[{"scopus_import":"1","file":[{"checksum":"a9383dd978ca2c50b7dded6c0bb2cd49","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"19415","file_size":6364878,"date_updated":"2025-03-17T10:53:32Z","date_created":"2025-03-17T10:53:32Z","file_name":"2025_NatureComm_Janik.pdf","content_type":"application/pdf"}],"publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"author":[{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","full_name":"Janik, Marian","last_name":"Janik","first_name":"Marian","orcid":"0009-0003-9037-8831"},{"id":"53f93ea2-803f-11ed-ab7e-b283135794ef","last_name":"Roux","full_name":"Roux, Kevin Etienne Robert","first_name":"Kevin Etienne Robert"},{"id":"18777c01-896a-11ed-bdf8-e4851dc07d16","last_name":"Borja Espinosa","full_name":"Borja Espinosa, Carla N","first_name":"Carla N"},{"first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","full_name":"Sagi, Oliver"},{"first_name":"Abdulhamid","id":"160D87FA-96B5-11E9-BF77-7626E6697425","full_name":"Baghdadi, Abdulhamid","last_name":"Baghdadi"},{"first_name":"Thomas","full_name":"Adletzberger, Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","last_name":"Adletzberger"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"first_name":"Marc","last_name":"Botifoll","full_name":"Botifoll, Marc"},{"full_name":"Garzón Manjón, Alba","last_name":"Garzón Manjón","first_name":"Alba"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"first_name":"Ioan M.","last_name":"Pop","full_name":"Pop, Ioan M."},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X"}],"article_type":"original","DOAJ_listed":"1","quality_controlled":"1","title":"Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors","_id":"19401","date_created":"2025-03-16T23:01:23Z","file_date_updated":"2025-03-17T10:53:32Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"year":"2025","intvolume":"        16","oa":1,"publication":"Nature Communications","volume":16,"day":"01","arxiv":1,"acknowledgement":"We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. We thank Simon Robson for proofreading the manuscript. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the HORIZON-RIA 101069515 project. This research was funded in whole or in part by the Austrian Science Fund (FWF) https://doi.org/10.55776/P32235, https://doi.org/10.55776/I5060 and https://doi.org/10.55776/P36507. For Open Access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. M.J. acknowledges funding from FellowQUTE 2024-01. K.R. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413. I.M.P. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission - NextGenerationEU (Regulation EU 2020/2094), through CSIC’s Quantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa programme from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD programme. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors acknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Centre at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM60.","related_material":{"record":[{"id":"18886","status":"public","relation":"research_data"},{"status":"public","id":"18144","relation":"earlier_version"}]},"abstract":[{"text":"High kinetic inductance superconductors are gaining increasing interest for the realisation of qubits, amplifiers and detectors. Moreover, thanks to their high impedance, quantum buses made of such materials enable large zero-point fluctuations of the voltage, boosting the coupling rates to spin and charge qubits. However, fully exploiting the potential of disordered or granular superconductors is challenging, as their inductance and, therefore, impedance at high values are difficult to control. Here, we report a reproducible fabrication of granular aluminium resonators by developing a wireless ohmmeter, which allows in situ measurements during film deposition and, therefore, control of the kinetic inductance of granular aluminium films. Reproducible fabrication of circuits with impedances (inductances) exceeding 13 kΩ (1 nH per square) is now possible. By integrating a 7.9 kΩ resonator with a germanium double quantum dot, we demonstrate strong charge-photon coupling with a rate of gc/2π = 566 ± 2 MHz. This broadly applicable method opens the path for novel qubits and high-fidelity, long-distance two-qubit gates.","lang":"eng"}],"month":"03","type":"journal_article","external_id":{"isi":["001434774800001"],"arxiv":["2407.03079"],"pmid":["40025007"]},"oa_version":"Published Version","citation":{"mla":"Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” <i>Nature Communications</i>, vol. 16, 2103, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-57252-4\">10.1038/s41467-025-57252-4</a>.","apa":"Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger, T., … Katsaros, G. (2025). Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-57252-4\">https://doi.org/10.1038/s41467-025-57252-4</a>","ieee":"M. Janik <i>et al.</i>, “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","short":"M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger, S. Calcaterra, M. Botifoll, A. Garzón Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M. Pop, G. Katsaros, Nature Communications 16 (2025).","chicago":"Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-57252-4\">https://doi.org/10.1038/s41467-025-57252-4</a>.","ama":"Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-57252-4\">10.1038/s41467-025-57252-4</a>","ista":"Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T, Calcaterra S, Botifoll M, Garzón Manjón A, Arbiol J, Chrastina D, Isella G, Pop IM, Katsaros G. 2025. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. Nature Communications. 16, 2103."},"ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2025-03-01T00:00:00Z","isi":1,"doi":"10.1038/s41467-025-57252-4","OA_type":"gold","project":[{"name":"Integrated Germanium Quantum Technology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"grant_number":"P32235","name":"Towards scalable hut wire quantum devices","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"status":"public","article_number":"2103","pmid":1,"APC_amount":"7068 EUR","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"M-Shop"}],"has_accepted_license":"1","article_processing_charge":"Yes","date_updated":"2026-10-02T11:05:09Z","fulldoi":"https://doi.org/10.1038/s41467-025-57252-4","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1},{"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"article_processing_charge":"Yes","has_accepted_license":"1","article_number":"115387","pmid":1,"publication_status":"published","issue":"3","fulldoi":"https://doi.org/10.1016/j.celrep.2025.115387","date_updated":"2026-10-20T08:20:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","external_id":{"pmid":["40057955"],"isi":["001443652700001"]},"oa_version":"Published Version","abstract":[{"text":"Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation.","lang":"eng"}],"month":"03","OA_type":"gold","isi":1,"doi":"10.1016/j.celrep.2025.115387","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"},{"name":"Mechanosensation in cell migration: the role of friction forces in cell polarization and directed migration","grant_number":"ALTF 1159-2018","_id":"269CD5C4-B435-11E9-9278-68D0E5697425"}],"status":"public","citation":{"apa":"Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A., … Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>","mla":"Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>, vol. 44, no. 3, 115387, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>.","ista":"Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R, Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. 44(3), 115387.","chicago":"Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>.","ama":"Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. 2025;44(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>","ieee":"S. Tavano <i>et al.</i>, “BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation,” <i>Cell Reports</i>, vol. 44, no. 3. Cell Press, 2025.","short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (2025)."},"ddc":["570"],"date_published":"2025-03-25T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"intvolume":"        44","oa":1,"corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"year":"2025","acknowledgement":"We are grateful to the colleagues who contributed to this work with discussions, technical advice, and feedback on the manuscript: Irene Steccari, David Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship (ALTF 1159-2018).","day":"25","volume":44,"publication":"Cell Reports","DOAJ_listed":"1","article_type":"original","author":[{"orcid":"0000-0001-9970-7804","first_name":"Ste","last_name":"Tavano","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","full_name":"Tavano, Ste"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","full_name":"Tasciyan, Saren","first_name":"Saren","orcid":"0000-0003-1671-393X"},{"id":"50F65CDC-AA30-11E9-A72B-8A12E6697425","last_name":"Tong","full_name":"Tong, Xin","first_name":"Xin"},{"first_name":"Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"orcid":"0000-0001-7659-9142","first_name":"Alexandra","full_name":"Schauer, Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","quality_controlled":"1","file":[{"file_size":9067797,"date_updated":"2025-03-17T10:26:54Z","date_created":"2025-03-17T10:26:54Z","file_name":"2025_CellReports_Tavano.pdf","content_type":"application/pdf","checksum":"57e05dd1598c807af0afdb32cec039d3","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"19413"}],"scopus_import":"1","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"publisher":"Cell Press","file_date_updated":"2025-03-17T10:26:54Z","_id":"19404","date_created":"2025-03-16T23:01:24Z"},{"citation":{"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. Cell Press, 2025.","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).","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>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>.","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>","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>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>","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, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>."},"ddc":["570"],"date_published":"2025-06-11T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.1016/j.bpr.2025.100211","OA_type":"gold","status":"public","project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination","grant_number":"CZI01"},{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"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."}],"related_material":{"record":[{"relation":"dissertation_contains","id":"20206","status":"public"},{"relation":"dissertation_contains","status":"public","id":"22744"}]},"month":"06","type":"journal_article","oa_version":"Published Version","date_updated":"2026-10-20T08:55:34Z","fulldoi":"https://doi.org/10.1016/j.bpr.2025.100211","publication_status":"published","issue":"2","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"100211","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"has_accepted_license":"1","article_processing_charge":"Yes","date_created":"2025-06-08T22:01:22Z","_id":"19795","file_date_updated":"2025-06-10T07:24:46Z","scopus_import":"1","file":[{"checksum":"4018c833f25a3ad3b57e3577fed70334","success":1,"access_level":"open_access","file_id":"19802","relation":"main_file","creator":"dernst","date_created":"2025-06-10T07:24:46Z","file_name":"2025_BiophysicalReports_Vorlaufer.pdf","date_updated":"2025-06-10T07:24:46Z","content_type":"application/pdf","file_size":7238179}],"publisher":"Cell Press","publication_identifier":{"eissn":["2667-0747"]},"DOAJ_listed":"1","article_type":"original","author":[{"last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob","first_name":"Jakob","orcid":"0009-0000-7590-3501"},{"last_name":"Semenov","id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","full_name":"Semenov, Nikolai","first_name":"Nikolai"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","full_name":"Javoor, Manjunath","orcid":"0000-0003-2311-2112","first_name":"Manjunath"},{"full_name":"Zens, Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","orcid":"0000-0002-9561-1239"},{"first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","first_name":"Mojtaba"},{"first_name":"Marek","id":"EE8452B8-C26A-11E9-B157-E80CE6697425","full_name":"Suplata, Marek","last_name":"Suplata"},{"first_name":"Wiebke","orcid":"0000-0003-0201-2315","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia","first_name":"Julia"},{"first_name":"Andreas","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","full_name":"Wartak, Andreas","last_name":"Wartak"},{"first_name":"Florian Km","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian Km"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G"}],"quality_controlled":"1","title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","volume":5,"publication":"Biophysical Reports","day":"11","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.).","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"year":"2025","intvolume":"         5","oa":1},{"citation":{"short":"E. Dawson, M. Hönigsberger, N. Kampleitner, A.V. Grasse, L. Lindorfer, J. Robb, F. Beikzadeh, F. Strahodinsky, H. Leitner, H. Rajendran, T. Schmitt, S. Cremer, Nature Communications 16 (2025).","ieee":"E. Dawson <i>et al.</i>, “Altruistic disease signalling in ant colonies,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ama":"Dawson E, Hönigsberger M, Kampleitner N, et al. Altruistic disease signalling in ant colonies. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-66175-z\">10.1038/s41467-025-66175-z</a>","ista":"Dawson E, Hönigsberger M, Kampleitner N, Grasse AV, Lindorfer L, Robb J, Beikzadeh F, Strahodinsky F, Leitner H, Rajendran H, Schmitt T, Cremer S. 2025. Altruistic disease signalling in ant colonies. Nature Communications. 16, 10511.","chicago":"Dawson, Erika, Michaela Hönigsberger, Niklas Kampleitner, Anna V Grasse, Lukas Lindorfer, Jennifer Robb, Farnaz Beikzadeh, et al. “Altruistic Disease Signalling in Ant Colonies.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-66175-z\">https://doi.org/10.1038/s41467-025-66175-z</a>.","apa":"Dawson, E., Hönigsberger, M., Kampleitner, N., Grasse, A. V., Lindorfer, L., Robb, J., … Cremer, S. (2025). Altruistic disease signalling in ant colonies. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-66175-z\">https://doi.org/10.1038/s41467-025-66175-z</a>","mla":"Dawson, Erika, et al. “Altruistic Disease Signalling in Ant Colonies.” <i>Nature Communications</i>, vol. 16, 10511, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-66175-z\">10.1038/s41467-025-66175-z</a>."},"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2025-12-01T00:00:00Z","OA_type":"gold","doi":"10.1038/s41467-025-66175-z","main_file_link":[{"url":"https://doi.org/10.1101/2024.02.27.582277","open_access":"1"}],"status":"public","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"text":"Sick individuals often conceal their disease status to group members, thereby preventing social exclusion or aggression. Here we show by behavioural, chemical, immunological and infection load analyses that sick ant pupae instead actively emit a chemical signal that in itself is sufficient to trigger their own destruction by colony members. In our experiments, this altruistic disease-signalling was performed only by worker but not queen pupae. The lack of signalling by queen pupae did not constitute cheating behaviour, but reflected their superior immune capabilities. Worker pupae suffered from extensive pathogen replication whereas queen pupae were able to restrain their infection. Our data suggest the evolution of a finely-tuned signalling system in which it is not the induction of an individual’s immune response, but rather its failure to overcome the infection, that triggers pupal signalling for sacrifice. This demonstrates a balanced interplay between individual and social immunity that efficiently achieves whole-colony health.","lang":"eng"}],"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/ants-signal-deadly-infection/","relation":"press_release"}],"record":[{"status":"public","id":"20471","relation":"research_data"}]},"month":"12","type":"journal_article","external_id":{"pmid":["41330896"]},"das_tickbox":"0","oa_version":"Published Version","fulldoi":"https://doi.org/10.1038/s41467-025-66175-z","date_updated":"2026-10-21T10:53:39Z","publication_status":"published","researchdata_availability":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"article_number":"10511","pmid":1,"APC_amount":"7068 EUR","department":[{"_id":"SyCr"},{"_id":"LifeSc"}],"has_accepted_license":"1","article_processing_charge":"Yes","date_created":"2025-01-27T11:28:05Z","_id":"18892","file_date_updated":"2025-12-15T13:30:33Z","supplementarymaterial":"no","scopus_import":"1","file":[{"creator":"dernst","relation":"main_file","file_id":"20826","access_level":"open_access","success":1,"checksum":"06244623bb7611c636652ecbc4787889","file_size":805323,"content_type":"application/pdf","date_updated":"2025-12-15T13:30:33Z","file_name":"2025_NatureComm_Dawson.pdf","date_created":"2025-12-15T13:30:33Z"}],"publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","DOAJ_listed":"1","author":[{"first_name":"Erika","last_name":"Dawson","full_name":"Dawson, Erika","id":"31B4E2D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hönigsberger","full_name":"Hönigsberger, Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","first_name":"Michaela"},{"full_name":"Kampleitner, Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","last_name":"Kampleitner","first_name":"Niklas"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"first_name":"Lukas","last_name":"Lindorfer","id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","full_name":"Lindorfer, Lukas"},{"last_name":"Robb","full_name":"Robb, Jennifer","id":"7bc2734a-e2c6-11ea-9824-a2ed5f0662a8","first_name":"Jennifer"},{"first_name":"Farnaz","full_name":"Beikzadeh Abbasi, Farnaz","last_name":"Beikzadeh Abbasi","id":"0344bfb9-3feb-11ee-87e9-c27edc800bcd"},{"id":"979E35EE-C996-11E9-8C7C-CF13E6697425","full_name":"Strahodinsky, Florian","last_name":"Strahodinsky","first_name":"Florian"},{"first_name":"Hanna","full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","last_name":"Leitner"},{"first_name":"Harikrishnan","last_name":"Rajendran","full_name":"Rajendran, Harikrishnan","id":"876b6b34-8ff4-11ec-97c9-8d95a7aae416"},{"first_name":"Thomas","last_name":"Schmitt","full_name":"Schmitt, Thomas"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"quality_controlled":"1","title":"Altruistic disease signalling in ant colonies","publication":"Nature Communications","volume":16,"day":"01","acknowledgement":"We thank Joergen Eilenberg and Nicolai V. Meyling for the fungal strain, and the ISTA Social Immunity team, Jonghyun Park and Yuko Ulrich for ant collection. We also thank the Social Immunity team, in particular David Moreno Martínez, Tanvi Madaan, Wilfrid Jean Louis and Jessica Kirchner, for experimental and molecular support, as well as Friedrich Fochler for technical support with the chemical analysis, and the ISTA Lab Support Facility, including the mass spectrometry unit, for general and chemical laboratory support. We further thank Marco Ribezzi for advice on 13C calculations and Ernst Pittenauer for discussion of the chemical data, Chris Pull and Michael Sixt for project discussion, and the Social Immunity team for comments on the manuscript. The study was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation Programme (No. 771402; EPIDEMICSonCHIP) to SC.","PlanS_conform":"1","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","year":"2025","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"MassSpec"}],"intvolume":"        16","oa":1},{"department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}],"article_processing_charge":"No","has_accepted_license":"1","publication_status":"draft","fulldoi":"https://doi.org/10.1101/2025.05.20.655037","date_updated":"2026-10-24T22:32:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","oa_version":"Preprint","das_tickbox":"1","abstract":[{"lang":"eng","text":"While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo."}],"related_material":{"record":[{"id":"21439","status":"public","relation":"research_data"},{"status":"public","id":"22963","relation":"later_version"},{"status":"public","id":"21423","relation":"dissertation_contains"}]},"month":"09","doi":"10.1101/2025.05.20.655037","status":"public","project":[{"name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.20.655037"}],"citation":{"ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>.","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.).","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. .","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>"},"ddc":["539","570"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2025-09-25T00:00:00Z","oa":1,"corr_author":"1","OA_place":"repository","language":[{"iso":"eng"}],"year":"2025","acknowledgement":"European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360","day":"25","publication":"bioRxiv","author":[{"id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova","full_name":"Dunajova, Zuzana","first_name":"Zuzana"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","orcid":"0000-0003-1671-393X","first_name":"Saren"},{"full_name":"Majek, Juraj","last_name":"Majek","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","first_name":"Juraj"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","last_name":"Merrin"},{"last_name":"Sahai","full_name":"Sahai, Erik","first_name":"Erik"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","_id":"21427","date_created":"2026-03-11T08:40:06Z"},{"abstract":[{"lang":"eng","text":"Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues."}],"related_material":{"record":[{"id":"19763","status":"public","relation":"dissertation_contains"}]},"month":"02","external_id":{"pmid":["39603235"],"isi":["001434279000001"]},"type":"journal_article","das_tickbox":"1","oa_version":"Published Version","ddc":["570"],"citation":{"ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Cell Press, pp. 567–580, 2025.","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580.","ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>","ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.","chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Cell Press, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>.","apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2025-02-24T00:00:00Z","OA_type":"hybrid","isi":1,"doi":"10.1016/j.devcel.2024.10.024","dataavailabilitystatement":"RNA-seq data has been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. Code for the quantification of fluorescence intensity (FI) profiles in differentiated cells on stencils, as well as for model simulations, is available on GitHub (https://github.com/dbrueckner/NeuralTubeColonies, https://doi.org/10.5281/zenodo.13335390","status":"public","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"pmid":1,"department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_status":"published","issue":"4","date_updated":"2026-10-24T22:32:24Z","fulldoi":"https://doi.org/10.1016/j.devcel.2024.10.024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"yes","file":[{"content_type":"application/pdf","file_name":"2025_DevelopmentalCell_Lehr.pdf","date_updated":"2025-04-16T10:54:07Z","date_created":"2025-04-16T10:54:07Z","file_size":6994499,"file_id":"19584","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"checksum":"bb58db4a908a1f4aabe4004706154541"}],"scopus_import":"1","publication_identifier":{"issn":["1534-5807"]},"publisher":"Cell Press","article_type":"original","author":[{"orcid":"0000-0001-8703-1093","first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","full_name":"Rus, Stefanie"},{"orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner"},{"first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","last_name":"Minchington"},{"full_name":"Greunz, Martina","id":"48A59534-F248-11E8-B48F-1D18A9856A87","last_name":"Greunz","first_name":"Martina"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna"}],"title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","quality_controlled":"1","file_date_updated":"2025-04-16T10:54:07Z","page":"567-580","_id":"18807","date_created":"2025-01-09T11:25:47Z","supplementarymaterial":"yes","corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"year":"2025","intvolume":"        60","oa":1,"volume":60,"publication":"Developmental Cell","acknowledgement":"We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","day":"24"},{"file":[{"success":1,"checksum":"f7d3dded6df2dcdb4818904cf2e1c183","file_id":"17153","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2024-06-17T09:36:51Z","file_name":"2024_ASHPC_Schloegl.pdf","date_updated":"2024-06-17T09:36:51Z","file_size":206746}],"publisher":"EuroCC Austria","publication_identifier":{"isbn":["9783200096455"]},"author":[{"last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois"},{"first_name":"Waleed","full_name":"Khalid, Waleed","last_name":"Khalid","id":"097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1"},{"full_name":"Elefante, Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer"}],"quality_controlled":"1","title":"How much memory per CPU core is requested?","date_created":"2024-06-14T09:06:36Z","_id":"17139","page":"46","file_date_updated":"2024-06-17T09:36:51Z","language":[{"iso":"eng"}],"year":"2024","oa":1,"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Grundlsee, Austria","start_date":"2024-06-10","end_date":"2024-06-13"},"publication":"ASHPC24 - Austrian-Slovenian HPC Meeting 2024","day":"13","month":"06","type":"conference_abstract","oa_version":"Published Version","ddc":["000"],"citation":{"ama":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core is requested? In: <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>. EuroCC Austria; 2024:46. doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>","chicago":"Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer. “How Much Memory per CPU Core Is Requested?” In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, 46. EuroCC Austria, 2024. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>.","ista":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian HPC Meeting, 46.","short":"A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46.","ieee":"A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per CPU core is requested?,” in <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, Grundlsee, Austria, 2024, p. 46.","apa":"Schlögl, A., Khalid, W., Elefante, S., &#38; Stadlbauer, S. (2024). How much memory per CPU core is requested? In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i> (p. 46). Grundlsee, Austria: EuroCC Austria. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>","mla":"Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, EuroCC Austria, 2024, p. 46, doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-06-13T00:00:00Z","doi":"10.25365/phaidra.463","status":"public","department":[{"_id":"ScienComp"}],"has_accepted_license":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.25365/phaidra.463","date_updated":"2024-06-17T09:40:37Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"27","acknowledgement":"We would like to thank the members of the Sweeney Lab (especially Stavros Papadopoulos and\r\nSophie Gobeil) for their contributions to this project and, in addition to the lab, Graziana Gatto\r\nand Mario de Bono, for discussion, and support. We are also grateful to Tom Jessell and Chris\r\nKintner for their scientific insight and mentorship during the conception of this project. This\r\nproject would also not have been possible with the technical support of the Matthias Nowak,\r\nVerena Mayer and the Aquatics as well as the Imaging and Optics Facility support teams\r\n(ISTA). In addition, we thank our funding sources for providing the resources to do these\r\nexperiments: FTI Strategy Lower Austria Dissertation Grant Number FT121-D-046 (D.V.);\r\nHorizon Europe ERC Starting Grant Number 101041551 (L.B.S., F.A.T. and D.V); Special\r\nResearch Program (SFB) of the Austrian Science Fund (FWF) Project number F7814-B (L.B.S);\r\nNINDS 5R35NS116858 (J.S.D); CZI grant DAF2020-225401 (DOI): 10.37921/120055ratwvi\r\n(R.H.); NIH grant number R01NS123116 (J.B.B); American Lebanese Syrian Associated\r\nCharities (ALSAC) (J.B.B.); German Academic Exchange Service (DAAD) IFI Grant Number\r\n57515251-91853472 (Z.H.); and Project A.L.S. (S.B-M.). ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1101/2024.09.20.614050","date_updated":"2025-05-14T11:40:13Z","publication":"bioRxiv","publication_status":"submitted","oa":1,"article_processing_charge":"No","department":[{"_id":"LoSw"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"acknowledged_ssus":[{"_id":"Bio"}],"year":"2024","language":[{"iso":"eng"}],"corr_author":"1","OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.09.20.614050"}],"project":[{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","grant_number":"FTI21-D-046"},{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits"},{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01","name":"Tools for automation and feedback microscopy"}],"status":"public","doi":"10.1101/2024.09.20.614050","OA_type":"green","date_published":"2024-09-27T00:00:00Z","date_created":"2025-04-07T08:48:28Z","_id":"19520","citation":{"apa":"Vijatovic, D., Toma, F. A., Harrington, Z. P., Sommer, C. M., Hauschild, R., Trevisan, A. J., … Sweeney, L. B. (n.d.). Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.09.20.614050\">https://doi.org/10.1101/2024.09.20.614050</a>","mla":"Vijatovic, David, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>.","short":"D. Vijatovic, F.A. Toma, Z.P. Harrington, C.M. Sommer, R. Hauschild, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, BioRxiv (n.d.).","ieee":"D. Vijatovic <i>et al.</i>, “Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis,” <i>bioRxiv</i>. .","ista":"Vijatovic D, Toma FA, Harrington ZP, Sommer CM, Hauschild R, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv, <a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>.","chicago":"Vijatovic, David, Florina Alexandra  Toma, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Alexandra J. Trevisan, Phillip Chapman, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.09.20.614050\">https://doi.org/10.1101/2024.09.20.614050</a>.","ama":"Vijatovic D, Toma FA, Harrington ZP, et al. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>"},"oa_version":"Preprint","title":"Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis","author":[{"full_name":"Vijatovic, David","id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","first_name":"David"},{"full_name":"Toma, Florina Alexandra ","id":"2f73f876-f128-11eb-9611-b96b5a30cb0e","last_name":"Toma","first_name":"Florina Alexandra "},{"first_name":"Zoe P","orcid":"0009-0008-0158-4032","full_name":"Harrington, Zoe P","last_name":"Harrington","id":"a8144562-32c9-11ee-b5ce-d9800628bda2"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"last_name":"Trevisan","full_name":"Trevisan, Alexandra J.","first_name":"Alexandra J."},{"first_name":"Phillip","full_name":"Chapman, Phillip","last_name":"Chapman"},{"full_name":"Julseth, Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","last_name":"Julseth","first_name":"Mara"},{"first_name":"Susan","last_name":"Brenner-Morton","full_name":"Brenner-Morton, Susan"},{"first_name":"Mariano I.","last_name":"Gabitto","full_name":"Gabitto, Mariano I."},{"first_name":"Jeremy S.","last_name":"Dasen","full_name":"Dasen, Jeremy S."},{"first_name":"Jay B.","full_name":"Bikoff, Jay B.","last_name":"Bikoff"},{"orcid":"0000-0001-9242-5601","first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"type":"preprint","month":"09","abstract":[{"text":"Vertebrates exhibit a wide range of motor behaviors, ranging from swimming to complex limb-based movements. Here we take advantage of frog metamorphosis, which captures a swim-to-limb-based movement transformation during the development of a single organism, to explore changes in the underlying spinal circuits. We find that the tadpole spinal cord contains small and largely homogeneous populations of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages. These neuronal populations only modestly increase in number and subtype heterogeneity with the emergence of free swimming. In contrast, during frog metamorphosis and the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron number and transcriptional heterogeneity, culminating in cohorts of neurons that exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively, results in severe but selective deficits in tail and limb function. Our work thus demonstrates that neural diversity scales exponentially with increasing behavioral complexity and illustrates striking evolutionary conservation in the molecular organization and function of motor circuits across species.","lang":"eng"}]},{"scopus_import":"1","file":[{"file_size":3057631,"content_type":"application/pdf","date_updated":"2024-12-03T08:56:53Z","date_created":"2024-12-03T08:56:53Z","file_name":"2024_PloSBio_Kim.pdf","relation":"main_file","creator":"dernst","file_id":"18608","access_level":"open_access","success":1,"checksum":"7de2dcb50deb65dde05c80082bb85a82"}],"publisher":"Public Library of Science","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"DOAJ_listed":"1","article_type":"original","author":[{"orcid":"0000-0003-2344-1039","first_name":"Olena","last_name":"Kim","full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuji","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji","last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315"},{"first_name":"Nils","last_name":"Brose","full_name":"Brose, Nils"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M"}],"quality_controlled":"1","title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","_id":"18603","date_created":"2024-12-01T23:01:54Z","file_date_updated":"2024-12-03T08:56:53Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"year":"2024","intvolume":"        22","oa":1,"volume":22,"publication":"PLoS Biology","day":"18","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.","related_material":{"record":[{"relation":"research_data","id":"18296","status":"public"}]},"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"}],"month":"11","type":"journal_article","external_id":{"pmid":["39556620"],"isi":["001358568700003"]},"oa_version":"Published Version","ddc":["570"],"citation":{"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>","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>.","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.","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>.","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.","short":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, P.M. Jonas, PLoS Biology 22 (2024)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-11-18T00:00:00Z","isi":1,"doi":"10.1371/journal.pbio.3002879","OA_type":"gold","status":"public","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"_id":"b1b85715-d554-11ed-a5ad-84a07fc9f18e","name":"Structural & functional basis of presynaptic plasticity","grant_number":"I06166"},{"grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"article_number":"e3002879","pmid":1,"APC_amount":"6248,82 EUR","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"has_accepted_license":"1","article_processing_charge":"Yes","date_updated":"2026-04-16T12:20:34Z","fulldoi":"https://doi.org/10.1371/journal.pbio.3002879","publication_status":"published","issue":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1},{"day":"11","contributor":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","contributor_type":"researcher","first_name":"Olena"},{"orcid":"0000-0003-0408-6094","contributor_type":"researcher","first_name":"Yuji","last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","contributor_type":"researcher","first_name":"Walter","orcid":"0000-0001-9735-5315"},{"last_name":"Brose","contributor_type":"researcher","first_name":"Nils "},{"first_name":"Ryuichi","contributor_type":"researcher","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","contributor_type":"supervisor","orcid":"0000-0001-5001-4804"}],"oa":1,"year":"2024","corr_author":"1","file_date_updated":"2024-10-11T10:04:23Z","_id":"18296","date_created":"2024-10-11T10:12:17Z","title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","author":[{"full_name":"Kim, Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","orcid":"0000-0003-2344-1039"}],"publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/zip","date_created":"2024-10-11T10:04:19Z","file_name":"Kim_et_al_2024_PlosBio_Source_data.zip","date_updated":"2024-10-11T10:04:19Z","file_size":164382,"file_id":"18297","access_level":"open_access","relation":"main_file","creator":"okim","success":1,"checksum":"0a977e7df54c418251b10dfd3f8a015c"},{"checksum":"5b9343d6b2035ac3185e390fad4d3830","success":1,"access_level":"open_access","file_id":"18298","creator":"okim","relation":"main_file","date_created":"2024-10-11T10:04:23Z","date_updated":"2024-10-11T10:04:23Z","file_name":"info.txt","content_type":"text/plain","file_size":654}],"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"],"ec_funded":1,"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_updated":"2026-09-14T08:48:01Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:18296","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"PeJo"},{"_id":"RySh"},{"_id":"EM-Fac"}],"status":"public","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:18296","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-10-11T00:00:00Z","citation":{"short":"O. Kim, (2024).","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.","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>.","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>","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>.","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>.","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>"},"ddc":["570"],"oa_version":"Submitted Version","type":"research_data","month":"10","related_material":{"record":[{"id":"18603","status":"public","relation":"used_in_publication"}]},"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"}]},{"publication_status":"published","date_updated":"2026-09-17T10:29:32Z","fulldoi":"https://doi.org/10.1038/s41684-024-01476-2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","researchdata_availability":"no","pmid":1,"department":[{"_id":"PreCl"}],"article_processing_charge":"No","has_accepted_license":"1","citation":{"ista":"Lauwereyns J, Bajramovic J, Bert B, Camenzind S, De Kock J, Elezović A, Erden S, Gonzalez-Uarquin F, Ulman YI, Hoffmann OI, Kitsara M, Kostomitsopoulos N, Neuhaus W, Petit-Demouliere B, Pollo S, Riso B, Schober S, Sotiropoulos A, Thomas A, Vitale A, Wilflingseder D, Ahluwalia A. 2024. Toward a common interpretation of the 3Rs principles in animal research. Lab Animal. 53, 347–350.","ama":"Lauwereyns J, Bajramovic J, Bert B, et al. Toward a common interpretation of the 3Rs principles in animal research. <i>Lab Animal</i>. 2024;53:347-350. doi:<a href=\"https://doi.org/10.1038/s41684-024-01476-2\">10.1038/s41684-024-01476-2</a>","chicago":"Lauwereyns, Jan, Jeffrey Bajramovic, Bettina Bert, Samuel Camenzind, Joery De Kock, Alisa Elezović, Sevilay Erden, et al. “Toward a Common Interpretation of the 3Rs Principles in Animal Research.” <i>Lab Animal</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41684-024-01476-2\">https://doi.org/10.1038/s41684-024-01476-2</a>.","short":"J. Lauwereyns, J. Bajramovic, B. Bert, S. Camenzind, J. De Kock, A. Elezović, S. Erden, F. Gonzalez-Uarquin, Y.I. Ulman, O.I. Hoffmann, M. Kitsara, N. Kostomitsopoulos, W. Neuhaus, B. Petit-Demouliere, S. Pollo, B. Riso, S. Schober, A. Sotiropoulos, A. Thomas, A. Vitale, D. Wilflingseder, A. Ahluwalia, Lab Animal 53 (2024) 347–350.","ieee":"J. Lauwereyns <i>et al.</i>, “Toward a common interpretation of the 3Rs principles in animal research,” <i>Lab Animal</i>, vol. 53. Springer Nature, pp. 347–350, 2024.","mla":"Lauwereyns, Jan, et al. “Toward a Common Interpretation of the 3Rs Principles in Animal Research.” <i>Lab Animal</i>, vol. 53, Springer Nature, 2024, pp. 347–50, doi:<a href=\"https://doi.org/10.1038/s41684-024-01476-2\">10.1038/s41684-024-01476-2</a>.","apa":"Lauwereyns, J., Bajramovic, J., Bert, B., Camenzind, S., De Kock, J., Elezović, A., … Ahluwalia, A. (2024). Toward a common interpretation of the 3Rs principles in animal research. <i>Lab Animal</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41684-024-01476-2\">https://doi.org/10.1038/s41684-024-01476-2</a>"},"ddc":["570"],"date_published":"2024-12-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"OA_type":"hybrid","isi":1,"doi":"10.1038/s41684-024-01476-2","status":"public","abstract":[{"lang":"eng","text":"Many scientific breakthroughs have depended on animal research, yet the ethical concerns surrounding the use of animals in experimentation have long prompted discussions about humane treatment and responsible scientific practice. First articulated by Russell and Burch, the 3Rs Principles of Replacement, Reduction, and Refinement have gained widespread recognition as basic guidelines for animal research. Over time, the 3Rs have transcended the research community, influencing policy decisions, animal welfare advocacy and public perception of animal experimentation. Despite their broad acceptance, interpretations of the 3Rs vary substantially, shaping statutory frameworks at various levels, with both technical and practical impacts."}],"month":"12","external_id":{"isi":["001355264100001"],"pmid":["39548348"]},"type":"journal_article","oa_version":"Published Version","das_tickbox":"0","volume":53,"publication":"Lab Animal","acknowledgement":"This publication is based upon work from the Ethics Crossover Group within the COST Action IMPROVE (“3Rs concepts to improve the quality of biomedical science”), CA21139, supported by COST (European Cooperation in Science and Technology). We acknowledge the input and advice from Dr. Susanna Louhimies.","day":"01","OA_place":"publisher","language":[{"iso":"eng"}],"year":"2024","intvolume":"        53","oa":1,"file_date_updated":"2024-12-03T14:07:04Z","date_created":"2024-11-24T23:01:49Z","_id":"18587","page":"347-350","supplementarymaterial":"no","file":[{"file_size":967252,"date_updated":"2024-12-03T14:07:04Z","file_name":"2024_LabAnimal_Lauwereyns.pdf","date_created":"2024-12-03T14:07:04Z","content_type":"application/pdf","checksum":"67fc140f761581a291591f075e49b88d","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"18614"}],"scopus_import":"1","publication_identifier":{"eissn":["1548-4475"],"issn":["0093-7355"]},"publisher":"Springer Nature","author":[{"full_name":"Lauwereyns, Jan","last_name":"Lauwereyns","first_name":"Jan"},{"first_name":"Jeffrey","last_name":"Bajramovic","full_name":"Bajramovic, Jeffrey"},{"last_name":"Bert","full_name":"Bert, Bettina","first_name":"Bettina"},{"first_name":"Samuel","last_name":"Camenzind","full_name":"Camenzind, Samuel"},{"full_name":"De Kock, Joery","last_name":"De Kock","first_name":"Joery"},{"first_name":"Alisa","full_name":"Elezović, Alisa","last_name":"Elezović"},{"full_name":"Erden, Sevilay","last_name":"Erden","first_name":"Sevilay"},{"first_name":"Fernando","full_name":"Gonzalez-Uarquin, Fernando","last_name":"Gonzalez-Uarquin"},{"last_name":"Ulman","full_name":"Ulman, Yesim Isil","first_name":"Yesim Isil"},{"last_name":"Hoffmann","full_name":"Hoffmann, Orsolya Ivett","first_name":"Orsolya Ivett"},{"last_name":"Kitsara","full_name":"Kitsara, Maria","first_name":"Maria"},{"last_name":"Kostomitsopoulos","full_name":"Kostomitsopoulos, Nikolaos","first_name":"Nikolaos"},{"first_name":"Winfried","full_name":"Neuhaus, Winfried","last_name":"Neuhaus"},{"last_name":"Petit-Demouliere","full_name":"Petit-Demouliere, Benoit","first_name":"Benoit"},{"last_name":"Pollo","full_name":"Pollo, Simone","first_name":"Simone"},{"full_name":"Riso, Brígida","last_name":"Riso","first_name":"Brígida"},{"full_name":"Schober, Sophie","last_name":"Schober","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie"},{"last_name":"Sotiropoulos","full_name":"Sotiropoulos, Athanassia","first_name":"Athanassia"},{"full_name":"Thomas, Aurélie","last_name":"Thomas","first_name":"Aurélie"},{"full_name":"Vitale, Augusto","last_name":"Vitale","first_name":"Augusto"},{"first_name":"Doris","full_name":"Wilflingseder, Doris","last_name":"Wilflingseder"},{"first_name":"Arti","full_name":"Ahluwalia, Arti","last_name":"Ahluwalia"}],"article_type":"letter_note","title":"Toward a common interpretation of the 3Rs principles in animal research","quality_controlled":"1"},{"scopus_import":"1","publication_identifier":{"issn":["0261-1929"],"eissn":["2632-3559"]},"publisher":"SAGE Publications","author":[{"first_name":"Maria","full_name":"Kitsara, Maria","last_name":"Kitsara"},{"full_name":"Smajlhodžić-Deljo, Merima","last_name":"Smajlhodžić-Deljo","first_name":"Merima"},{"last_name":"Gurbeta Pokvic","full_name":"Gurbeta Pokvic, Lejla","first_name":"Lejla"},{"first_name":"Bettina","last_name":"Bert","full_name":"Bert, Bettina"},{"first_name":"Nataliia","last_name":"Bubalo","full_name":"Bubalo, Nataliia"},{"first_name":"Sevilay","last_name":"Erden","full_name":"Erden, Sevilay"},{"last_name":"Franco","full_name":"Franco, Nuno Henrique","first_name":"Nuno Henrique"},{"full_name":"Chirico, Giuseppe","last_name":"Chirico","first_name":"Giuseppe"},{"first_name":"Jonathan","last_name":"Gómez Raja","full_name":"Gómez Raja, Jonathan"},{"last_name":"Gonzalez-Uarquin","full_name":"Gonzalez-Uarquin, Fernando","first_name":"Fernando"},{"first_name":"Annemarie","full_name":"Lang, Annemarie","last_name":"Lang"},{"first_name":"Nicole","full_name":"Linklater, Nicole","last_name":"Linklater"},{"first_name":"Sandra","last_name":"Mojsova","full_name":"Mojsova, Sandra"},{"last_name":"Olsson","full_name":"Olsson, I. Anna S.","first_name":"I. Anna S."},{"first_name":"Ioanna","last_name":"Sandvig","full_name":"Sandvig, Ioanna"},{"first_name":"Alexandra","full_name":"Schaffert, Alexandra","last_name":"Schaffert"},{"last_name":"Schmit","full_name":"Schmit, Marthe","first_name":"Marthe"},{"full_name":"Schober, Sophie","last_name":"Schober","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie"},{"first_name":"Bogdan","last_name":"Sevastre","full_name":"Sevastre, Bogdan"},{"last_name":"Wilflingseder","full_name":"Wilflingseder, Doris","first_name":"Doris"},{"first_name":"Arti","last_name":"Ahluwalia","full_name":"Ahluwalia, Arti"},{"first_name":"Winfried","last_name":"Neuhaus","full_name":"Neuhaus, Winfried"}],"article_type":"original","title":"Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE)","quality_controlled":"1","_id":"18310","date_created":"2024-10-13T22:01:51Z","page":"326-333","supplementarymaterial":"no","language":[{"iso":"eng"}],"year":"2024","intvolume":"        52","volume":52,"publication":"Alternatives to Laboratory Animals","day":"01","month":"11","external_id":{"pmid":["39333027"],"isi":["001348633700007"]},"type":"journal_article","oa_version":"None","das_tickbox":"0","citation":{"ama":"Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, et al. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). <i>Alternatives to Laboratory Animals</i>. 2024;52(6):326-333. doi:<a href=\"https://doi.org/10.1177/02611929241286024\">10.1177/02611929241286024</a>","chicago":"Kitsara, Maria, Merima Smajlhodžić-Deljo, Lejla Gurbeta Pokvic, Bettina Bert, Nataliia Bubalo, Sevilay Erden, Nuno Henrique Franco, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” <i>Alternatives to Laboratory Animals</i>. SAGE Publications, 2024. <a href=\"https://doi.org/10.1177/02611929241286024\">https://doi.org/10.1177/02611929241286024</a>.","ista":"Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, Bert B, Bubalo N, Erden S, Franco NH, Chirico G, Gómez Raja J, Gonzalez-Uarquin F, Lang A, Linklater N, Mojsova S, Olsson IAS, Sandvig I, Schaffert A, Schmit M, Schober S, Sevastre B, Wilflingseder D, Ahluwalia A, Neuhaus W. 2024. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory Animals. 52(6), 326–333.","ieee":"M. Kitsara <i>et al.</i>, “Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE),” <i>Alternatives to Laboratory Animals</i>, vol. 52, no. 6. SAGE Publications, pp. 326–333, 2024.","short":"M. Kitsara, M. Smajlhodžić-Deljo, L. Gurbeta Pokvic, B. Bert, N. Bubalo, S. Erden, N.H. Franco, G. Chirico, J. Gómez Raja, F. Gonzalez-Uarquin, A. Lang, N. Linklater, S. Mojsova, I.A.S. Olsson, I. Sandvig, A. Schaffert, M. Schmit, S. Schober, B. Sevastre, D. Wilflingseder, A. Ahluwalia, W. Neuhaus, Alternatives to Laboratory Animals 52 (2024) 326–333.","apa":"Kitsara, M., Smajlhodžić-Deljo, M., Gurbeta Pokvic, L., Bert, B., Bubalo, N., Erden, S., … Neuhaus, W. (2024). Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). <i>Alternatives to Laboratory Animals</i>. SAGE Publications. <a href=\"https://doi.org/10.1177/02611929241286024\">https://doi.org/10.1177/02611929241286024</a>","mla":"Kitsara, Maria, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” <i>Alternatives to Laboratory Animals</i>, vol. 52, no. 6, SAGE Publications, 2024, pp. 326–33, doi:<a href=\"https://doi.org/10.1177/02611929241286024\">10.1177/02611929241286024</a>."},"date_published":"2024-11-01T00:00:00Z","OA_type":"closed access","doi":"10.1177/02611929241286024","isi":1,"status":"public","pmid":1,"department":[{"_id":"PreCl"}],"article_processing_charge":"No","issue":"6","publication_status":"published","date_updated":"2026-09-17T10:30:08Z","fulldoi":"https://doi.org/10.1177/02611929241286024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","researchdata_availability":"no"},{"quality_controlled":"1","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","author":[{"first_name":"Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia"},{"first_name":"Rushikesh","last_name":"Shinde","full_name":"Shinde, Rushikesh"},{"full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","orcid":"0000-0002-8176-4824","first_name":"Madison"},{"orcid":"0000-0002-3415-4628","first_name":"Matilda","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Szep, Gregory","last_name":"Szep","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","first_name":"Gregory"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","full_name":"Steccari, Irene","first_name":"Irene"},{"first_name":"David","full_name":"Labrousse Arias, David","last_name":"Labrousse Arias","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425"},{"full_name":"Zheden, Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","first_name":"Vanessa"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew","first_name":"Andrew"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"article_type":"original","publisher":"Springer Nature","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"scopus_import":"1","file":[{"success":1,"checksum":"7891ebe7c900ae47469ab127031dd1ec","file_id":"17267","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_name":"2024_NaturePhysics_CaballeroMancebo.pdf","date_updated":"2024-07-16T12:12:43Z","date_created":"2024-07-16T12:12:43Z","file_size":9897883}],"supplementarymaterial":"yes","page":"310-321","_id":"14846","date_created":"2024-01-21T23:00:57Z","file_date_updated":"2024-07-16T12:12:43Z","oa":1,"intvolume":"        20","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"year":"2024","language":[{"iso":"eng"}],"corr_author":"1","day":"01","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).","publication":"Nature Physics","volume":20,"das_tickbox":"1","oa_version":"Published Version","type":"journal_article","external_id":{"isi":["001138880800005"],"pmid":["38370025"]},"month":"02","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/","description":"News on ISTA Website"}]},"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."}],"status":"public","project":[{"grant_number":"I03601","name":"Control of embryonic cleavage pattern","_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"isi":1,"dataavailabilitystatement":"Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding author on request","doi":"10.1038/s41567-023-02302-1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-02-01T00:00:00Z","ddc":["530"],"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>.","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>","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.","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>","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>.","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."},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"pmid":1,"researchdata_availability":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-01T08:33:51Z","fulldoi":"https://doi.org/10.1038/s41567-023-02302-1","publication_status":"published"},{"fulldoi":"https://doi.org/10.1016/j.cub.2023.11.067","date_updated":"2026-10-01T08:33:05Z","issue":"1","publication_status":"published","researchdata_availability":"upon request","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","pmid":1,"doi":"10.1016/j.cub.2023.11.067","dataavailabilitystatement":"All original microscopy data any additional information reported in this paper is available from the lead contact upon request. All original code is available from the lead contact upon request","isi":1,"status":"public","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ddc":["570"],"citation":{"mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>.","apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., &#38; Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","ieee":"F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” <i>Current Biology</i>, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.","ista":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8.","ama":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. 2024;34(1):171-182.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>","chicago":"Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-01-08T00:00:00Z","type":"journal_article","external_id":{"pmid":["38134934"],"isi":["001154500400001"]},"das_tickbox":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells."}],"month":"01","day":"08","acknowledgement":"We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H.","volume":34,"publication":"Current Biology","intvolume":"        34","oa":1,"language":[{"iso":"eng"}],"corr_author":"1","year":"2024","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"supplementarymaterial":"yes","page":"171-182.e8","_id":"14795","date_created":"2024-01-14T23:00:56Z","file_date_updated":"2024-01-16T10:53:31Z","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","first_name":"Feyza N"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_type":"original","quality_controlled":"1","title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","scopus_import":"1","file":[{"success":1,"checksum":"51220b76d72a614208f84bdbfbaf9b72","file_id":"14813","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2024_CurrentBiology_Arslan.pdf","date_updated":"2024-01-16T10:53:31Z","date_created":"2024-01-16T10:53:31Z","file_size":5183861}],"publisher":"Elsevier","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]}},{"supplementarymaterial":"yes","_id":"15048","date_created":"2024-03-03T23:00:50Z","page":"1-18","file_date_updated":"2024-03-04T07:24:43Z","article_type":"original","author":[{"first_name":"Alexandra","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer"},{"first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha"},{"first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"quality_controlled":"1","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","scopus_import":"1","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","success":1,"file_size":14839986,"file_name":"2024_Development_Schauer.pdf","date_created":"2024-03-04T07:24:43Z","date_updated":"2024-03-04T07:24:43Z","content_type":"application/pdf"}],"publisher":"Company of Biologists","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"day":"01","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","volume":151,"publication":"Development","intvolume":"       151","oa":1,"language":[{"iso":"eng"}],"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2024","doi":"10.1242/dev.202316","dataavailabilitystatement":"A custom MATLAB script for analyzing cell dispersal has been deposited in the ISTA library (doi:10.15479/AT:ISTA:14926)","isi":1,"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"status":"public","citation":{"mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. Company of Biologists, pp. 1–18, 2024.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18."},"ddc":["570"],"date_published":"2024-02-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"type":"journal_article","external_id":{"isi":["001170580200001"],"pmid":["38372390"]},"oa_version":"Published Version","das_tickbox":"1","related_material":{"record":[{"status":"public","id":"14926","relation":"research_data"}]},"abstract":[{"text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.","lang":"eng"}],"month":"02","date_updated":"2026-10-01T08:32:34Z","fulldoi":"https://doi.org/10.1242/dev.202316","issue":"4","publication_status":"published","researchdata_availability":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"CaHe"},{"_id":"Bio"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","pmid":1},{"license":"https://opensource.org/licenses/MIT","year":"2024","corr_author":"1","has_accepted_license":"1","oa":1,"department":[{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-01T08:32:33Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:14926","day":"02","month":"02","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"15048","relation":"used_in_publication"}]},"file":[{"creator":"rhauschild","relation":"main_file","file_id":"14927","access_level":"open_access","success":1,"checksum":"df7f358ae19a176cf710c0a802ce31b1","file_size":736,"content_type":"application/octet-stream","file_name":"README.md","date_updated":"2024-02-02T14:40:31Z","date_created":"2024-02-02T14:40:31Z"},{"file_size":3543,"content_type":"application/x-zip-compressed","date_created":"2024-02-02T14:40:31Z","date_updated":"2024-02-02T14:40:31Z","file_name":"Supplementary_file_1.zip","success":1,"checksum":"10194cc11619eccd8f4b24472e465b7f","relation":"main_file","creator":"rhauschild","file_id":"14928","access_level":"open_access"}],"title":"Matlab script for analysis of clone dispersal","author":[{"first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"}],"type":"software","date_published":"2024-02-02T00:00:00Z","tmp":{"short":"MIT","legal_code_url":"https://opensource.org/licenses/MIT","name":"The MIT License"},"_id":"14926","date_created":"2024-02-02T14:42:26Z","file_date_updated":"2024-02-02T14:40:31Z","ddc":["570"],"citation":{"ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>.","short":"R. Hauschild, (2024).","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of Science and Technology Austria, 2024.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>","mla":"Hauschild, Robert. <i>Matlab Script for Analysis of Clone Dispersal</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>."},"status":"public","doi":"10.15479/AT:ISTA:14926"},{"oa":1,"intvolume":"        15","acknowledged_ssus":[{"_id":"EM-Fac"}],"year":"2024","OA_place":"publisher","language":[{"iso":"eng"}],"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.","day":"29","volume":15,"publication":"Nature Communications","title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","quality_controlled":"1","author":[{"last_name":"Kofler","full_name":"Kofler, Lisa","first_name":"Lisa"},{"full_name":"Grundmann, Lorenz","last_name":"Grundmann","first_name":"Lorenz"},{"last_name":"Gerhalter","full_name":"Gerhalter, Magdalena","first_name":"Magdalena"},{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"first_name":"Juliane","full_name":"Merl-Pham, Juliane","last_name":"Merl-Pham"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin"},{"last_name":"Vareka","full_name":"Vareka, Martin","first_name":"Martin"},{"last_name":"Breinbauer","full_name":"Breinbauer, Rolf","first_name":"Rolf"},{"first_name":"Stefanie M.","full_name":"Hauck, Stefanie M.","last_name":"Hauck"},{"first_name":"David","last_name":"Haselbach","full_name":"Haselbach, David"},{"full_name":"Bergler, Helmut","last_name":"Bergler","first_name":"Helmut"}],"DOAJ_listed":"1","article_type":"original","publication_identifier":{"eissn":["2041-1723"]},"publisher":"Springer Nature","file":[{"checksum":"7c044538a47182c826d1b526c52958a2","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"17946","file_size":3735024,"date_updated":"2024-09-09T08:56:12Z","file_name":"2024_NatureComm_Kofler.pdf","date_created":"2024-09-09T08:56:12Z","content_type":"application/pdf"}],"scopus_import":"1","supplementarymaterial":"yes","file_date_updated":"2024-09-09T08:56:12Z","date_created":"2024-09-08T22:01:10Z","_id":"17885","article_processing_charge":"Yes","has_accepted_license":"1","department":[{"_id":"EM-Fac"}],"pmid":1,"article_number":"7511","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","researchdata_availability":"yes","publication_status":"published","date_updated":"2026-10-01T11:05:46Z","fulldoi":"https://doi.org/10.1038/s41467-024-51754-3","das_tickbox":"1","oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["39209816"],"isi":["001457895200001"]},"month":"08","abstract":[{"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.","lang":"eng"}],"status":"public","isi":1,"OA_type":"gold","doi":"10.1038/s41467-024-51754-3","dataavailabilitystatement":"Strains generated in this study are available from the corresponding authors upon request. For cryo-EM model building, published pre-60S models PDB-6EM3, PDB-6EM4, PDB-6C0F, PDB-6EM1 and PDB-8V87 were used. Motion-corrected micrographs with annotated particle locations were deposited in EMPIAR with the accession number EMPIAR-12237. The cryo-EM maps of clusters 1 to 4 with the combined datasets were deposited in the EMDB with the accession numbers EMD-51122, EMD-51126, EMD-51128, and EMD-51129. The reconstructions for the treated dataset were deposited with the accession numbers EMD-51175, EMD-51176, EMD-51177, and EMD-51178, while the untreated reconstructions of reported clusters can be found via EMD-51164, EMD-51165, EMD-51166, EMD-51167. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE101 partner repository with the dataset identifier PXD046691. Source data are provided with this paper.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-08-29T00:00:00Z","ddc":["570"],"citation":{"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>.","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>","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>","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>.","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.","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).","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."}},{"oa":1,"intvolume":"       631","year":"2024","corr_author":"1","language":[{"iso":"eng"}],"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.","day":"18","volume":631,"publication":"Nature","title":"Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis","quality_controlled":"1","article_type":"original","author":[{"orcid":"0000-0001-6120-3723","first_name":"Florian R","last_name":"Gärtner","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hellen","full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold"},{"last_name":"Stutte","full_name":"Stutte, Susanne","first_name":"Susanne"},{"last_name":"Fu","full_name":"Fu, Wenwen","first_name":"Wenwen"},{"full_name":"Weitz, Jutta","last_name":"Weitz","first_name":"Jutta"},{"full_name":"Dueck, Anne","last_name":"Dueck","first_name":"Anne"},{"first_name":"Bhavishya","full_name":"Nelakuditi, Bhavishya","last_name":"Nelakuditi"},{"full_name":"Fumagalli, Valeria","last_name":"Fumagalli","first_name":"Valeria"},{"last_name":"Van Den Heuvel","full_name":"Van Den Heuvel, Dominic","first_name":"Dominic"},{"first_name":"Larissa","last_name":"Belz","full_name":"Belz, Larissa"},{"first_name":"Gulnoza","full_name":"Sobirova, Gulnoza","last_name":"Sobirova"},{"first_name":"Zhe","last_name":"Zhang","full_name":"Zhang, Zhe"},{"full_name":"Titova, Anna","last_name":"Titova","first_name":"Anna"},{"last_name":"Navarro","full_name":"Navarro, Alejandro Martinez","first_name":"Alejandro Martinez"},{"last_name":"Pekayvaz","full_name":"Pekayvaz, Kami","first_name":"Kami"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"first_name":"Louisa","last_name":"Von Baumgarten","full_name":"Von Baumgarten, Louisa"},{"last_name":"Kranich","full_name":"Kranich, Jan","first_name":"Jan"},{"full_name":"Straub, Tobias","last_name":"Straub","first_name":"Tobias"},{"first_name":"Bastian","last_name":"Popper","full_name":"Popper, Bastian"},{"last_name":"Zheden","full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","first_name":"Vanessa"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Chenglong","last_name":"Guo","full_name":"Guo, Chenglong"},{"first_name":"Guido","last_name":"Piontek","full_name":"Piontek, Guido"},{"full_name":"Von Stillfried, Saskia","last_name":"Von Stillfried","first_name":"Saskia"},{"full_name":"Boor, Peter","last_name":"Boor","first_name":"Peter"},{"full_name":"Colonna, Marco","last_name":"Colonna","first_name":"Marco"},{"last_name":"Clauß","full_name":"Clauß, Sebastian","first_name":"Sebastian"},{"first_name":"Christian","last_name":"Schulz","full_name":"Schulz, Christian"},{"first_name":"Thomas","full_name":"Brocker, Thomas","last_name":"Brocker"},{"first_name":"Barbara","full_name":"Walzog, Barbara","last_name":"Walzog"},{"first_name":"Christoph","last_name":"Scheiermann","full_name":"Scheiermann, Christoph"},{"full_name":"Aird, William C.","last_name":"Aird","first_name":"William C."},{"last_name":"Nerlov","full_name":"Nerlov, Claus","first_name":"Claus"},{"first_name":"Konstantin","last_name":"Stark","full_name":"Stark, Konstantin"},{"last_name":"Petzold","full_name":"Petzold, Tobias","first_name":"Tobias"},{"first_name":"Stefan","last_name":"Engelhardt","full_name":"Engelhardt, Stefan"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Rudelius, Martina","last_name":"Rudelius","first_name":"Martina"},{"full_name":"Oostendorp, Robert A.J.","last_name":"Oostendorp","first_name":"Robert A.J."},{"first_name":"Matteo","full_name":"Iannacone, Matteo","last_name":"Iannacone"},{"full_name":"Heinig, Matthias","last_name":"Heinig","first_name":"Matthias"},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publisher":"Springer Nature","file":[{"content_type":"application/pdf","date_updated":"2024-07-22T06:16:11Z","file_name":"2024_Nature_Gaertner.pdf","date_created":"2024-07-22T06:16:11Z","file_size":15704819,"file_id":"17286","access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"checksum":"aa004afc72d2489f0fb0fcbc9919fbbd"}],"scopus_import":"1","supplementarymaterial":"yes","file_date_updated":"2024-07-22T06:16:11Z","date_created":"2024-07-21T22:01:02Z","_id":"17284","page":"645-653","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"researchdata_availability":"upon request","publication_status":"published","fulldoi":"https://doi.org/10.1038/s41586-024-07671-y","date_updated":"2026-10-01T11:17:11Z","das_tickbox":"1","oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["38987596"],"isi":["001281636500020"]},"month":"07","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"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/heiniglab/gaertner_megakaryocytes"}]},"project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"status":"public","dataavailabilitystatement":"Imaging and flow cytometry raw data are available on request. scRNA-seq data are accessible at the GEO (GSE261996). Bulk RNA-seq data are accessible at the GEO (GSE185488). Source data are provided with this paper.","doi":"10.1038/s41586-024-07671-y","isi":1,"date_published":"2024-07-18T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["570"],"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.","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.","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>","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>.","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.","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>","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>."}},{"quality_controlled":"1","title":"Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","DOAJ_listed":"1","article_type":"original","author":[{"last_name":"Homola","full_name":"Homola, Miroslav","first_name":"Miroslav"},{"full_name":"Büttner, Renate Carina","last_name":"Büttner","id":"3b7984c9-17ff-11ed-b6fe-f943c4a5b626","first_name":"Renate Carina"},{"first_name":"Tibor","full_name":"Füzik, Tibor","last_name":"Füzik"},{"first_name":"Pavel","last_name":"Křepelka","full_name":"Křepelka, Pavel"},{"full_name":"Holbová, Radka","last_name":"Holbová","first_name":"Radka"},{"last_name":"Nováček","full_name":"Nováček, Jiří","first_name":"Jiří"},{"full_name":"Chaillet, Marten L.","last_name":"Chaillet","first_name":"Marten L."},{"full_name":"Žák, Jakub","last_name":"Žák","first_name":"Jakub"},{"last_name":"Grybchuk","full_name":"Grybchuk, Danyil","first_name":"Danyil"},{"first_name":"Friedrich","full_name":"Förster, Friedrich","last_name":"Förster"},{"last_name":"Wilson","full_name":"Wilson, William H.","first_name":"William H."},{"last_name":"Schroeder","full_name":"Schroeder, Declan C.","first_name":"Declan C."},{"last_name":"Plevka","full_name":"Plevka, Pavel","first_name":"Pavel"}],"publisher":"American Association for the Advancement of Science","publication_identifier":{"eissn":["2375-2548"]},"scopus_import":"1","file":[{"checksum":"291dd7ceccbe6bfd8e0a9157584f88e9","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"18921","file_size":40623405,"date_updated":"2025-01-27T14:40:08Z","file_name":"2024_ScienceAdv_Homola.pdf","date_created":"2025-01-27T14:40:08Z","content_type":"application/pdf"}],"supplementarymaterial":"yes","date_created":"2025-01-27T14:32:34Z","_id":"18920","file_date_updated":"2025-01-27T14:40:08Z","oa":1,"intvolume":"        10","year":"2024","language":[{"iso":"eng"}],"OA_place":"publisher","day":"01","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.","volume":10,"publication":"Science Advances","oa_version":"Published Version","das_tickbox":"1","type":"journal_article","external_id":{"pmid":["38598627"]},"month":"04","related_material":{"link":[{"relation":"software","url":" https://github.com/fuzikt/tomostarpy."}],"record":[{"relation":"research_data","id":"23025","status":"public"}]},"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"}],"status":"public","doi":"10.1126/sciadv.adk1954","OA_type":"gold","dataavailabilitystatement":"Cryo-EM maps and structure coordinates were deposited to the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), respectively, with the following accession numbers: (i) EhV-201 virion vertex reconstructed using a single-particle approach and a mask with the diameter of 50 nm (EMD-17650); (ii) EhV-201 virion vertex reconstructed using sub-tomogram averaging and a mask with the diameter of 50 nm (EMD-17649); (iii) EhV-201 virion vertex reconstructed using sub-tomogram averaging and a mask with the diameter of 50 nm and a mask covering only the capsid layer (EMD-19036) and the fitted structure of AlphaFold2 predicted EhV-201 major capsid protein and penton protein (PDB 8RBT); (iv) EhV-201 virion vertex reconstructed by sub-tomogram averaging and a mask with the diameter of 120 nm (EMD-17651); and (v) composite map of the EhV201 virion (EMD-19035) and corresponding structure of icosahedral asymmetric unit (PDB 8RBS). All custom scripts used during tomographic reconstruction have been made available at https://github.com/fuzikt/tomostarpy. Additional files have been made available at https://doi.org/10.5061/dryad.p5hqbzkw0: (i) cryo-ET tilt series of lamellas of control and EhV-201 infected E. huxleyi cells; (ii) segmentations of cryo-tomograms of infected and control cells; (iii) block face imaging data series of high-pressure frozen and resin-embedded E. huxleyi infected by EhV-201; (iv) scripts used during tomographic reconstruction; (v) fluorescence microscopy images of E. huxleyi infected by EhV-201; and (vi) mass spectrometry report of EhV-201 virion protein composition. Cryo-ET tilt series used for EhV-201 virion structure determination were deposited to EMPIAR and linked to the file EMD-17649. All other data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.","date_published":"2024-04-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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).","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.","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>.","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.","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>.","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>"},"ddc":["570"],"has_accepted_license":"1","article_processing_charge":"Yes","department":[{"_id":"EM-Fac"}],"pmid":1,"article_number":"eadk1954 ","researchdata_availability":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1126/sciadv.adk1954","date_updated":"2026-10-01T11:15:30Z","issue":"15","publication_status":"published"},{"date_published":"2024-08-27T00:00:00Z","citation":{"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>.","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>","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.","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>.","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>"},"project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}],"status":"public","doi":"10.1007/978-1-0716-4019-7_8","month":"08","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."}],"oa_version":"None","das_tickbox":"0","type":"book_chapter","researchdata_availability":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"date_updated":"2026-10-01T11:17:28Z","fulldoi":"https://doi.org/10.1007/978-1-0716-4019-7_8","publication_status":"published","article_processing_charge":"No","alternative_title":["Neuromethods"],"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"_id":"18052","page":"123-137","date_created":"2024-09-10T12:32:38Z","supplementarymaterial":"no","publisher":"Springer Nature","publication_identifier":{"issn":["0893-2336"],"eisbn":["9781071640197"],"eissn":["1940-6045"],"isbn":["9781071640180"]},"scopus_import":"1","quality_controlled":"1","title":"Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning","author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David"},{"orcid":"0000-0001-9732-3815","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"publication":"New Aspects in Analyzing the Synaptic Organization of the Brain","edition":"1","day":"27","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.","year":"2024","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"place":"New York","corr_author":"1","editor":[{"first_name":"Joachim H.R. ","last_name":"Lübke","full_name":"Lübke, Joachim H.R. "},{"full_name":"Rollenhagen, Astrid","last_name":"Rollenhagen","first_name":"Astrid"}]}]