i>Nature</i>. 2024;631:645-653. doi:<a href=\"https://doi.org/10.1038/s41586-024-07671-y\">10.1038/s41586-024-07671-y</a>","ista":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S, Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M, Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 631, 645–653.","short":"F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck, B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang, A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich, T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried, P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann, W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild, M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631 (2024) 645–653.","mla":"Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” <i>Nature</i>, vol. 631, Springer Nature, 2024, pp. 645–53, doi:<a href=\"https://doi.org/10.1038/s41586-024-07671-y\">10.1038/s41586-024-07671-y</a>."},"abstract":[{"text":"Platelet homeostasis is essential for vascular integrity and immune defence1,2. Although the process of platelet formation by fragmenting megakaryocytes (MKs; thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis) remains unclear3,4. Here we use intravital imaging to track the cellular dynamics of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver IFNα to the MK niche triggering local on-demand proliferation and maturation of MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet homeostasis at steady state and under stress. pDCs are best known for their ability to function as vigilant detectors of viral infection5. We show that virus-induced activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis. Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis. Together, we identify a pDC-dependent homeostatic circuit that involves innate immune sensing and demand-adapted release of inflammatory mediators to maintain homeostasis of the megakaryocytic lineage.","lang":"eng"}],"date_updated":"2025-09-08T08:14:25Z","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"corr_author":"1","date_created":"2024-07-21T22:01:02Z","oa":1,"publisher":"Springer Nature","day":"18","_id":"17284","status":"public","acknowledgement":"We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03); FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744 (F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213 (F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation (DFG, project IDs 322900939, 432698239 and 445703531), European Research Council (ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E. are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics Munich). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 833440 to S.M.). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"article_type":"original","pmid":1,"year":"2024","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","external_id":{"isi":["001281636500020"],"pmid":["38987596"]},"author":[{"last_name":"Gärtner","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","full_name":"Gärtner, Florian R"},{"first_name":"Hellen","full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold"},{"full_name":"Stutte, Susanne","first_name":"Susanne","last_name":"Stutte"},{"full_name":"Fu, Wenwen","first_name":"Wenwen","last_name":"Fu"},{"last_name":"Weitz","first_name":"Jutta","full_name":"Weitz, Jutta"},{"full_name":"Dueck, Anne","first_name":"Anne","last_name":"Dueck"},{"first_name":"Bhavishya","full_name":"Nelakuditi, Bhavishya","last_name":"Nelakuditi"},{"last_name":"Fumagalli","full_name":"Fumagalli, Valeria","first_name":"Valeria"},{"last_name":"Van Den Heuvel","first_name":"Dominic","full_name":"Van Den Heuvel, Dominic"},{"full_name":"Belz, Larissa","first_name":"Larissa","last_name":"Belz"},{"first_name":"Gulnoza","full_name":"Sobirova, Gulnoza","last_name":"Sobirova"},{"last_name":"Zhang","first_name":"Zhe","full_name":"Zhang, Zhe"},{"last_name":"Titova","first_name":"Anna","full_name":"Titova, Anna"},{"last_name":"Navarro","full_name":"Navarro, Alejandro Martinez","first_name":"Alejandro Martinez"},{"last_name":"Pekayvaz","first_name":"Kami","full_name":"Pekayvaz, Kami"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"last_name":"Von Baumgarten","full_name":"Von Baumgarten, Louisa","first_name":"Louisa"},{"last_name":"Kranich","first_name":"Jan","full_name":"Kranich, Jan"},{"first_name":"Tobias","full_name":"Straub, Tobias","last_name":"Straub"},{"last_name":"Popper","first_name":"Bastian","full_name":"Popper, Bastian"},{"full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0002-9438-4783","last_name":"Zheden"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Chenglong","full_name":"Guo, Chenglong","last_name":"Guo"},{"last_name":"Piontek","full_name":"Piontek, Guido","first_name":"Guido"},{"last_name":"Von Stillfried","first_name":"Saskia","full_name":"Von Stillfried, Saskia"},{"full_name":"Boor, Peter","first_name":"Peter","last_name":"Boor"},{"last_name":"Colonna","full_name":"Colonna, Marco","first_name":"Marco"},{"first_name":"Sebastian","full_name":"Clauß, Sebastian","last_name":"Clauß"},{"last_name":"Schulz","full_name":"Schulz, Christian","first_name":"Christian"},{"last_name":"Brocker","first_name":"Thomas","full_name":"Brocker, Thomas"},{"last_name":"Walzog","full_name":"Walzog, Barbara","first_name":"Barbara"},{"last_name":"Scheiermann","full_name":"Scheiermann, Christoph","first_name":"Christoph"},{"last_name":"Aird","full_name":"Aird, William C.","first_name":"William C."},{"last_name":"Nerlov","first_name":"Claus","full_name":"Nerlov, Claus"},{"full_name":"Stark, Konstantin","first_name":"Konstantin","last_name":"Stark"},{"last_name":"Petzold","first_name":"Tobias","full_name":"Petzold, Tobias"},{"full_name":"Engelhardt, Stefan","first_name":"Stefan","last_name":"Engelhardt"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"last_name":"Rudelius","full_name":"Rudelius, Martina","first_name":"Martina"},{"full_name":"Oostendorp, Robert A.J.","first_name":"Robert A.J.","last_name":"Oostendorp"},{"first_name":"Matteo","full_name":"Iannacone, Matteo","last_name":"Iannacone"},{"last_name":"Heinig","first_name":"Matthias","full_name":"Heinig, Matthias"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"intvolume":"       631","project":[{"grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"page":"645-653","publication_status":"published","file":[{"content_type":"application/pdf","date_updated":"2024-07-22T06:16:11Z","file_size":15704819,"relation":"main_file","success":1,"creator":"dernst","access_level":"open_access","file_id":"17286","date_created":"2024-07-22T06:16:11Z","file_name":"2024_Nature_Gaertner.pdf","checksum":"aa004afc72d2489f0fb0fcbc9919fbbd"}],"oa_version":"Published Version"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"article_number":"7511","article_type":"original","acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"department":[{"_id":"EM-Fac"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"08","year":"2024","quality_controlled":"1","intvolume":"        15","external_id":{"isi":["001457895200001"],"pmid":["39209816"]},"author":[{"first_name":"Lisa","full_name":"Kofler, Lisa","last_name":"Kofler"},{"last_name":"Grundmann","full_name":"Grundmann, Lorenz","first_name":"Lorenz"},{"full_name":"Gerhalter, Magdalena","first_name":"Magdalena","last_name":"Gerhalter"},{"first_name":"Michael","full_name":"Prattes, Michael","last_name":"Prattes"},{"last_name":"Merl-Pham","full_name":"Merl-Pham, Juliane","first_name":"Juliane"},{"last_name":"Zisser","first_name":"Gertrude","full_name":"Zisser, Gertrude"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","last_name":"Hodirnau"},{"full_name":"Vareka, Martin","first_name":"Martin","last_name":"Vareka"},{"last_name":"Breinbauer","full_name":"Breinbauer, Rolf","first_name":"Rolf"},{"full_name":"Hauck, Stefanie M.","first_name":"Stefanie M.","last_name":"Hauck"},{"first_name":"David","full_name":"Haselbach, David","last_name":"Haselbach"},{"last_name":"Bergler","full_name":"Bergler, Helmut","first_name":"Helmut"}],"file":[{"file_id":"17946","access_level":"open_access","creator":"dernst","success":1,"relation":"main_file","file_size":3735024,"file_name":"2024_NatureComm_Kofler.pdf","checksum":"7c044538a47182c826d1b526c52958a2","date_created":"2024-09-09T08:56:12Z","date_updated":"2024-09-09T08:56:12Z","content_type":"application/pdf"}],"oa_version":"Published Version","publication_status":"published","publication":"Nature Communications","date_published":"2024-08-29T00:00:00Z","type":"journal_article","scopus_import":"1","OA_type":"gold","title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","has_accepted_license":"1","DOAJ_listed":"1","ddc":["570"],"OA_place":"publisher","abstract":[{"lang":"eng","text":"The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities."}],"date_updated":"2025-09-08T09:13:01Z","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"volume":15,"doi":"10.1038/s41467-024-51754-3","file_date_updated":"2024-09-09T08:56:12Z","citation":{"ieee":"L. Kofler <i>et al.</i>, “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-51754-3\">https://doi.org/10.1038/s41467-024-51754-3</a>.","apa":"Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-51754-3\">https://doi.org/10.1038/s41467-024-51754-3</a>","ista":"Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 15, 7511.","ama":"Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-51754-3\">10.1038/s41467-024-51754-3</a>","short":"L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser, I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach, H. Bergler, Nature Communications 15 (2024).","mla":"Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” <i>Nature Communications</i>, vol. 15, 7511, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-51754-3\">10.1038/s41467-024-51754-3</a>."},"acknowledgement":"We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit, Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae, Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus de la Cruz for sharing strains or providing antibodies. We thank the members of the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. This research was funded in whole, or in part, by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451] and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","status":"public","article_processing_charge":"Yes","date_created":"2024-09-08T22:01:10Z","oa":1,"publisher":"Springer Nature","day":"29","_id":"17885"},{"title":"Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning","type":"book_chapter","scopus_import":"1","place":"New York","publication":"New Aspects in Analyzing the Synaptic Organization of the Brain","ec_funded":1,"date_published":"2024-08-27T00:00:00Z","corr_author":"1","date_created":"2024-09-10T12:32:38Z","day":"27","publisher":"Springer Nature","_id":"18052","edition":"1","status":"public","acknowledgement":"This research was supported by the European Research Council Advanced Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"ama":"Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR, Rollenhagen A, eds. <i>New Aspects in Analyzing the Synaptic Organization of the Brain</i>. 1st ed. New York: Springer Nature; 2024:123-137. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4019-7_8\">10.1007/978-1-0716-4019-7_8</a>","ista":"Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137.","chicago":"Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” In <i>New Aspects in Analyzing the Synaptic Organization of the Brain</i>, edited by Joachim H.R.  Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-4019-7_8\">https://doi.org/10.1007/978-1-0716-4019-7_8</a>.","apa":"Kleindienst, D., Costanzo, T., &#38; Shigemoto, R. (2024). Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In J. H. R. Lübke &#38; A. Rollenhagen (Eds.), <i>New Aspects in Analyzing the Synaptic Organization of the Brain</i> (1st ed., pp. 123–137). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4019-7_8\">https://doi.org/10.1007/978-1-0716-4019-7_8</a>","ieee":"D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in <i>New Aspects in Analyzing the Synaptic Organization of the Brain</i>, 1st ed., J. H. R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.","mla":"Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” <i>New Aspects in Analyzing the Synaptic Organization of the Brain</i>, edited by Joachim H.R.  Lübke and Astrid Rollenhagen, 1st ed., Springer Nature, 2024, pp. 123–37, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4019-7_8\">10.1007/978-1-0716-4019-7_8</a>.","short":"D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., Springer Nature, New York, 2024, pp. 123–137."},"doi":"10.1007/978-1-0716-4019-7_8","abstract":[{"lang":"eng","text":"Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is an electron microscope (EM) sample preparation technique which allows for high-resolution visualization of membrane proteins with high sensitivity. However, image acquisition of specific replica profiles such as synapses in a large field of EM view needs a valid experience and a long time for manual searching. Here, we describe how to utilize deep learning for automatizing image acquisition of specific profiles of interest in replica samples. This protocol facilitates the labor-intensive collection of EM images, in particular for rare profiles. We provide instructions for using SerialEM image acquisition software in conjunction with object detection by our newly developed deep learning software DarEM, to automatically acquire tilt series of all synapses in a selected region. We then show how to perform a mostly automated analysis of gold particle labeling in the acquired images by utilizing Darea software."}],"date_updated":"2025-04-14T07:27:15Z","publication_identifier":{"isbn":["9781071640180"],"eissn":["1940-6045"],"eisbn":["9781071640197"],"issn":["0893-2336"]},"year":"2024","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"alternative_title":["Neuromethods"],"acknowledged_ssus":[{"_id":"EM-Fac"}],"page":"123-137","publication_status":"published","editor":[{"first_name":"Joachim H.R. ","full_name":"Lübke, Joachim H.R. ","last_name":"Lübke"},{"full_name":"Rollenhagen, Astrid","first_name":"Astrid","last_name":"Rollenhagen"}],"oa_version":"None","author":[{"last_name":"Kleindienst","full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"orcid":"0000-0001-9732-3815","last_name":"Costanzo","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539"}]},{"year":"2024","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","keyword":["Hippocampal mossy fiber synapses","short-term potentiation","long-term potentiation","presynaptic plasticity","electron microscopy","freeze-fracture replica labeling","paired recordings","forskolin","cyclic adenosine monophosphate (cAMP)","protein kinase A (PKA)","neuromodulation","synaptic vesicle pools","presynaptic Ca2+ channels","Munc13","docking","priming","active zone"],"month":"10","department":[{"_id":"PeJo"},{"_id":"RySh"},{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"content_type":"application/zip","date_updated":"2024-10-11T10:04:19Z","relation":"main_file","file_size":164382,"success":1,"creator":"okim","access_level":"open_access","file_id":"18297","date_created":"2024-10-11T10:04:19Z","file_name":"Kim_et_al_2024_PlosBio_Source_data.zip","checksum":"0a977e7df54c418251b10dfd3f8a015c"},{"file_size":654,"relation":"main_file","success":1,"creator":"okim","access_level":"open_access","file_id":"18298","date_created":"2024-10-11T10:04:23Z","file_name":"info.txt","checksum":"5b9343d6b2035ac3185e390fad4d3830","content_type":"text/plain","date_updated":"2024-10-11T10:04:23Z"}],"oa_version":"Submitted Version","author":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","full_name":"Kim, Olena","last_name":"Kim","orcid":"0000-0003-2344-1039"}],"project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692"}],"title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","has_accepted_license":"1","contributor":[{"last_name":"Kim","contributor_type":"researcher","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"},{"orcid":"0000-0003-0408-6094","last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Yuji"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","contributor_type":"researcher","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"last_name":"Brose","contributor_type":"researcher","first_name":"Nils "},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","contributor_type":"researcher","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","contributor_type":"supervisor","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"ddc":["570"],"type":"research_data","related_material":{"record":[{"relation":"used_in_publication","id":"18603","status":"public"}]},"ec_funded":1,"date_published":"2024-10-11T00:00:00Z","oa":1,"date_created":"2024-10-11T10:12:17Z","corr_author":"1","_id":"18296","day":"11","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","status":"public","doi":"10.15479/AT:ISTA:18296","citation":{"ieee":"O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons.” Institute of Science and Technology Austria, 2024.","apa":"Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>","chicago":"Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>.","ista":"Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>.","ama":"Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>","short":"O. Kim, (2024).","mla":"Kim, Olena. <i>Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>."},"file_date_updated":"2024-10-11T10:04:23Z","date_updated":"2026-04-16T12:20:33Z","abstract":[{"text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.","lang":"eng"}]},{"author":[{"id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","full_name":"Chen, JingJing","last_name":"Chen"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"full_name":"Chen, Chong","first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"},{"last_name":"Arai","first_name":"Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Arai, Itaru"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","full_name":"Kim, Olena","last_name":"Kim","orcid":"0000-0003-2344-1039"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383"}],"intvolume":"       112","publication_status":"published","page":"755-771.e9","oa_version":"Published Version","file":[{"content_type":"application/pdf","date_updated":"2025-04-23T14:02:08Z","relation":"main_file","file_size":8192355,"success":1,"creator":"dernst","file_id":"19614","access_level":"open_access","date_created":"2025-04-23T14:02:08Z","file_name":"2024_Neuron_Chen.pdf","checksum":"30098b4f0209556ddfb3540a23d07ca5"}],"department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"article_type":"original","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","year":"2024","month":"03","PlanS_conform":"1","issue":"5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024."},"file_date_updated":"2025-04-23T14:02:08Z","doi":"10.1016/j.neuron.2023.12.002","language":[{"iso":"eng"}],"volume":112,"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"date_updated":"2026-08-06T22:30:29Z","abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"_id":"14843","day":"06","publisher":"Elsevier","date_created":"2024-01-21T23:00:56Z","oa":1,"corr_author":"1","article_processing_charge":"Yes (via OA deal)","status":"public","acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15101"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","description":"News on ISTA Website"}]},"scopus_import":"1","type":"journal_article","date_published":"2024-03-06T00:00:00Z","ec_funded":1,"publication":"Neuron","OA_place":"publisher","ddc":["570"],"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","has_accepted_license":"1","OA_type":"hybrid"},{"article_type":"original","article_number":"add6495","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"keyword":["Multidisciplinary"],"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","quality_controlled":"1","year":"2023","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"intvolume":"         9","author":[{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"full_name":"Javoor, Manjunath","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","orcid":"0000-0003-2311-2112"},{"full_name":"Datler, Julia","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","last_name":"Datler"},{"last_name":"Döring","first_name":"Hermann","full_name":"Döring, Hermann"},{"last_name":"Hofer","full_name":"Hofer, Florian","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"orcid":"0000-0001-8370-6161","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","full_name":"Dimchev, Georgi A"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X","last_name":"Hodirnau"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"external_id":{"isi":["000964550100015"],"pmid":["36662867"]},"oa_version":"Published Version","file":[{"checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","file_name":"2023_ScienceAdvances_Faessler.pdf","date_created":"2023-01-23T07:45:54Z","file_id":"12335","access_level":"open_access","creator":"dernst","success":1,"file_size":1756234,"relation":"main_file","date_updated":"2023-01-23T07:45:54Z","content_type":"application/pdf"}],"publication_status":"published","date_published":"2023-01-20T00:00:00Z","publication":"Science Advances","scopus_import":"1","related_material":{"record":[{"status":"public","id":"14562","relation":"research_data"},{"id":"18766","relation":"dissertation_contains","status":"public"}]},"type":"journal_article","ddc":["570"],"has_accepted_license":"1","title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","publication_identifier":{"issn":["2375-2548"]},"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.</jats:p>","lang":"eng"}],"date_updated":"2026-04-07T12:59:44Z","file_date_updated":"2023-01-23T07:45:54Z","citation":{"ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. 2023;9(3). doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495.","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>.","ieee":"F. Fäßler <i>et al.</i>, “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” <i>Science Advances</i>, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>.","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023)."},"doi":"10.1126/sciadv.add6495","volume":9,"language":[{"iso":"eng"}],"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\nThis 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.","status":"public","article_processing_charge":"No","publisher":"American Association for the Advancement of Science","day":"20","_id":"12334","corr_author":"1","oa":1,"date_created":"2023-01-23T07:26:42Z"},{"year":"2023","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia","start_date":"2023-06-13"},"page":"59-59","publication_status":"published","file":[{"content_type":"application/pdf","date_updated":"2023-07-18T09:18:55Z","date_created":"2023-07-18T09:18:55Z","checksum":"ec8e4295d54171032cdd1b01423eb4a6","file_name":"2023_ASHPC_Schloegl.pdf","relation":"main_file","file_size":316959,"success":1,"creator":"dernst","file_id":"13249","access_level":"open_access"}],"oa_version":"Submitted Version","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","last_name":"Elefante"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","last_name":"Hodirnau"}],"has_accepted_license":"1","title":"Running Windows-applications on a Linux HPC cluster using WINE","ddc":["000"],"type":"conference_abstract","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","date_published":"2023-07-01T00:00:00Z","oa":1,"date_created":"2023-06-23T11:01:23Z","corr_author":"1","_id":"13161","day":"01","publisher":"EuroCC Austria","article_processing_charge":"No","status":"public","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","language":[{"iso":"eng"}],"file_date_updated":"2023-07-18T09:18:55Z","citation":{"ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, Maribor, Slovenia, 2023, pp. 59–59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. 2023. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>. EuroCC Austria; 2023:59-59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, 59–59. EuroCC Austria, 2023.","apa":"Schlögl, A., Elefante, S., &#38; Hodirnau, V.-V. (2023). Running Windows-applications on a Linux HPC cluster using WINE. In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i> (pp. 59–59). Maribor, Slovenia: EuroCC Austria.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 59–59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, EuroCC Austria, 2023, pp. 59–59."},"date_updated":"2026-07-06T13:01:46Z"},{"volume":34,"language":[{"iso":"eng"}],"citation":{"ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>."},"doi":"10.1093/plcell/koac071","abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"date_updated":"2025-05-14T11:06:15Z","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"date_created":"2022-03-08T13:47:51Z","oa":1,"publisher":"Oxford University Press","day":"01","_id":"10841","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","status":"public","article_processing_charge":"No","type":"journal_article","scopus_import":"1","publication":"Plant Cell","date_published":"2022-06-01T00:00:00Z","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"author":[{"last_name":"Dahhan","full_name":"Dahhan, DA","first_name":"DA"},{"last_name":"Reynolds","first_name":"GD","full_name":"Reynolds, GD"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"last_name":"Eeckhout","full_name":"Eeckhout, D","first_name":"D"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"first_name":"K","full_name":"Yperman, K","last_name":"Yperman"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter"},{"last_name":"Vang","full_name":"Vang, N","first_name":"N"},{"full_name":"Yan, X","first_name":"X","last_name":"Yan"},{"first_name":"I","full_name":"Hwang, I","last_name":"Hwang"},{"last_name":"Heese","first_name":"A","full_name":"Heese, A"},{"first_name":"G","full_name":"De Jaeger, G","last_name":"De Jaeger"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Van Damme","full_name":"Van Damme, D","first_name":"D"},{"last_name":"Pan","full_name":"Pan, J","first_name":"J"},{"first_name":"SY","full_name":"Bednarek, SY","last_name":"Bednarek"}],"intvolume":"        34","project":[{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"page":"2150-2173","publication_status":"published","oa_version":"Preprint","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"isi":1,"article_type":"original","acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"year":"2022","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","month":"06"},{"article_processing_charge":"Yes (via OA deal)","status":"public","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","_id":"12239","publisher":"Elsevier","day":"03","oa":1,"date_created":"2023-01-16T09:51:49Z","corr_author":"1","publication_identifier":{"issn":["1674-2052"]},"date_updated":"2025-04-15T07:32:09Z","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"doi":"10.1016/j.molp.2022.09.003","file_date_updated":"2023-01-30T07:46:51Z","citation":{"ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542."},"volume":15,"language":[{"iso":"eng"}],"ddc":["580"],"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","has_accepted_license":"1","date_published":"2022-10-03T00:00:00Z","publication":"Molecular Plant","scopus_import":"1","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"04d5c12490052d03e4dc4412338a43dd","file_name":"2022_MolecularPlant_Johnson.pdf","date_created":"2023-01-30T07:46:51Z","file_id":"12435","access_level":"open_access","creator":"dernst","success":1,"file_size":2307251,"relation":"main_file","date_updated":"2023-01-30T07:46:51Z","content_type":"application/pdf"}],"publication_status":"published","page":"1533-1542","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630"}],"intvolume":"        15","author":[{"orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"orcid":"0000-0001-9732-3815","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","full_name":"Costanzo, Tommaso"},{"last_name":"Dahhan","full_name":"Dahhan, Dana A.","first_name":"Dana A."},{"first_name":"Sebastian Y.","full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"keyword":["Plant Science","Molecular Biology"],"month":"10","issue":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","year":"2022","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"article_type":"original","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}]},{"language":[{"iso":"eng"}],"volume":29,"citation":{"ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural &#38; Molecular Biology. 29(9), 942–953.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. 2022;29(9):942-953. doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>","ieee":"M. Prattes <i>et al.</i>, “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural &#38; Molecular Biology 29 (2022) 942–953."},"file_date_updated":"2023-01-30T10:00:04Z","doi":"10.1038/s41594-022-00832-5","abstract":[{"lang":"eng","text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases."}],"date_updated":"2023-08-04T09:52:20Z","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"date_created":"2023-01-16T09:59:06Z","oa":1,"day":"12","publisher":"Springer Nature","_id":"12262","acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","status":"public","article_processing_charge":"No","type":"journal_article","scopus_import":"1","publication":"Nature Structural & Molecular Biology","date_published":"2022-09-12T00:00:00Z","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","has_accepted_license":"1","ddc":["570"],"external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"author":[{"last_name":"Prattes","full_name":"Prattes, Michael","first_name":"Michael"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina","first_name":"Christina"},{"first_name":"Gertrude","full_name":"Zisser, Gertrude","last_name":"Zisser"},{"full_name":"Sailer, Carolin","first_name":"Carolin","last_name":"Sailer"},{"first_name":"Vasileios","full_name":"Kargas, Vasileios","last_name":"Kargas"},{"last_name":"Loibl","first_name":"Mathias","full_name":"Loibl, Mathias"},{"full_name":"Gerhalter, Magdalena","first_name":"Magdalena","last_name":"Gerhalter"},{"last_name":"Kofler","full_name":"Kofler, Lisa","first_name":"Lisa"},{"full_name":"Warren, Alan J.","first_name":"Alan J.","last_name":"Warren"},{"first_name":"Florian","full_name":"Stengel, Florian","last_name":"Stengel"},{"first_name":"David","full_name":"Haselbach, David","last_name":"Haselbach"},{"full_name":"Bergler, Helmut","first_name":"Helmut","last_name":"Bergler"}],"intvolume":"        29","page":"942-953","publication_status":"published","file":[{"checksum":"2d5c3ec01718fefd7553052b0b8a0793","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","date_created":"2023-01-30T10:00:04Z","file_id":"12447","access_level":"open_access","creator":"dernst","success":1,"relation":"main_file","file_size":9935057,"date_updated":"2023-01-30T10:00:04Z","content_type":"application/pdf"}],"oa_version":"Published Version","department":[{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"article_type":"original","acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"year":"2022","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","month":"09","keyword":["Molecular Biology","Structural Biology"]},{"isi":1,"pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"article_type":"original","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"issue":"7927","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","year":"2022","quality_controlled":"1","intvolume":"       609","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","call_identifier":"FWF"}],"external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"author":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368"},{"first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana","last_name":"Gelová","orcid":"0000-0003-4783-1752"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843"},{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Živanović","full_name":"Živanović, Branka D.","first_name":"Branka D."},{"full_name":"Zou, Minxia","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou"},{"full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas","last_name":"Fiedler"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","full_name":"Giannini, Caterina","last_name":"Giannini"},{"last_name":"Grones","first_name":"Peter","full_name":"Grones, Peter"},{"last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","full_name":"Hrtyan, Mónika"},{"full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"last_name":"Kuhn","first_name":"Andre","full_name":"Kuhn, Andre"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan"},{"last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","full_name":"Randuch, Marek"},{"first_name":"Nikola","full_name":"Rýdza, Nikola","last_name":"Rýdza"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Teplova","full_name":"Teplova, Anastasiia","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"full_name":"Kinoshita, Toshinori","first_name":"Toshinori","last_name":"Kinoshita"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"last_name":"Rakusová","first_name":"Hana","full_name":"Rakusová, Hana"}],"file":[{"file_name":"Friml Nature 2022_merged.pdf","checksum":"a6055c606aefb900bf62ae3e7d15f921","date_created":"2023-11-02T17:12:37Z","access_level":"open_access","file_id":"14483","creator":"amally","success":1,"file_size":79774945,"relation":"main_file","date_updated":"2023-11-02T17:12:37Z","content_type":"application/pdf"}],"oa_version":"Submitted Version","page":"575-581","publication_status":"published","ec_funded":1,"publication":"Nature","date_published":"2022-09-15T00:00:00Z","type":"journal_article","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19395"},{"status":"public","id":"20364","relation":"dissertation_contains"}]},"has_accepted_license":"1","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","ddc":["580"],"date_updated":"2026-04-07T11:52:15Z","abstract":[{"lang":"eng","text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization."}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"volume":609,"citation":{"mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022."},"doi":"10.1038/s41586-022-05187-x","file_date_updated":"2023-11-02T17:12:37Z","article_processing_charge":"No","status":"public","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","date_created":"2023-01-16T10:04:48Z","oa":1,"corr_author":"1","_id":"12291","day":"15","publisher":"Springer Nature"},{"ec_funded":1,"publication":"Oxford Open Neuroscience","date_published":"2022-07-07T00:00:00Z","type":"journal_article","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12726"},{"status":"public","id":"14530","relation":"dissertation_contains"}]},"title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","has_accepted_license":"1","ddc":["570"],"date_updated":"2026-04-07T13:29:13Z","abstract":[{"lang":"eng","text":"The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general."}],"publication_identifier":{"eissn":["2753-149X"]},"volume":1,"language":[{"iso":"eng"}],"doi":"10.1093/oons/kvac009","citation":{"mla":"Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1, kvac009, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>.","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022).","ista":"Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM, Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 1(1), kvac009.","ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. 2022;1(1). doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>","apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>","chicago":"Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>.","ieee":"A. H. Hansen <i>et al.</i>, “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1. Oxford University Press, 2022."},"file_date_updated":"2023-08-16T08:00:30Z","article_processing_charge":"No","acknowledgement":"A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics Facility, Lab Support Facility and Preclinical Facility.","status":"public","oa":1,"date_created":"2022-02-25T07:52:11Z","corr_author":"1","_id":"10791","day":"07","publisher":"Oxford University Press","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"pmid":1,"article_type":"original","article_number":"kvac009","department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","year":"2022","quality_controlled":"1","intvolume":"         1","project":[{"grant_number":"618444","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"external_id":{"pmid":["38596707"]},"author":[{"last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"last_name":"Riedl","orcid":"0000-0003-4844-6311","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena"},{"first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne","last_name":"Laukoter","orcid":"0000-0002-7903-3010"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","full_name":"Nicolas, Armel"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"last_name":"Tsai","full_name":"Tsai, Li Huei","first_name":"Li Huei"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"file":[{"creator":"dernst","access_level":"open_access","file_id":"14061","relation":"main_file","file_size":4846551,"success":1,"date_created":"2023-08-16T08:00:30Z","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","checksum":"822e76e056c07099d1fb27d1ece5941b","date_updated":"2023-08-16T08:00:30Z","content_type":"application/pdf"}],"oa_version":"Published Version","publication_status":"published"}]